Congenital Anomalies in a Neonate With Partial Monosomy of Chromosome 21 q Arm: A Case Report

Praisy Joy; Sudeshna Datta; Sanjukta Sahoo; Tapas Kumar Som; Prabhas R Tripathy; Manisha R Gaikwad; Pavithra Ayyanar; Sunil K Raghav

doi:10.7759/cureus.98751

. 2025 Dec 8;17(12):e98751. doi: 10.7759/cureus.98751

Congenital Anomalies in a Neonate With Partial Monosomy of Chromosome 21 q Arm: A Case Report

Praisy Joy ^1,^✉, Sudeshna Datta ², Sanjukta Sahoo ¹, Tapas Kumar Som ³, Prabhas R Tripathy ¹, Manisha R Gaikwad ¹, Pavithra Ayyanar ⁴, Sunil K Raghav ²

Editors: Alexander Muacevic, John R Adler

PMCID: PMC12779367 PMID: 41510431

Abstract

Congenital anomalies are a major cause of infant morbidity and mortality. Whole-genome sequencing provides a potential tool for solving diagnostic dilemmas in such instances. We report an interesting case of a neonate from India with holoprosencephaly and multiple associated anomalies, including dysmorphic features and ventricular septal defect. Karyotype analysis revealed mitotic instability. Both ring chromosome 21 and deletions in the q arm of chromosome 21 were observed in the metaphase spreads. To characterize the genomic abnormality more precisely, whole genome sequencing was performed, which identified a partial monosomy involving the 21q22.11-q22.3 region. This case demonstrates how whole-genome sequencing effectively identifies copy number variations and complex structural abnormalities, providing valuable insights into the genetic basis of congenital abnormalities.

Keywords: 21q deletion, congenital anomalies (ca), next generation sequencing (ngs), partial 21 monosomy, ring chromosome 21, structural variants (sv), whole genome sequencing (wgs)

Introduction

A congenital anomaly (CA) is defined as “a structural, functional, behavioural, or metabolic abnormality present during the intrauterine period that may be detected prenatally or at birth” [1]. CAs profoundly impact the health and well-being of individuals, families, healthcare systems, and communities, as they cause early miscarriage and fetal and infant death. They can be classified as major or minor anomalies according to the International Classification of Disease guidelines by the World Health Organization [2]. Major anomalies affect the infant’s life expectancy and physical or social functions, whereas minor anomalies have little or no impact on health [2]. Although CAs occur globally, its burden is higher in developing countries [3]. In India, the incidence ranges from 0.84% to 2.9%, making it the fourth leading cause (8.6%) of neonatal mortality and the sixth leading cause of under-five mortality [4]. Common anomalies are neural tube defects, congenital heart diseases, cleft lip and palate, and limb abnormalities. With the emergence of 4D ultrasound and advances in sequencing techniques, the trend in detection has increased over the years. There is a genetic aetiology in 30-40% of such cases.

Methods to understand the aetiology of CA include karyotyping, fluorescence in situ hybridisation (FISH), comparative genomic hybridization (CGH) array, and next-generation sequencing (NGS) techniques. In recent times, NGS is one of the most powerful methods for the diagnosis of congenital abnormalities and rare Mendelian disorders. It is widely used to detect single-nucleotide variants (SNVs) and structural variants (SVs) [5]. SVs are large genomic alterations of at least 50 nucleotides or larger. They are generally classified as unbalanced gains or losses of DNA (copy-number variants, CNVs) or balanced rearrangements (inversions and translocations) [5]. Complex SVs disrupt large genomic regions and account for germline and somatic disorders [6].

Here, we present a case of a neonate with multiple congenital anomalies and evidence of unstable mitotic behaviour. Cytogenetic analysis was found to have a mosaic pattern, with 10 metaphases demonstrating a ring chromosome 21 and 15 metaphases with a deletion of the long arm of chromosome 21. For further exploration of the underlying genetic aetiology, whole genome sequencing (WGS) was performed. WGS detected a partial monosomy of approximately 15.2 Mb on chromosome 21, extending from 21q22.11-q22.3 (chr21:31,118,415-46,286,297, hg38).

Case presentation

Materials and methods

Ethical Clearance

Patient was enrolled in an institutional review board-approved research study (IEC Number: T/IM-NF/Anatomy/23/44). The procedures followed were in accordance with the ethical standards of the institution’s committee on human research and were in keeping with international standards.

Whole Genome Sequencing and Preprocessing

WGS was performed using the Nextera DNA Flex (Illumina, San Diego, CA, USA) library prep kit according to the manufacturer’s guidelines. Following library preparation and quantification, we performed paired-end sequencing (150 bp) of the library using the Novaseq 6000 sequencing instrument (Illumina). The raw BCL files were demultiplexed, and the quality of the fastq files was checked using the FASTQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter sequences and low-quality bases were trimmed using fastp (v0.39) to minimize sequencing errors [7]. High-quality paired-end reads were then aligned to the hg38 human reference genome using the BWA-MEM aligner (v0.7.17) [8]. Picard MarkDuplicates tool (2.26.5) (http://broadinstitute.github.io/picard) was used to mark the PCR duplicate reads, which were excluded from downstream analysis. Base quality score recalibration and variant calling were performed using GATK (v4.1.2.0) according to GATK Best Practices recommendations [9-11].

Identification of CNVs and Gene Prioritization Analysis

DELLY’s (v1.0.3) [12] read-depth profile analysis was used for the detection of CNVs. We used two R packages (R Foundation for Statistical Computing, Vienna, Austria) to annotate the genes in the CNV region: org.Hs.eg.db [13] and AnnotationDbi [14]. We mapped the RefSeq EntrezID to chromosomal cytobands, gene symbols, Online Mendelian Inheritance in Man (OMIM) identifiers, and gene biotypes using various org.Hs.eg.db package functions. Then, using a custom R script, we filtered for chromosome 21 and merged all the above variables.

Identification and Annotation of SVs

For SV calling and genotyping, we used three callers: DELLY [12], MANTA (v1.6.0) [15] and smoove (https://github.com/brentp/smoove?tab=readme-ov-file) with default parameters to ensure concurrent and accurate SV calling. For all three callers, SVs with split-read support of ≤ 3 were filtered out. The identified SVs were merged using the SURVIVOR (v 1.0.7) [16]-merge function within a 1 kb breakpoint window, considering SV. Only SVs detected by all three methods and ≥50 bp in length were retained; variants >1 Mb were excluded due to detection limitations in short-read sequencing. We first annotated SVs with population-level allele frequency (AF) information using the SVAFotate tool with “-f 0.8, -a best mis -c 0” parameters [17]. SVAFotate aggregates and combines allele frequencies from multiple population datasets, such as CCDG [18], gnomAD [5], 1000G [19], and TOPMed [20]. To identify rare and unique SVs in our dataset, we excluded common SVs (Max_AF >= 0.01). For functional annotation, we used AnnotSV (v3.4.4) [21] with the GRCh38 build of the human genome. The resulting output file includes gene-based annotations, information on repeats, genic intolerance, and overlapping features from various databases such as the Database of Genomic Variants [22], 1000 Genomes [19], gnomAD [5], ExAC databases [23], disease-based annotation from OMIM [24], pathogenic features from dbVar [25], Exomiser score [26] and American College of Medical Genetics and Genomics (ACMG) categories [27]. We extracted the GnomAD pLI (probability of being loss-of-function intolerant) scores from annotSV results to understand the gene constraint of the identified SVs in the genomic regions. pLI is a score that indicates the probability of a gene being intolerant to a loss-of-function (LoF) variation. A gene with a pLI score >= 0.9 is considered extremely LoF intolerant. We used the VarElect, a free online phenotype-dependent variant prioritizer for screening genes in the CNV region. We queried all genes present in the CNV region with disease phenotypes of the patient and exported the result in Excel (Microsoft, Redmond, WA, USA) [28].

Functional Enrichment Analysis

Gene ontology (GO) analyses for the genes impacted with SVs were performed in R using the package ClusterProfiler [29]. The plots for the paper were created using GGPLOT2 package in R. The karyotype plot and visualization of reciprocal deletion and duplication were created using the karyoplotR [30] and Gviz [31] packages, respectively.

Clinical Details

A one-day-old male baby was admitted to the neonatal intensive care unit (NICU) with multiple anomalies. The baby was born to a nonconsanguineously married couple who had a previous spontaneous abortion during early pregnancy. This was their second pregnancy and the antenatal period was unremarkable. Ultrasound scans done during the last trimester of pregnancy showed hydrocephalus. Quickening was not felt. The baby was 1.340 kg at birth, born by normal vaginal delivery at 37 weeks. The baby did not cry at birth. APGAR Score at 1 and 5 minutes was 2 and 3. The baby had severe perinatal asphyxia. Initially, bag and mask ventilation was done, and since there were no respiratory efforts, the baby was intubated and started on a ventilator. Blood gas analysis was not done. The baby passed away on the same day seven hours after birth due to multiple congenital anomalies. On examination, the baby had microphthalmia, hypertelorism, corneal clouding, micrognathia, bilateral anotia, central cleft lip (harelip) and cleft palate, arthrogryposis (fixed flexion deformity), bilateral congenital talipes equinovarus (CTEV), wide-spaced nipple, pectus excavatum, scoliosis, genu recurvatum, and bilateral large extended big toe (Figure 1A). However, there were no polydactyly or scalp defects. The baby had a ventricular septal defect on the echocardiogram. A neurosonogram showed holoprosencephaly. Karyotype was done which had a resolution of 9 Mb at the Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Bhubaneswar. Karyotyping showed mos 46, X, r(21) (::p13->q22::) / 46, XY, del(21) (q?) [59%,41%] (Figure 1B, 1C). There was unstable mitotic behaviour that was noted. We wanted to do whole-genome sequencing to clear the diagnostic dilemma. The cause of death was severe perinatal asphyxia (hypoxic-ischemic encephalopathy (HIE) grade 3). Then, the fetal autopsy done in the Department of Pathology, AIIMS, Bhubaneswar, showed holoprosencephaly. No other internal anomalies were noted.

A) The neonate in the NICU. Dysmorphism in the form of microophthalmia, hypertelorism, wide spaced nipples, pectus excavatum, club foot and big toe is seen in this photo.

B) Karyotype showing 21 q deletion.

C) Karyotype showing ring chromosome in chromosome 21.

Results

WGS Identifies Partial Monosomy in Chromosome 21

CNV analysis revealed a 15.2 Mb partial monosomy in the long arm of chromosome 21, extending from 21q22.11-q22.3 (chr21:31,118,415 - 46,286,297, hg38) (Figure 2A). The number of genes spanning this region is 505. Among them, the majority are non-coding RNAs (41.19%), followed by protein-coding genes (37.23%) and pseudogenes (15.84%) (Appendix 1 panel A, Appendix 2). Of the protein-coding genes, 19.6% are associated with OMIM disease phenotype (Appendix 2). Notably, KCNJ6, PCNT2 are involved in brain morphogenesis [32], while HPE1 is associated with holoprosencephaly [33]. Deletions in SYNJ1, ITSN1, SLC5A3/SMIT1, and KCNE2, located in the distal part of 21q22.11, are associated with neurobehavioral symptoms [34,35], whereas deletions in the critical region 21q22.11, such as KCNE1 and DSCR1, lead to congenital heart defects [35].

A) Figure showing copy number variation (CNV) - Deletion of 21q in one arm of chromosome 21.

B) Gene-phenotype plot for the genes observed in the CNV region. Legend denotes the VarElect score.

C) Gene ontology (GO) BP enrichment analysis for the genes affected by structural variants (SVs). P-values were calculated using the non-parametric Wilcoxon rank-sum test, and adjusted p-values were calculated based on the Bonferroni correction procedure.

D) Visualization of reciprocal deletion and duplication on chromosome 19. Red is for deletion, and blue is for duplication.

Using VarElect [28] for phenotype-driven gene prioritization, we identified 89 genes associated with patient’s clinical features (Appendix 3). Applying a score threshold of ≥15, we identified seven top candidates, with the CBS gene showing the highest score of 75.41. The gene encodes cystathionine beta-synthase, and mutations in which cause homocystinuria, a multisystemic autosomal recessive disorder of the connective tissue, muscles, central nervous system (CNS), and cardiovascular system [36]. Pectus excavatum is common in homocystinuria patients, and it is also present in our case. Although CBS was phenotypically relevant, no pathogenic mutations were detected. Additionally, COL6A1 and COL6A2 (Bethlem myopathy genes) and DYRK1A (linked to intellectual disability syndrome and ocular anomalies) [37-40] were identified as key candidates.

SV Analysis Identifies Reciprocal Deletion and Duplication

In addition to CNV analysis, we identified 2,380 SVs using split-read, read-pair, and assembly-based approaches (Methods). The majority were deletions (94.51%), followed by duplications (2.3%), inversions (1.93%), and translocations (1.01%) (Appendix 1 panel B). Chromosome 21 exhibited the least number of SVs among all chromosomes, limited to deletions and insertions (Appendix 1 panel C). To identify patient-specific variants, SVs were annotated with AF from multiple cohorts and classified as rare (Max_AF < 0.01; n = 70) or unique (Max_AF = 0; n = 93). Of them, 119 SVs were predicted to affect 106 genes across coding, untranslated region (UTR), and intronic regions (Appendix 4).

GO analysis of these genes indicated enrichment in the biological processes associated with nervous system development (Figure 2C). Gene constraint analysis (gnomAD pLI ≥ 0.9) identified 18 SVs. Among these SVs, we found a reciprocal deletion and duplication on chromosome 19 (chr19:4,005,230-4,159,441) comprising three genes: MAP2K2, PIAS4, ZBTB7A (Figure 2D, 2E). MAP2K2, a key kinase in the RAS/MAPK pathway, is implicated in cardio-facio-cutaneous (CFC) syndrome [41]. ZBTB7A is a transcriptional repressor and is linked to developmental delay and neurological defects [42], and PIAS4 encodes a RING finger protein which interacts with the androgen receptor, is associated with abnormal head size phenotypes (macrocephaly or microcephaly) [43]. However, the effects of the reciprocal deletion and duplication on the patient phenotype remain unknown.

Discussion

21q deletion syndrome (ORPHA:574) is a rare chromosomal anomaly (less than 1 in 1000000 births) characterized by the loss of variable portions of a segment of the long arm of chromosome 21 leading to an increased risk of birth defects, developmental delay and intellectual deficit. The phenotypes range from mild to severe depending on the location and size of the area deleted.

In this report, we present a complex case with multiple congenital anomalies and early neonatal death, characterized by mosaic chromosomal abnormalities involving chromosome 21. Conventional cytogenetic analysis revealed a mosaic karyotype consisting of cells with ring morphology and others with deletion of the long arm of chromosome 21; mos 46, X, r21 (::p13->q22::) / 46, XY, del21 (q?) [59%,41%]. Ring chromosomes (RCs) are rare structural chromosomal anomalies with an estimated incidence of 1 in 50,000 live births [44]. RCs are found in 10-12% of cases involving chromosomes 18, 20, and X, and in 5-9% of cases involving chromosomes 13, 14, 15, 21, 22, and Y [44]. Autosomal RCs are usually unstable and may lead to different mosaic genetic constitutions [45]. Similar to the phenotypes observed in our case, a previous study has reported microcephaly, mild asymmetry of the face, depressed nasal bridge, squint in both eyes, flat occiput, large ears, broad trunk, wide nipple, and pectus excavatum in a 29-month-old patient. Cytogenetic analysis revealed a mosaic karyotype mos 46,XX,r21(p11.1q22.1?2)/45,XX, del21/46,XX [46].

To further elucidate the structural abnormalities, WGS was performed. CNV analysis revealed a terminal deletion of 15.2 Mb on chromosome 21q22.11-q22.3 confirming the long arm deletion from cytogenetic analysis. However, we could not detect the ring chromosome or its breakpoint. This observation infers that the ring chromosome found might be an unstable rearrangement, with a progressive loss of distal genetic material occurring through mitotic divisions.

Chromosome 21q deletions present a wide phenotypic spectrum from mild to severe. Studies have reported three deletion regions. Region 1 extended from centromere to 31.2 Mb encompassing 50 genes, region 2 extended from 31.2 Mb to 36 Mb encompassing 80 genes causing a very severe phenotype and region 3 extended from 36 Mb and 37.5 Mb to telomere encompassing 130 genes causing a mild phenotype [35,47]. In our study, we report a partial monosomy of 15.2 Mb extending from 21q22.11-21q22.3. Here we observe deletions in region 2 and region 3, and similar to the findings of severe phenotypes associated with deletions in these regions [35,47] our patient too demonstrated lower birth weight, microphthalmia, hypertelorism, micrognathia, central cleft lip (harelip) and cleft palate, arthrogryposis, wide spaced nipple, pectus excavatum, bilateral large extended big toe, ventricular septal defect and holoprosencephaly. Previous studies have established that several genes within the deleted 21q22.11-q22.3 region are critical to neurodevelopmental and cardiac phenotypes [32-35]. In this study, we utilized VarElect, a phenotype-based gene prioritization tool, and found 89 genes to be directly associated with the patient's clinical features. Among the top-scoring genes (score ≥15) were CBS, RIPK4, HPE1, and DYRK1A. For instance, CBS is involved in homocysteine metabolism, and its disruption leads to homocystinuria, often associated with pectus excavatum, a feature also observed in our case. Despite its strong association with the clinical phenotype, we did not find any pathogenic mutations in the gene. The exact effect of these SVs on the phenotype of the patient is still unknown; their overall effect, together with the CNV at chromosome 21, could play a role in the clinical presentation.

Moon and Yum described an unusual case involving a newborn who initially showed signs consistent with HIE, such as low muscle tone, breathing problems, trouble feeding, and persistent seizures within the first day of life [48]. Brain MRI demonstrated widespread abnormal signals, suggesting possible perinatal asphyxia. Nevertheless, the lack of definite hypoxic events around birth and the atypical clinical progression led to further testing. Chromosome analysis identified a de novo ring chromosome 21 with a terminal deletion, confirming a genetic disorder rather than a brain injury caused by lack of oxygen. This case highlights the need to consider genetic causes in newborns with unexplained neurological symptoms, especially when imaging resembles HIE. The authors point out that ring chromosome 21 can produce a range of symptoms, including severe neurological problems at birth. This report contributes to the limited knowledge on newborn presentations of ring chromosome 21 and underscores the risk of misdiagnosis in cases that mimic acquired perinatal brain injury [48]. Our case also had a history of severe perinatal asphyxia suggestive of HIE.

Conclusions

This report details a case of ring chromosome 21 exhibiting a severe phenotype, characterized by a 15.2 Mb deletion along with reciprocal deletion and duplication events on chromosome 19, as identified through whole genome sequencing. We have done the cytogenetic and molecular characterisation to delineate the cause and dilemma in the diagnosis of this case with multiple congenital anomalies. 21q deletions have a wide phenotypic spectrum of presentation. Genetic counselling and prenatal diagnosis will go a long way to help families with such disorders.

Appendices

Appendix 1

A) Pie plot showing the percentage of genes in the copy-number variant (CNV) region belonging to various feature type.

B) Pie plot showing the percentage of total structural variants (SVs) discovered. DEL, DUP, INV, TRA denote deletion, duplication, inversion and translocations.

c) Stacked bar plot showing the total number of each type of SVs discovered across chromosomes.

Appendix 2

Table 1. Genes annotated in the copy-number variant (CNV) region.

EntrezID	Cytoband	GeneSymbol	GeneType	Gene/Locus_MIM_number	Phenotype	Phenotype_MIM_number
539	21q22.11	ATP5PO	protein-coding	600828	Mitochondrial complex V (ATP synthase) deficiency, nuclear type 7	620359
757	21q22.11	TMEM50B	protein-coding	617894
2618	21q22.11	GART	protein-coding	138440
3454	21q22.11	IFNAR1	protein-coding	107450	Immunodeficiency 106, susceptibility to viral infections	619935
3455	21q22.11	IFNAR2	protein-coding	602376	{Hepatitis B virus, susceptibility to}	610424
3460	21q22.11	IFNGR2	protein-coding	147569	Immunodeficiency 28, mycobacteriosis	614889
3588	21q22.11	IL10RB	protein-coding	123889	{Hepatitis B virus, susceptibility to}	610424
6453	21q22.11	ITSN1	protein-coding	602442
6526	21q22.11	SLC5A3	protein-coding	600444
6647	21q22.11	SOD1	protein-coding	105400
6651	21q22.11	SON	protein-coding	182465	ZTTK syndrome	617140
7074	21q22.11	TIAM1	protein-coding	600687	Neurodevelopmental disorder with language delay and seizures	619908
7339	21q22.11	UBE3AP2	pseudo
8867	21q22.11	SYNJ1	protein-coding	604297	Developmental and epileptic encephalopathy 53	617389
9073	21q22.11	CLDN8	protein-coding	611231
9875	21q22.11	URB1	protein-coding	608865
9946	21q22.11	CRYZL1	protein-coding	603920
9992	21q22.11	KCNE2	protein-coding	603796	Atrial fibrillation, familial, 4	611493
10215	21q22.11	OLIG2	protein-coding	606386
29980	21q22.11	DONSON	protein-coding	251230
30811	21q22.11	HUNK	protein-coding	606532
54022	21q22.11	RPS5P3	pseudo
54048	21q22.11	HMGN1P2	pseudo
54065	21q22.11	SMIM11	protein-coding
54067	21q22.11	C21orf62-AS1	ncRNA
54069	21q22.11	MIS18A	protein-coding	618137
54099	21q22.11	FBXW11P1	pseudo
54943	21q22.11	DNAJC28	protein-coding
56245	21q22.11	C21orf62	protein-coding
56246	21q22.11	MRAP	protein-coding	607398
56683	21q22.11	CFAP298	protein-coding	615494	Ciliary dyskinesia, primary, 26	615500
57466	21q22.11	SCAF4	protein-coding	616023	Fliedner-Zweier syndrome	620511
59271	21q22.11	EVA1C	protein-coding
64968	21q22.11	MRPS6	protein-coding	611973
84996	21q22.11	URB1-AS1	ncRNA
94104	21q22.11	PAXBP1	protein-coding	617621
114036	21q22.11	LINC00310	ncRNA
116448	21q22.11	OLIG1	protein-coding	606385
140258	21q22.11	KRTAP13-1	protein-coding	608718
140290	21q22.11	TCP10L	protein-coding	608365
150051	21q22.11	TIAM1-AS1	ncRNA
254950	21q22.11	KRTAP15-1	protein-coding
266919	21q22.11	LINC00307	ncRNA
284827	21q22.11	KRTAP13-4	protein-coding
337878	21q22.11	KRTAP7-1	protein-coding
337879	21q22.11	KRTAP8-1	protein-coding
337880	21q22.11	KRTAP11-1	protein-coding	600064
337882	21q22.11	KRTAP19-1	protein-coding
337959	21q22.11	KRTAP13-2	protein-coding
337960	21q22.11	KRTAP13-3	protein-coding
337963	21q22.11	KRTAP23-1	protein-coding
337964	21q22.11	KRTAP13-5P	pseudo
337965	21q22.11	KRTAP13-6P	pseudo
337966	21q22.11	KRTAP6-1	protein-coding
337967	21q22.11	KRTAP6-2	protein-coding
337968	21q22.11	KRTAP6-3	protein-coding
337969	21q22.11	KRTAP19-2	protein-coding
337970	21q22.11	KRTAP19-3	protein-coding
337971	21q22.11	KRTAP19-4	protein-coding
337972	21q22.11	KRTAP19-5	protein-coding
337973	21q22.11	KRTAP19-6	protein-coding
337974	21q22.11	KRTAP19-7	protein-coding
337975	21q22.11	KRTAP20-1	protein-coding
337976	21q22.11	KRTAP20-2	protein-coding
337977	21q22.11	KRTAP21-1	protein-coding
337978	21q22.11	KRTAP21-2	protein-coding
337979	21q22.11	KRTAP22-1	protein-coding
337980	21q22.11	KRTAP8-2P	pseudo
337981	21q22.11	KRTAP8-3P	pseudo
337982	21q22.11	KRTAP19-9P	pseudo
337983	21q22.11	KRTAP19-10P	pseudo
337984	21q22.11	KRTAP19-11P	pseudo
337985	21q22.11	KRTAP20-3	protein-coding
337986	21q22.11	KRTAP21-4P	pseudo
388818	21q22.11	KRTAP26-1	protein-coding
391279	21q22.11	OR7E23P	pseudo
643803	21q22.11	KRTAP24-1	protein-coding	618927
643812	21q22.11	KRTAP27-1	protein-coding
677846	21q22.11	SNORA80A	snoRNA
728299	21q22.11	KRTAP19-8	protein-coding
728409	21q22.11	LINC01548	ncRNA
100128766	21q22.11	RPL8P2	pseudo
100129168	21q22.11	MTRES1P2	pseudo
100130240	21q22.11	RPS5P2	pseudo
100131268	21q22.11	TPT1P1	pseudo
100131902	21q22.11	KRTAP25-1	protein-coding
100151640	21q22.11	EXOSC3P1	pseudo
100151643	21q22.11	KRTAP20-4	protein-coding
100151645	21q22.11	USF1P1	pseudo
100288287	21q22.11	KRTAP22-2	protein-coding
100288323	21q22.11	KRTAP21-3	protein-coding
100288432	21q22.11	IL10RB-DT	ncRNA
100422891	21q22.11	MIR4327	ncRNA
100499261	21q22.11	BTF3P6	pseudo
100506215	21q22.11	PAXBP1-AS1	ncRNA
100506334	21q22.11	LINC00649	ncRNA
100551499	21q22.11	LINC00159	ncRNA
100873732	21q22.11	RNA5SP490	pseudo
100874202	21q22.11	MIS18A-AS1	ncRNA
101928078	21q22.11	LOC101928078	pseudo
101928107	21q22.11	LOC101928107	ncRNA
101928126	21q22.11	LOC101928126	ncRNA
101930746	21q22.11	LINC00945	ncRNA
102465248	21q22.11	MIR6501	ncRNA
102724449	21q22.11	SOD1-DT	ncRNA
102724502	21q22.11	LINC01690	ncRNA
105372772	21q22.11	LOC105372772	ncRNA
105372773	21q22.11	LOC105372773	ncRNA
105372774	21q22.11	LOC105372774	ncRNA
105372775	21q22.11	LOC105372775	ncRNA
105372776	21q22.11	LOC105372776	ncRNA
105372777	21q22.11	LOC105372777	ncRNA
105372779	21q22.11	MRAP-AS1	ncRNA
105372787	21q22.11	LOC105372787	ncRNA
105372789	21q22.11	LOC105372789	ncRNA
105372790	21q22.11	LOC105372790	ncRNA
105372791	21q22.11	LOC105372791	ncRNA
105377136	21q22.11	LOC105377136	ncRNA
106144524	21q22.11	HUNK-AS1	ncRNA
106479491	21q22.11	RN7SL740P	pseudo
107985488	21q22.11	LOC107985488	ncRNA
110091775	21q22.11	CFAP298-TCP10L	protein-coding
124900469	21q22.11	LOC124900469	snoRNA
124900470	21q22.11	LOC124900470	snoRNA
124905008	21q22.11	LOC124905008	ncRNA
124905009	21q22.11	LOC124905009	ncRNA
124905010	21q22.11	LOC124905010	ncRNA
124905011	21q22.11	LOC124905011	ncRNA
124905012	21q22.11	LOC124905012	ncRNA
124905013	21q22.11	LOC124905013	ncRNA
127882475	21q22.11	IFNAR2-IL10RB	protein-coding
861	21q22.12	RUNX1	protein-coding	151385	Leukemia, acute myeloid	601626
873	21q22.12	CBR1	protein-coding	114830
874	21q22.12	CBR3	protein-coding	603608
1827	21q22.12	RCAN1	protein-coding	602917
3753	21q22.12	KCNE1	protein-coding	176261	Jervell and Lange-Nielsen syndrome 2	612347
8410	21q22.12	RPS9P1	pseudo
8488	21q22.12	RPL3P1	pseudo
8489	21q22.12	RPL23AP3	pseudo
9980	21q22.12	DOP1B	protein-coding	604803
23515	21q22.12	MORC3	protein-coding	610078
54021	21q22.12	SRSF9P1	pseudo
54024	21q22.12	RPS26P1	pseudo
54025	21q22.12	RPS20P1	pseudo
54026	21q22.12	RPL34P3	pseudo
54031	21q22.12	RIMKLBP1	pseudo
54036	21q22.12	PPP1R2P2	pseudo
54064	21q22.12	LINC00160	ncRNA
54093	21q22.12	SETD4	protein-coding
54102	21q22.12	CLIC6	protein-coding	615321
80215	21q22.12	RUNX1-IT1	ncRNA
266693	21q22.12	EZH2P1	pseudo
387315	21q22.12	MTND2P1	pseudo
388820	21q22.12	SMIM34	protein-coding
728556	21q22.12	MEMO1P1	pseudo
768219	21q22.12	MIR802	ncRNA	616090
100133286	21q22.12	CBR1-AS1	ncRNA
100506385	21q22.12	LINC01426	ncRNA
100506403	21q22.12	LOC100506403	ncRNA
100506428	21q22.12	CBR3-AS1	ncRNA
100996609	21q22.12	LINC01436	ncRNA
101241877	21q22.12	ATP5MFP1	pseudo
101928147	21q22.12	C21orf140	protein-coding
101928269	21q22.12	LOC101928269	ncRNA
105369295	21q22.12	SETD4-AS1	ncRNA
105369306	21q22.12	LOC105369306	ncRNA
105372793	21q22.12	LOC105372793	ncRNA
106481493	21q22.12	RNU6-992P	pseudo
107985515	21q22.12	LOC107985515	ncRNA
112267915	21q22.12	LOC112267915	ncRNA
124900475	21q22.12	LOC124900475	snoRNA
124905014	21q22.12	RUNX1-AS1	ncRNA
124905015	21q22.12	LOC124905015	ncRNA
124905016	21q22.12	LOC124905016	ncRNA
124905072	21q22.12	LOC124905072	snoRNA
8208	21q22.12-q22.13	CHAF1B	protein-coding	601245
1859	21q22.13	DYRK1A	protein-coding	600855	Intellectual developmental disorder, autosomal dominant 7	614104
3141	21q22.13	HLCS	protein-coding	253270
3763	21q22.13	KCNJ6	protein-coding	600877	Keppen-Lubinsky syndrome	614098
6493	21q22.13	SIM2	protein-coding	600892
7267	21q22.13	TTC3	protein-coding	602259
10281	21q22.13	DSCR4	ncRNA	604829
10311	21q22.13	VPS26C	protein-coding	605298
23562	21q22.13	CLDN14	protein-coding	605608	Deafness, autosomal recessive 29	614035
51227	21q22.13	PIGP	protein-coding	605938	Developmental and epileptic encephalopathy 55	617599
53820	21q22.13	RIPPLY3	protein-coding	609892
54035	21q22.13	PSMD4P1	pseudo
84677	21q22.13	DSCR8	ncRNA	613396
257203	21q22.13	DSCR9	ncRNA
259234	21q22.13	DSCR10	ncRNA
359737	21q22.13	MRPL20P1	pseudo
503646	21q22.13	DPRXP5	pseudo
100188792	21q22.13	MAFD3	unknown
100288590	21q22.13	LOC100288590	pseudo
100873733	21q22.13	RNA5SP491	pseudo
100874006	21q22.13	TTC3-AS1	ncRNA
100874060	21q22.13	SPATA20P1	pseudo
100874294	21q22.13	HLCS-IT1	ncRNA
100874327	21q22.13	DSCR4-IT1	ncRNA
101928368	21q22.13	LOC101928368	ncRNA
105369301	21q22.13	CLDN14-AS1	ncRNA
105369305	21q22.13	LOC105369305	ncRNA
105369308	21q22.13	LOC105369308	ncRNA
105372797	21q22.13	LOC105372797	ncRNA
105372798	21q22.13	LOC105372798	ncRNA
105372799	21q22.13	KCNJ6-AS1	ncRNA
105372801	21q22.13	LOC105372801	ncRNA
106479873	21q22.13	RNU6-696P	pseudo
106481108	21q22.13	RN7SL678P	pseudo
107985492	21q22.13	LOC107985492	ncRNA
108281168	21q22.13	LOC108281168	biological-region
122455337	21q22.13	HLCS-AS1	ncRNA
124905017	21q22.13	LOC124905017	ncRNA
124905018	21q22.13	LOC124905018	ncRNA
124905019	21q22.13	LOC124905019	ncRNA
124905020	21q22.13	LOC124905020	ncRNA
124905070	21q22.13	LOC124905070	snoRNA
128193292	21q22.13	LNCTSI	ncRNA
3772	21q22.13-q22.2	KCNJ15	protein-coding	602106
100188797	21q22.13-qter	BMND6	unknown
1826	21q22.2	DSCAM	protein-coding	602523
2078	21q22.2	ERG	protein-coding	165080	Lymphatic malformation 14	620602
2114	21q22.2	ETS2	protein-coding	164740
3150	21q22.2	HMGN1	protein-coding	163920
5121	21q22.2	PCP4	protein-coding	601629
6450	21q22.2	SH3BGR	protein-coding	602230
7485	21q22.2	GET1	protein-coding	602915
8624	21q22.2	PSMG1	protein-coding	605296
10317	21q22.2	B3GALT5	protein-coding	604066
54014	21q22.2	BRWD1	protein-coding	617824	Ciliary dyskinesia, primary, 51	620438
114041	21q22.2	B3GALT5-AS1	ncRNA
150082	21q22.2	LCA5L	protein-coding
150084	21q22.2	IGSF5	protein-coding	610638
191585	21q22.2	PLAC4	ncRNA	613770
282569	21q22.2	BACE2-IT1	ncRNA
284835	21q22.2	LINC00323	ncRNA
391282	21q22.2	RPL23AP12	pseudo
400866	21q22.2	LINC00114	ncRNA	611723
400867	21q22.2	ETS2-AS1	ncRNA
692146	21q22.2	RPS26P4	pseudo
729056	21q22.2	JCADP1	pseudo
100420924	21q22.2	RNF6P1	pseudo
100421629	21q22.2	METTL21AP1	pseudo
100423023	21q22.2	MIR3197	ncRNA
100431168	21q22.2	MYL6P2	pseudo
100506492	21q22.2	DSCAM-AS1	ncRNA
100616148	21q22.2	MIR4760	ncRNA
100861429	21q22.2	YRDCP3	pseudo
100862727	21q22.2	TIMM9P2	pseudo
100873797	21q22.2	RPSAP64	pseudo
100874093	21q22.2	BRWD1-AS1	ncRNA
100874326	21q22.2	DSCAM-IT1	ncRNA
100874428	21q22.2	SNRPGP13	pseudo
101060045	21q22.2	PCBP2P1	pseudo
101928398	21q22.2	LOC101928398	ncRNA
101928435	21q22.2	LINC01700	ncRNA
102466972	21q22.2	MIR6508	ncRNA
102724678	21q22.2	LINC01423	ncRNA
102724740	21q22.2	LINC02940	ncRNA
103091865	21q22.2	BRWD1-AS2	ncRNA
105369294	21q22.2	LOC105369294	ncRNA
105372802	21q22.2	LOC105372802	ncRNA
105372804	21q22.2	LOC105372804	ncRNA
106480743	21q22.2	BRWD1-IT1	ncRNA
106865373	21q22.2	GET1-SH3BGR	protein-coding
107548109	21q22.2	LOC107548109	biological-region
107548111	21q22.2	LOC107548111	biological-region
107985480	21q22.2	LOC107985480	ncRNA
107985484	21q22.2	LINC02943	ncRNA
107985499	21q22.2	LOC107985499	ncRNA
107985500	21q22.2	LOC107985500	ncRNA
107985513	21q22.2	LOC107985513	ncRNA
108281150	21q22.2	LOC108281150	biological-region
111099028	21q22.2	LOC111099028	biological-region
124900473	21q22.2	LOC124900473	snoRNA
124905066	21q22.2	LOC124905066	pseudo
124905074	21q22.2	LOC124905074	snoRNA
25825	21q22.2-q22.3	BACE2	protein-coding	605668
104	21q22.3	ADARB1	protein-coding	601218	Neurodevelopmental disorder with hypotonia, microcephaly, and seizures	618862
326	21q22.3	AIRE	protein-coding	240300
754	21q22.3	PTTG1IP	protein-coding	603784
755	21q22.3	CFAP410	protein-coding	602271
875	21q22.3	CBS	protein-coding	236200
1291	21q22.3	COL6A1	protein-coding	120220	Bethlem myopathy 1A	158810
1292	21q22.3	COL6A2	protein-coding	120240	?Myosclerosis, congenital	255600
1409	21q22.3	CRYAA	protein-coding	123580	Cataract 9, multiple types	604219
1476	21q22.3	CSTB	protein-coding	254800
1637	21q22.3	DCR	other	190685	Down syndrome	190685
3244	21q22.3	HPE1	unknown
3275	21q22.3	PRMT2	protein-coding	601961
3689	21q22.3	ITGB2	protein-coding	116920
4047	21q22.3	LSS	protein-coding	600909	Alopecia-intellectual disability syndrome 4	618840
4599	21q22.3	MX1	protein-coding	147150
4600	21q22.3	MX2	protein-coding	147890
4731	21q22.3	NDUFV3	protein-coding	602184
5116	21q22.3	PCNT	protein-coding	210720
5152	21q22.3	PDE9A	protein-coding	602973
5211	21q22.3	PFKL	protein-coding	171860	Hemolytic anemia due to phosphofructokinase deficiency
5316	21q22.3	PKNOX1	protein-coding	602100
5822	21q22.3	PWP2	protein-coding	601475
6285	21q22.3	S100B	protein-coding	176990
6573	21q22.3	SLC19A1	protein-coding	600424	?Megaloblastic anemia, folate-responsive	601775
6612	21q22.3	SUMO3	protein-coding	602231
7031	21q22.3	TFF1	protein-coding	113710
7032	21q22.3	TFF2	protein-coding	182590
7033	21q22.3	TFF3	protein-coding	600633
7109	21q22.3	TRAPPC10	protein-coding	602103	Neurodevelopmental disorder with microcephaly, short stature, and speech delay	620027
7113	21q22.3	TMPRSS2	protein-coding	602060
7226	21q22.3	TRPM2	protein-coding	603749
7307	21q22.3	U2AF1	protein-coding	191317
7327	21q22.3	UBE2G2	protein-coding	603124
8209	21q22.3	GATD3	protein-coding	601659
8566	21q22.3	PDXK	protein-coding	179020	Neuropathy, hereditary motor and sensory, type VIC, with optic atrophy	618511
8568	21q22.3	RRP1	protein-coding	610653
8888	21q22.3	MCM3AP	protein-coding	603294	Peripheral neuropathy, autosomal recessive, with or without impaired intellectual development	618124
9619	21q22.3	ABCG1	protein-coding	603076
10785	21q22.3	WDR4	protein-coding	605924	Galloway-Mowat syndrome 6	618347
10841	21q22.3	FTCD	protein-coding	229100
11077	21q22.3	HSF2BP	protein-coding	604554	Premature ovarian failure 19	619245
23076	21q22.3	RRP1B	protein-coding	610654
23181	21q22.3	DIP2A	protein-coding	607711
23275	21q22.3	POFUT2	protein-coding	610249
23308	21q22.3	ICOSLG	protein-coding	605717	?Immunodeficiency 119	620825
25966	21q22.3	C2CD2	protein-coding	617581
29947	21q22.3	DNMT3L	protein-coding	606588
49854	21q22.3	ZBTB21	protein-coding	616485
53347	21q22.3	UBASH3A	protein-coding	605736
54020	21q22.3	SLC37A1	protein-coding	608094
54027	21q22.3	RPL31P1	pseudo
54029	21q22.3	RPL23AP4	pseudo
54039	21q22.3	PCBP3	protein-coding	608502
54043	21q22.3	MYL6P1	pseudo
54045	21q22.3	IMMTP1	pseudo
54049	21q22.3	H2AZP1	pseudo
54058	21q22.3	C21orf58	protein-coding
54059	21q22.3	YBEY	protein-coding	617461
54082	21q22.3	TSPEAR-AS1	ncRNA
54084	21q22.3	TSPEAR	protein-coding	612920	?Deafness, autosomal recessive 98	614861
54089	21q22.3	LINC00112	ncRNA
54090	21q22.3	LINC00111	ncRNA
54097	21q22.3	FAM3B	protein-coding	608617
54101	21q22.3	RIPK4	protein-coding	214350
54145	21q22.3	H2BC12L	protein-coding
56894	21q22.3	AGPAT3	protein-coding	614794
63977	21q22.3	PRDM15	protein-coding	617692
64699	21q22.3	TMPRSS3	protein-coding	601072
80781	21q22.3	COL18A1	protein-coding	120328	Glaucoma, primary closed-angle	618880
81543	21q22.3	LRRC3	protein-coding	617620
84221	21q22.3	SPATC1L	protein-coding	612412
84536	21q22.3	LINC01547	ncRNA
85395	21q22.3	SLX9	protein-coding
89765	21q22.3	RSPH1	protein-coding	609314	Ciliary dyskinesia, primary, 24	615481
89766	21q22.3	UMODL1	protein-coding	613859
90625	21q22.3	ERVH48-1	protein-coding
114038	21q22.3	LINC00313	ncRNA
114042	21q22.3	LINC00334	ncRNA
114043	21q22.3	TSPEAR-AS2	ncRNA
114044	21q22.3	MCM3AP-AS1	ncRNA
150094	21q22.3	SIK1	protein-coding	605705	Developmental and epileptic encephalopathy 30	616341
150135	21q22.3	LINC00479	ncRNA
150142	21q22.3	ZNF295-AS1	ncRNA
150147	21q22.3	UMODL1-AS1	ncRNA
246704	21q22.3	LINC00315	ncRNA
284836	21q22.3	LINC00319	ncRNA
284837	21q22.3	AATBC	ncRNA
343819	21q22.3	MRPL51P2	pseudo
353323	21q22.3	KRTAP12-2	protein-coding
353332	21q22.3	KRTAP12-1	protein-coding
353333	21q22.3	KRTAP10-10	protein-coding
378825	21q22.3	PICSAR	ncRNA	617191
378832	21q22.3	COL18A1-AS1	ncRNA
386672	21q22.3	KRTAP10-4	protein-coding
386674	21q22.3	KRTAP10-6	protein-coding
386675	21q22.3	KRTAP10-7	protein-coding
386676	21q22.3	KRTAP10-9	protein-coding
386677	21q22.3	KRTAP10-1	protein-coding
386678	21q22.3	KRTAP10-11	protein-coding
386679	21q22.3	KRTAP10-2	protein-coding
386680	21q22.3	KRTAP10-5	protein-coding
386681	21q22.3	KRTAP10-8	protein-coding
386682	21q22.3	KRTAP10-3	protein-coding
386683	21q22.3	KRTAP12-3	protein-coding
386684	21q22.3	KRTAP12-4	protein-coding
386685	21q22.3	KRTAP10-12	protein-coding
387492	21q22.3	DSTNP1	pseudo
387494	21q22.3	RPL18AP2	pseudo
388830	21q22.3	LINC00316	ncRNA
642852	21q22.3	LINC00205	ncRNA
727699	21q22.3	LINC00163	ncRNA	610259
727701	21q22.3	LINC00165	ncRNA
728039	21q22.3	SSR4P1	pseudo
100126693	21q22.3	LINC00322	ncRNA
100129027	21q22.3	PCBP3-AS1	ncRNA
100505746	21q22.3	ITGB2-AS1	ncRNA
100847013	21q22.3	MIR5692B	ncRNA
100861507	21q22.3	FTCD-AS1	ncRNA
100861510	21q22.3	LRRC3-DT	ncRNA
100862692	21q22.3	DIP2A-IT1	ncRNA
100873205	21q22.3	MTCO1P3	pseudo
100873206	21q22.3	MTND5P1	pseudo
100873332	21q22.3	MTND6P21	pseudo
100873734	21q22.3	RNA5SP492	pseudo
100873880	21q22.3	TMEM97P1	pseudo
100874224	21q22.3	KRTAP10-13P	pseudo
100874236	21q22.3	COL18A1-AS2	ncRNA
100874510	21q22.3	PSMA6P3	pseudo
101928212	21q22.3	LOC101928212	ncRNA
101928233	21q22.3	LINC01671	ncRNA
101928255	21q22.3	LOC101928255	ncRNA
101928284	21q22.3	PDE9A-AS1	ncRNA
101928311	21q22.3	LINC01668	ncRNA
101928369	21q22.3	LOC101928369	ncRNA
101928399	21q22.3	LINC01679	ncRNA
101928607	21q22.3	TRPM2-AS	ncRNA
101928689	21q22.3	LINC01424	ncRNA
101928745	21q22.3	BNAT1	ncRNA
101928796	21q22.3	LOC101928796	ncRNA
101930094	21q22.3	RSPH1-DT	ncRNA
102464825	21q22.3	MIR6070	ncRNA
102465488	21q22.3	MIR6814	ncRNA
102465489	21q22.3	MIR6815	ncRNA
102723380	21q22.3	LOC102723380	ncRNA
102724800	21q22.3	LOC102724800	ncRNA
102725065	21q22.3	LOC102725065	ncRNA
105372808	21q22.3	PCSEAT	ncRNA
105372809	21q22.3	LOC105372809	ncRNA
105372812	21q22.3	LOC105372812	ncRNA
105372813	21q22.3	LOC105372813	ncRNA
105372814	21q22.3	LOC105372814	ncRNA
105372815	21q22.3	LOC105372815	ncRNA
105372817	21q22.3	LOC105372817	ncRNA
105372821	21q22.3	LOC105372821	ncRNA
105372824	21q22.3	LOC105372824	ncRNA
105372825	21q22.3	LOC105372825	ncRNA
105372826	21q22.3	LOC105372826	ncRNA
105372829	21q22.3	LOC105372829	ncRNA
105372832	21q22.3	LOC105372832	ncRNA
105372833	21q22.3	DNMT3L-AS1	ncRNA
105372836	21q22.3	LOC105372836	ncRNA
105372839	21q22.3	LOC105372839	ncRNA
105372840	21q22.3	LINC01694	ncRNA
105372841	21q22.3	LOC105372841	ncRNA
105372842	21q22.3	LOC105372842	ncRNA
105377137	21q22.3	LINC03039	ncRNA
105377138	21q22.3	LINC01678	ncRNA
105377139	21q22.3	LOC105377139	ncRNA
106480072	21q22.3	RNU6-1150P	pseudo
106481303	21q22.3	RNU6-396P	pseudo
106481452	21q22.3	RNU6-859P	pseudo
106481542	21q22.3	RNU6-1149P	pseudo
106481742	21q22.3	FRGCA	ncRNA
106635524	21q22.3	SNORA91	snoRNA
107075260	21q22.3	MTCYBP21	pseudo
107985478	21q22.3	LOC107985478	ncRNA
107985485	21q22.3	LOC107985485	ncRNA
107985502	21q22.3	LOC107985502	ncRNA
107985504	21q22.3	LOC107985504	ncRNA
107987299	21q22.3	LOC107987299	ncRNA
107987300	21q22.3	LOC107987300	ncRNA
107987303	21q22.3	LOC107987303	ncRNA
108251799	21q22.3	LOC108251799	biological-region
108254685	21q22.3	LOC108254685	biological-region
108281139	21q22.3	LOC108281139	biological-region
108281151	21q22.3	LOC108281151	biological-region
109029533	21q22.3	LOC109029533	biological-region
109623452	21q22.3	SNORD159	snoRNA
111099027	21q22.3	LOC111099027	biological-region
111216286	21q22.3	LINC02575	ncRNA
112268487	21q22.3	KRTAP12-5P	pseudo
122152369	21q22.3	COL6A2-DT	ncRNA
124900467	21q22.3	LOC124900467	protein-coding
124900472	21q22.3	LOC124900472	snoRNA
124905021	21q22.3	LOC124905021	ncRNA
124905022	21q22.3	LOC124905022	ncRNA
124905023	21q22.3	LOC124905023	ncRNA
124905024	21q22.3	LOC124905024	ncRNA
124905025	21q22.3	LOC124905025	ncRNA
124905026	21q22.3	LOC124905026	ncRNA
124905027	21q22.3	LOC124905027	protein-coding
124905028	21q22.3	LOC124905028	ncRNA
124905029	21q22.3	LOC124905029	ncRNA
124905030	21q22.3	LOC124905030	ncRNA
124905031	21q22.3	LOC124905031	ncRNA
124905032	21q22.3	LOC124905032	ncRNA
124905033	21q22.3	LOC124905033	ncRNA
124905034	21q22.3	LOC124905034	ncRNA
124905035	21q22.3	LOC124905035	ncRNA
124905036	21q22.3	HEPFAL	ncRNA
124905037	21q22.3	LOC124905037	ncRNA
124905038	21q22.3	LOC124905038	ncRNA
124905039	21q22.3	LOC124905039	ncRNA
124905040	21q22.3	LOC124905040	ncRNA
124905041	21q22.3	LOC124905041	ncRNA
124905042	21q22.3	LOC124905042	ncRNA
124905043	21q22.3	LOC124905043	ncRNA
124905044	21q22.3	LOC124905044	ncRNA
124905045	21q22.3	LOC124905045	ncRNA
124905046	21q22.3	LOC124905046	ncRNA
124905058	21q22.3	LOC124905058	ncRNA
124905060	21q22.3	LOC124905060	pseudo
124905062	21q22.3	LOC124905062	snRNA
124905068	21q22.3	LOC124905068	snoRNA
124905069	21q22.3	LOC124905069	snoRNA
128092249	21q22.3	LOC128092249	protein-coding
130890644	21q22.3	MX1-AS1	ncRNA

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Appendix 3

Table 2. Gene-phenotype correlation list from VarElect.

Symbol	Description	Category	Matched Phenotypes	Matched Phenotypes Scount	Global Rank (Total Genes 12465)	-LOG10(P)	Score	Average Disease Causing Likelihood
CBS	Cystathionine Beta-Synthase	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect, Wide\-spaced nipples, Holoprosencephaly	9	54	2.810805	75.41	0.547264
RIPK4	Receptor Interacting Serine/Threonine Kinase 4	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Ventricular septal defect, Wide\-spaced nipples	7	294	2.074851	30.71	0.540287
HPE1	Holoprosencephaly 1, Alobar	Genetic Locus	Microphthalmia, Hypertelorism, Cleft lip, Cleft palate, Ventricular septal defect, Holoprosencephaly	6	269	2.113446	29.97	0
DYRK1A	Dual Specificity Tyrosine Phosphorylation Regulated Kinase 1A	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect	7	486	1.856562	23.69	0.810935
COL18A1	Collagen Type XVIII Alpha 1 Chain	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect, Wide\-spaced nipples, Holoprosencephaly	9	702	1.696861	21.51	0.062167
COL6A1	Collagen Type VI Alpha 1 Chain	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect, Wide\-spaced nipples	8	817	1.630977	18.43	0.052352
COL6A2	Collagen Type VI Alpha 2 Chain	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect	7	957	1.562287	15.37	0.068567
SOD1	Superoxide Dismutase 1	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Ventricular septal defect, Holoprosencephaly	7	1024	1.532899	14.66	0.774798
LSS	Lanosterol Synthase	Protein Coding	Microphthalmia, Hypertelorism, Cleft lip, Cleft palate, Ventricular septal defect, Holoprosencephaly	6	1106	1.499443	12.67	0.484029
PCNT	Pericentrin	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect, Holoprosencephaly	8	1382	1.402691	12.57	0.003366
SLC19A1	Solute Carrier Family 19 Member 1	Protein Coding	Cleft lip, Cleft palate, Ventricular septal defect, Holoprosencephaly	4	926	1.576588	11.9	0.336461
CSTB	Cystatin B	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect, Wide\-spaced nipples, Holoprosencephaly	9	1635	1.329681	11.6	0.733491
DONSON	DNA Replication Fork Stabilization Factor DONSON	Protein Coding	Microphthalmia, Micrognathia, Cleft lip, Cleft palate	4	961	1.560475	11.57	0.404012
RUNX1	RUNX Family Transcription Factor 1	Protein Coding	Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect	6	1287	1.43362	11.34	0.491055
TRAPPC10	Trafficking Protein Particle Complex Subunit 10	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Ventricular septal defect, Holoprosencephaly	7	1459	1.379143	11.2	0.50591
SIK1	Salt Inducible Kinase 1	Protein Coding	Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Ventricular septal defect	5	1241	1.449427	10.64	0.269487
IFNAR1	Interferon Alpha And Beta Receptor Subunit 1	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect, Holoprosencephaly	8	1883	1.268348	9.9	0.343348
S100B	S100 Calcium Binding Protein B	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect	7	2008	1.240435	8.69	0.728072
KCNE1	Potassium Voltage-Gated Channel Subfamily E Regulatory Subunit 1	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect, Wide\-spaced nipples	8	2178	1.205141	8.58	0.531162
CFAP410	Cilia And Flagella Associated Protein 410	Protein Coding	Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum	5	1806	1.286481	8.09	0.192971
WDR4	WD Repeat Domain 4	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate	5	1843	1.277673	7.96	0.248393
SON	SON DNA And RNA Binding Protein	Protein Coding	Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Ventricular septal defect	5	1978	1.246972	7.48	0.594756
SYNJ1	Synaptojanin 1	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Ventricular septal defect, Wide\-spaced nipples	7	2392	1.164437	7.42	0.428713
SIM2	SIM BHLH Transcription Factor 2	Protein Coding	Microphthalmia, Hypertelorism, Cleft lip, Cleft palate, Ventricular septal defect, Holoprosencephaly	6	2192	1.202358	7.37	0.487994
OLIG2	Oligodendrocyte Transcription Factor 2	Protein Coding	Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect	6	2210	1.198806	7.33	0
KCNE2	Potassium Voltage-Gated Channel Subfamily E Regulatory Subunit 2	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum, Ventricular septal defect, Wide\-spaced nipples	8	2935	1.07559	6.57	0.592285
PRDM15	PR/SET Domain 15	Protein Coding	Microphthalmia, Hypertelorism, Cleft lip, Cleft palate, Ventricular septal defect, Holoprosencephaly	6	2683	1.114578	6.2	0.573968
DNMT3L	DNA Methyltransferase 3 Like	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Ventricular septal defect, Holoprosencephaly	7	3551	0.992848	5.07	0.253846
HMGN1	High Mobility Group Nucleosome Binding Domain 1	Protein Coding	Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Pectus excavatum	5	3014	1.064055	5.06	0.247919
HUNK	Hormonally Up-Regulated Neu-Associated Kinase	Protein Coding	Microphthalmia, Hypertelorism, Cleft lip, Cleft palate, Pectus excavatum, Wide\-spaced nipples	6	3624	0.98401	4.62	0.324749
GART	Phosphoribosylglycinamide Formyltransferase, Phosphoribosylglycinamide Synthetase, Phosphoribosylaminoimidazole Synthetase	Protein Coding	Hypertelorism, Micrognathia, Cleft lip, Cleft palate	4	3120	1.049044	4.38	0.296779
SCAF4	SR-Related CTD Associated Factor 4	Protein Coding	Hypertelorism, Micrognathia, Pectus excavatum, Ventricular septal defect	4	3580	0.989316	3.8	0.768482
MCM3AP	Minichromosome Maintenance Complex Component 3 Associated Protein	Protein Coding	Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Ventricular septal defect	5	4022	0.938757	3.75	0.498954
ZBTB21	Zinc Finger And BTB Domain Containing 21	Protein Coding	Hypertelorism, Cleft lip, Cleft palate, Ventricular septal defect	4	3670	0.978533	3.7	0.536187
HLCS	Holocarboxylase Synthetase	Protein Coding	Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Ventricular septal defect	5	4201	0.919846	3.57	0.636247
SMIM11	Small Integral Membrane Protein 11	Protein Coding	Microphthalmia, Cleft lip, Cleft palate, Ventricular septal defect	4	4006	0.940488	3.38	0.61613
CRYZL1	Crystallin Zeta Like 1	Protein Coding	Hypertelorism, Micrognathia, Cleft lip, Cleft palate, Ventricular septal defect	5	4423	0.897482	3.33	0.620438
PIGP	Phosphatidylinositol Glycan Anchor Biosynthesis Class P	Protein Coding	Cleft lip, Cleft palate, Ventricular septal defect	3	3578	0.989558	3.29	0.216345
TSPEAR	Thrombospondin Type Laminin G Domain And EAR Repeats	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft palate, Ventricular septal defect	5	4640	0.876681	3.16	0.266227
ITSN1	Intersectin 1	Protein Coding	Cleft lip, Cleft palate, Ventricular septal defect	3	4175	0.922542	2.79	0.664135
SUMO3	Small Ubiquitin Like Modifier 3	Protein Coding	Microphthalmia, Cleft lip, Cleft palate	3	4337	0.906009	2.66	0.67305
TMPRSS2	Transmembrane Serine Protease 2	Protein Coding	Hypertelorism, Micrognathia, Pectus excavatum, Ventricular septal defect, Wide\-spaced nipples	5	5394	0.811288	2.53	0.315989
IFNGR2	Interferon Gamma Receptor 2	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft palate, Holoprosencephaly	5	5438	0.807759	2.49	0.402133
TMPRSS3	Transmembrane Serine Protease 3	Protein Coding	Cleft lip, Cleft palate, Pectus excavatum	3	4759	0.865683	2.33	0.158363
URB1	URB1 Ribosome Biogenesis Homolog	Protein Coding	Cleft palate, Pectus excavatum	2	4555	0.88471	2.06	0
KCNJ6	Potassium Inwardly Rectifying Channel Subfamily J Member 6	Protein Coding	Hypertelorism, Micrognathia, Cleft palate	3	5464	0.805688	1.91	0.883012
CRYAA	Crystallin Alpha A	Protein Coding	Microphthalmia, Cleft palate	2	5047	0.840165	1.8	0.7352
FTCD	Formimidoyltransferase Cyclodeaminase	Protein Coding	Cleft lip, Cleft palate	2	5194	0.827697	1.71	0.162659
ERG	ETS Transcription Factor ERG	Protein Coding	Hypertelorism, Micrognathia, Pectus excavatum, Ventricular septal defect	4	6396	0.73729	1.69	0.830623
ATP5PO	ATP Synthase Peripheral Stalk Subunit OSCP	Protein Coding	Hypertelorism, Micrognathia, Ventricular septal defect	3	6608	0.723129	1.35	0.334732
MORC3	MORC Family CW-Type Zinc Finger 3	Protein Coding	Micrognathia, Cleft palate	2	5943	0.769193	1.33	0.807403
MX1	MX Dynamin Like GTPase 1	Protein Coding	Micrognathia, Cleft palate	2	5943	0.769193	1.33	0.43731
CLDN14	Claudin 14	Protein Coding	Hypertelorism, Micrognathia, Cleft palate	3	6658	0.719855	1.32	0.534441
SETD4	SET Domain Containing 4	Protein Coding	Micrognathia, Cleft palate, Ventricular septal defect	3	6687	0.717967	1.3	0.547486
TFF2	Trefoil Factor 2	Protein Coding	Microphthalmia, Micrognathia	2	6063	0.760511	1.28	0.36645
U2AF1	U2 Small Nuclear RNA Auxiliary Factor 1	Protein Coding	Hypertelorism, Micrognathia, Cleft palate	3	7346	0.677148	1.25	0.77858
AIRE	Autoimmune Regulator	Protein Coding	Hypertelorism, Pectus excavatum, Ventricular septal defect	3	7462	0.670343	1.21	0.259796
H2BC12L	H2B Clustered Histone 12 Like	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft palate	4	8048	0.637511	1.09	0
IMMTP1	Inner Membrane Mitochondrial Protein Pseudogene 1	Pseudogene	Microphthalmia, Hypertelorism, Micrognathia, Cleft palate	4	8048	0.637511	1.09	0
CHAF1B	Chromatin Assembly Factor 1 Subunit B	Protein Coding	Microphthalmia, Hypertelorism, Micrognathia, Cleft palate	4	8048	0.637511	1.09	0.55132
BACE2	Beta-Secretase 2	Protein Coding	Cleft palate, Ventricular septal defect	2	6643	0.720834	1.08	0.848639
ADARB1	Adenosine Deaminase RNA Specific B1	Protein Coding	Cleft palate, Ventricular septal defect, Holoprosencephaly	3	7905	0.645297	1.01	0.865561
GATD3	Glutamine Amidotransferase Class 1 Domain Containing 3	Protein Coding	Hypertelorism, Cleft lip, Ventricular septal defect	3	8025	0.638754	0.96	0.308967
TIAM1	TIAM Rac1 Associated GEF 1	Protein Coding	Ventricular septal defect	1	7491	0.668659	0.69	0.460805
DSCAM	DS Cell Adhesion Molecule	Protein Coding	Hypertelorism, Ventricular septal defect	2	8565	0.610471	0.66	0.741066
RCAN1	Regulator Of Calcineurin 1	Protein Coding	Ventricular septal defect	1	7616	0.661472	0.65	0.663669
FAM3B	FAM3 Metabolism Regulating Signaling Molecule B	Protein Coding	Cleft lip, Cleft palate	2	8924	0.592639	0.55	0.32568
LINC01671	Long Intergenic Non-Protein Coding RNA 1671	RNA Gene	Cleft lip	1	9245	0.577292	0.35	0
PDE9A	Phosphodiesterase 9A	Protein Coding	Cleft lip	1	9245	0.577292	0.35	0.666175
ITGB2	Integrin Subunit Beta 2	Protein Coding	Microphthalmia, Micrognathia	2	10463	0.523542	0.32	0.714501
PWP2	PWP2 Small Subunit Processome Component	Protein Coding	Hypertelorism, Holoprosencephaly	2	10479	0.522879	0.32	0.241039
DCR	Down Syndrome Chromosome Region	Genetic Locus	Ventricular septal defect	1	9847	0.549895	0.31	0
MIR802	MicroRNA 802	RNA Gene	Ventricular septal defect	1	9847	0.549895	0.31	0
VPS26C	VPS26 Endosomal Protein Sorting Factor C	Protein Coding	Ventricular septal defect	1	10025	0.542114	0.29	0.712495
DSCR4	Down Syndrome Critical Region 4	RNA Gene	Ventricular septal defect	1	10025	0.542114	0.29	0.595025
SPATC1L	Spermatogenesis And Centriole Associated 1 Like	Protein Coding	Microphthalmia, Hypertelorism	2	10771	0.510943	0.27	0.119095
POFUT2	Protein O-Fucosyltransferase 2	Protein Coding	Cleft lip	1	10688	0.514302	0.2	0.434408
ETS2	ETS Proto-Oncogene 2, Transcription Factor	Protein Coding	Hypertelorism	1	10756	0.511548	0.19	0.656116
IFNAR2	Interferon Alpha And Beta Receptor Subunit 2	Protein Coding	Cleft palate	1	10775	0.510781	0.19	0.422986
IGSF5	Immunoglobulin Superfamily Member 5	Protein Coding	Cleft lip	1	11076	0.498816	0.14	0.107325
KCNJ6-AS1	KCNJ6 Antisense RNA 1	RNA Gene	Micrognathia	1	11108	0.497563	0.13	0
UBASH3A	Ubiquitin Associated And SH3 Domain Containing A	Protein Coding	Microphthalmia	1	11130	0.496703	0.13	0.271878
KCNJ15	Potassium Inwardly Rectifying Channel Subfamily J Member 15	Protein Coding	Microphthalmia	1	11130	0.496703	0.13	0.434616
TRPM2	Transient Receptor Potential Cation Channel Subfamily M Member 2	Protein Coding	Holoprosencephaly	1	11469	0.483673	0.11	0.128253
ICOSLG	Inducible T Cell Costimulator Ligand	Protein Coding	Micrognathia	1	11516	0.481897	0.11	0.271789
DIP2A	Disco Interacting Protein 2 Homolog A	Protein Coding	Micrognathia	1	11639	0.477283	0.1	0.607098
SLC37A1	Solute Carrier Family 37 Member 1	Protein Coding	Hypertelorism	1	11856	0.46926	0.1	0.468879
KRTAP10-12	Keratin Associated Protein 10-12	Protein Coding	Hypertelorism	1	11856	0.46926	0.1	0.110913
TSPEAR-AS1	TSPEAR Antisense RNA 1	RNA Gene	Microphthalmia	1	12292	0.453576	0.07	0

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Appendix 4

Table 3. Functional annotation of structural variants.

AnnotSV_ID

SV_chrom

SV_start

SV_end

SV_length

SV_type

Samples_ID

REF

ALT

QUAL

FILTER

INFO

FORMAT

ILS_AP001

ILS_AP001_1

ILS_AP001_2

Annotation_mode

CytoBand

Gene_name

Closest_left

Closest_right

Gene_count

Tx_version

Tx_start

Tx_end

Overlapped_tx_length

Overlapped_CDS_length

Overlapped_CDS_percent

Frameshift

Exon_count

Location

Location2

Dist_nearest_SS

Nearest_SS_type

Intersect_start

Intersect_end

RE_gene

P_gain_phen

P_gain_hpo

P_gain_source

P_gain_coord

P_loss_phen

P_loss_hpo

P_loss_source

P_loss_coord

P_ins_phen

P_ins_hpo

P_ins_source

P_ins_coord

po_P_gain_phen

po_P_gain_hpo

po_P_gain_source

po_P_gain_coord

po_P_gain_percent

po_P_loss_phen

po_P_loss_hpo

po_P_loss_source

po_P_loss_coord

po_P_loss_percent

P_snvindel_nb

P_snvindel_phen

B_gain_source

B_gain_coord

B_gain_AFmax

B_loss_source

B_loss_coord

B_loss_AFmax

B_ins_source

B_ins_coord

B_ins_AFmax

B_inv_source

B_inv_coord

B_inv_AFmax

po_B_gain_allG_source

po_B_gain_allG_coord

po_B_gain_someG_source

po_B_gain_someG_coord

po_B_loss_allG_source

po_B_loss_allG_coord

po_B_loss_someG_source

po_B_loss_someG_coord

GC_content_left

GC_content_right

Repeat_coord_left

Repeat_type_left

Repeat_coord_right

Repeat_type_right

Gap_left

Gap_right

SegDup_left

SegDup_right

ENCODE_blacklist_left

ENCODE_blacklist_characteristics_left

ENCODE_blacklist_right

ENCODE_blacklist_characteristics_right

ACMG

DDD_HI_percent

ExAC_delZ

ExAC_dupZ

ExAC_cnvZ

ExAC_synZ

ExAC_misZ

GenCC_disease

GenCC_moi

GenCC_classification

GenCC_pmid

NCBI_gene_ID

OMIM_ID

OMIM_phenotype

OMIM_inheritance

OMIM_morbid

OMIM_morbid_candidate

LOEUF_bin

GnomAD_pLI

ExAC_pLI

Exomiser_gene_pheno_score

Human_pheno_evidence

Mouse_pheno_evidence

Fish_pheno_evidence

AnnotSV_ranking_score

AnnotSV_ranking_criteria

ACMG_class

ILS_AP001_2

12_107608877_107608984_DEL_1

1.08E+08

-106

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:22826:0:0:0:0:0

TTAAAATAAAATAAAATAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAATAAAATAAAATATAAAATAAAATATAAAATAAAATAAA

780

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-106;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=12;END=107608983;CIPOS=0,28;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=186910_1;Best_CCDG_Mismatch_OFP=0.00934579;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.1459;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_12:107608906-107608976;Best_TOPMed_OFP=0.672897;Best_TOPMed_AF=0.170773;Best_TOPMed_Het=29656;Best_TOPMed_HomAlt=3748;Best_TOPMed_PopMax_AF=0.383399;Best_TOPMed_Mismatch_ID=INV_12:107505762-107866958;Best_TOPMed_Mismatch_OFP=0.000296236;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0.672897;ThousG_Count=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr12_b0743d0d;Best_gnomAD_OFP=0.186736;Best_gnomAD_AF=0.132533;Best_gnomAD_Het=15993;Best_gnomAD_HomAlt=305;Best_gnomAD_PopMax_AF=0.283157;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_INS_chr12_5965628a;Best_gnomAD_Mismatch_OFP=0.141663;Best_gnomAD_Mismatch_SVTYPE=INS;Best_gnomAD_Mismatch_AF=8.9e-05;Best_gnomAD_Mismatch_Het=11;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:107:0,0:+:780:DEL:DEL00038933:NA:NA:chr12_107608877-chr12_107608984

0/1:NA:106:0,0:+:694:DEL:MantaDEL_22826_0_0_0_0_0:TTAAAATAAAATAAAATAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAATAAAATAAAATATAAAATAAAATATAAAATAAAATAAA:T:chr12_107608877-chr12_107608983

0/1:NA:78:0,0:+:380:DEL:7348:NA:NA:chr12_107608905-chr12_107608983

split

q23.3

ABTB3

NM_001018072

1.07E+08

1.08E+08

108

intron4-intron4

CDS

1205

1.08E+08

IMH

12:40539485-113039119

0.1121

121551

full=3

0/1

10_1560472_1560587_DEL_1

1560472

1560587

-114

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:36333:0:0:0:0:0

CACCCTGGGTCGTCACACACGCGTGAACACACGGGGGGCACCCTGGGTCGTCACACACGCGTGAACACACGGGGGGCACCCTGGGTCGTCACACACGCGTGAACACACGGGGGGT

802

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-114;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=10;END=1560586;CIPOS=0,0;CIEND=-40,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=143996;Best_CCDG_OFP=0.652174;Best_CCDG_AF=0.644;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=461311;Best_CCDG_Mismatch_OFP=0.000281707;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=6.839e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0.652174;TOPMed_Count=0;Best_TOPMed_ID=DEL_10:1560473-1560546;Best_TOPMed_OFP=0.652174;Best_TOPMed_AF=0.796027;Best_TOPMed_Het=36576;Best_TOPMed_HomAlt=63698;Best_TOPMed_PopMax_AF=0.945155;Best_TOPMed_Mismatch_ID=DUP_10:1544002-1577700;Best_TOPMed_Mismatch_OFP=0.00341246;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_13251;Best_ThousG_OFP=0.652174;Best_ThousG_AF=0.622854;Best_ThousG_Het=1628;Best_ThousG_HomAlt=1181;Best_ThousG_PopMax_AF=0.742928;ThousG_SV_Cov=0.652174;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr10_cf2eea75;Best_gnomAD_OFP=0.652174;Best_gnomAD_AF=0.501124;Best_gnomAD_Het=45144;Best_gnomAD_HomAlt=7973;Best_gnomAD_PopMax_AF=0.584797;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr10_8c7c0436;Best_gnomAD_Mismatch_OFP=0.733823;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.044062;Best_gnomAD_Mismatch_Het=4474;Best_gnomAD_Mismatch_HomAlt=9;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

1/1:NA:115:0,0:+:480:DEL:DEL00030007:NA:NA:chr10_1560472-chr10_1560587

1/1:NA:114:0,0:+:802:DEL:MantaDEL_36333_0_0_0_0_0:CACCCTGGGTCGTCACACACGCGTGAACACACGGGGGGCACCCTGGGTCGTCACACACGCGTGAACACACGGGGGGCACCCTGGGTCGTCACACACGCGTGAACACACGGGGGGT:C:chr10_1560472-chr10_1560586

1/1:NA:74:0,0:+:561:DEL:5864:NA:NA:chr10_1560472-chr10_1560546

split

p15.3

ADARB2

NM_018702

1177312

1737525

116

intron1-intron1

CDS

176463

1560471

1560587

43.56

-1.24883

-2.53125

-2.42223

0.97635

2.868325

105

8.56E-01

7.38E-01

full=3

1/1

11_26289563_26289683_DEL_1

26289563

26289683

-119

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:28029:0:1:0:0:0

TACATATACACATATATCCTATATGTGTGTATATGTACATATACACACATATATTCTATATGTGTGTATATGTACATATACACACATATATTCTATATGTGTGTATATGTACATATACAC

534

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-119;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=11;END=26289682;CIPOS=0,7;CIEND=-35,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=552441;Best_CCDG_Mismatch_OFP=0.512821;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=0.0002393;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_11:26168982-26306759;Best_TOPMed_OFP=0.00087096;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=1.20192e-05;Best_TOPMed_Mismatch_ID=DUP_11:25900270-26725298;Best_TOPMed_Mismatch_OFP=0.000145449;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_22611;Best_ThousG_OFP=0.666667;Best_ThousG_AF=0.012901;Best_ThousG_Het=80;Best_ThousG_HomAlt=1;Best_ThousG_PopMax_AF=0.030354;Best_ThousG_Mismatch_ID=HGSV_21276;Best_ThousG_Mismatch_OFP=1.75885e-06;Best_ThousG_Mismatch_SVTYPE=INV;Best_ThousG_Mismatch_AF=0.413492;Best_ThousG_Mismatch_Het=2648;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr11_c1e64f6d;Best_gnomAD_OFP=0.701754;Best_gnomAD_AF=0.00694;Best_gnomAD_Het=867;Best_gnomAD_HomAlt=2;Best_gnomAD_PopMax_AF=0.024629;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr11_2e30ec4e;Best_gnomAD_Mismatch_OFP=0.00388489;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:120:0,0:+:342:DEL:DEL00034436:NA:NA:chr11_26289563-chr11_26289683

0/1:NA:119:0,0:+:534:DEL:MantaDEL_28029_0_1_0_0_0:TACATATACACATATATCCTATATGTGTGTATATGTACATATACACACATATATTCTATATGTGTGTATATGTACATATACACACATATATTCTATATGTGTGTATATGTACATATACAC:T:chr11_26289563-chr11_26289682

0/1:NA:77:0,0:+:333:DEL:6464:NA:NA:chr11_26289570-chr11_26289647

split

p14.2

ANO3

NM_001313726

26188807

26663289

121

intron1-intron1

CDS

19961

26289562

26289683

dbVar;gnomAD-SV_v3_DEL_chr11_f71dd9b5

chr11:8142635-35706287;chr11:26289521-26290235

0.048

IMH

11:1621661-71538522

0.0179

26.37

0.115654

2.632122

dystonia 24

Strong;Supportive

23200863;23200863[PMID];24151159;24442708;25356970;25847575;32116979;33388357;34307749

63982

610110

Dystonia 24, 615034 (3) AD

yes

1.25E-17

4.09E-13

full=1

0/1

9_94833891_94833964_DEL_1

94833891

94833964

-72

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:210906:0:1:0:0:0

TGAGAGTATTATTTTTTGCAACTCGTAAATCATTAATGGATCTAGGCAATGATCATTTTGTGTTTCCTAATGG

780

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-72;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=9;END=94833963;CIPOS=0,3;CIEND=0,1;STRANDS=+;Max_AF=0.008931;Max_Het=1691;Max_HomAlt=116;Max_PopMax_AF=0.024843;CCDG_Count=0;Best_CCDG_Mismatch_ID=433601_2;Best_CCDG_Mismatch_OFP=0.0136986;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.00701;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=1;Best_TOPMed_ID=DEL_9:94833892-94833963;Best_TOPMed_OFP=1;Best_TOPMed_AF=0.006613;Best_TOPMed_Het=1691;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.0105446;Best_TOPMed_Mismatch_ID=INV_9:94710576-96645135;Best_TOPMed_Mismatch_OFP=3.77347e-05;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_163726;Best_ThousG_OFP=0.958904;Best_ThousG_AF=0.003122;Best_ThousG_Het=16;Best_ThousG_HomAlt=2;Best_ThousG_PopMax_AF=0.01183;ThousG_SV_Cov=0.958904;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr9_19fb53af;Best_gnomAD_OFP=0.958904;Best_gnomAD_AF=0.008931;Best_gnomAD_Het=894;Best_gnomAD_HomAlt=116;Best_gnomAD_PopMax_AF=0.024843;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_CPX_chr9_d1c64a8f;Best_gnomAD_Mismatch_OFP=0.00498668;Best_gnomAD_Mismatch_SVTYPE=CPX;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:73:0,0:+:780:DEL:DEL00028776:NA:NA:chr9_94833891-chr9_94833964

0/1:NA:72:0,0:+:448:DEL:MantaDEL_210906_0_1_0_0_0:TGAGAGTATTATTTTTTGCAACTCGTAAATCATTAATGGATCTAGGCAATGATCATTTTGTGTTTCCTAATGG:T:chr9_94833891-chr9_94833963

0/1:NA:69:0,0:+:404:DEL:5645:NA:NA:chr9_94833894-chr9_94833963

split

q22.32

AOPEP

XM_011519130

94726698

94875323

intron5-intron5

CDS

32888

94833890

94833964

dbVar

chr9:94691779-95015950

0.01

IMH

9:65437055-134286391;9:80897170-125694547;9:89671548-130954998;9:94308786-96947962

0.4714

84909

619600

Dystonia 31, 619565 (3) AR

yes

full=3

0/1

11_941537_942183_DEL_1

941537

942183

-645

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:25802:0:1:0:1:0

CTCCCAAAGTGCTGGGGTTACAGGCATGAGCCACTGTGGCTGGCTGCTTTCTTATTCTTTTTTTTTTTTGAGATGGAGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCACTGCAATCTCTGACTCCCAGGTTCAAGCGATTCTCCCACCTCAGCCTCCCAAGTAGCTGGGACTACAGGCATGCACCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGACATGGGGTTTTGCCATGTGGCTAGGCTGGTGTTGAACTCCTGATCTCAAGTGATCTGGTGGCCTTGGCCTCCCAAAGTGGTGGGATTACAAGCATGAACCACCATGCCCGGCCTCTCATGCTTAAATGAAGTAGTAATACCTGACCTTTTATTTTTTATCTATTTATATTTGAGATGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTAGCGTGATCTTGGCTCACTGCAACCTCCGCCTCCCAGGTTCACTCCATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGCGCCCACCACCATGCCCGGCTAATTTTTTGTATTTTTAGTAGAGAGGGGGGTTTCACCCTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCTGCCCGCCTCGGCT

803

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-645;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=11;END=942182;CIPOS=0,33;CIEND=0,1;STRANDS=+;Max_AF=0.004036;Max_Het=503;Max_HomAlt=1;Max_PopMax_AF=0.005769;CCDG_Count=1;Best_CCDG_ID=158981;Best_CCDG_OFP=0.948916;Best_CCDG_AF=3.42e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=465260;Best_CCDG_Mismatch_OFP=0.0522442;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=6.839e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0.948916;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DUP_11:857950-949631;Best_TOPMed_Mismatch_OFP=0.00704602;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=1;Best_ThousG_ID=HGSV_21064;Best_ThousG_OFP=0.948916;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.000832;Best_ThousG_Mismatch_ID=HGSV_21049;Best_ThousG_Mismatch_OFP=0.00345867;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=2;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr11_938ba06e;Best_gnomAD_OFP=0.890093;Best_gnomAD_AF=0.000169;Best_gnomAD_Het=19;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.00161;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr11_2a0f5d05;Best_gnomAD_Mismatch_OFP=0.0523501;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.000119;Best_gnomAD_Mismatch_Het=15;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=0.995356

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:646:20,6:+:803:DEL:DEL00033964:NA:NA:chr11_941537-chr11_942183

0/1:NA:645:0,0:+:370:DEL:MantaDEL_25802_0_1_0_1_0:CTCCCAAAGTGCTGGGGTTACAGGCATGAGCCACTGTGGCTGGCTGCTTTCTTATTCTTTTTTTTTTTTGAGATGGAGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCACTGCAATCTCTGACTCCCAGGTTCAAGCGATTCTCCCACCTCAGCCTCCCAAGTAGCTGGGACTACAGGCATGCACCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGACATGGGGTTTTGCCATGTGGCTAGGCTGGTGTTGAACTCCTGATCTCAAGTGATCTGGTGGCCTTGGCCTCCCAAAGTGGTGGGATTACAAGCATGAACCACCATGCCCGGCCTCTCATGCTTAAATGAAGTAGTAATACCTGACCTTTTATTTTTTATCTATTTATATTTGAGATGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTAGCGTGATCTTGGCTCACTGCAACCTCCGCCTCCCAGGTTCACTCCATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGCGCCCACCACCATGCCCGGCTAATTTTTTGTATTTTTAGTAGAGAGGGGGGTTTCACCCTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCTGCCCGCCTCGGCT:C:chr11_941537-chr11_942182

0/1:NA:612:0,0:+:278:DEL:6370:NA:NA:chr11_941570-chr11_942182

split

p15.5

AP2A2

NM_001242837

925869

1012240

647

intron1-intron1

CDS

15448

941536

942183

dbVar

chr11:851409-1025480;chr11:857076-1025480;chr11:876861-979340;chr11:924172-1011626;chr11:939003-951343

0.01

72.44

0.24731

-0.33825

-0.15288

0.071349

4.232065

schizophrenia

Limited

23042115

161

1.0000e

1.00E+00

full=3

0/1

22_44860912_44860969_DEL_1

44860912

44860969

-56

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:95612:0:1:0:0:0

TTGGAGAATGTCACTTCTTGGTTTTACAACAATTTTTTTTCTCCCTGTTGCTTGACA

653

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-56;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=22;END=44860968;CIPOS=0,1;CIEND=0,1;STRANDS=+;Max_AF=0.000781;Max_Het=18;Max_HomAlt=0;Max_PopMax_AF=0.004274;CCDG_Count=0;Best_CCDG_ID=308768;Best_CCDG_OFP=0.00374237;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=504733;Best_CCDG_Mismatch_OFP=0.00542289;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_22:44858643-44861351;Best_TOPMed_OFP=0.0210332;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.26535e-06;Best_TOPMed_Mismatch_ID=INV_22:44757699-44872616;Best_TOPMed_Mismatch_OFP=0.000496002;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_96575;Best_ThousG_OFP=0.982456;Best_ThousG_AF=0.000781;Best_ThousG_Het=5;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.004274;Best_ThousG_Mismatch_ID=HGSV_96574;Best_ThousG_Mismatch_OFP=0.00901471;Best_ThousG_Mismatch_SVTYPE=CPX;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.982456;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr22_e53f8373;Best_gnomAD_OFP=0.982456;Best_gnomAD_AF=0.000143;Best_gnomAD_Het=18;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.0042;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr22_abddc20b;Best_gnomAD_Mismatch_OFP=0.00712411;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=1.7e-05;Best_gnomAD_Mismatch_Het=2;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:57:0,0:+:653:DEL:DEL00062432:NA:NA:chr22_44860912-chr22_44860969

1/1:NA:56:0,0:+:486:DEL:MantaDEL_95612_0_1_0_0_0:TTGGAGAATGTCACTTCTTGGTTTTACAACAATTTTTTTTCTCCCTGTTGCTTGACA:T:chr22_44860912-chr22_44860968

0/1:NA:55:0,0:+:272:DEL:11382:NA:NA:chr22_44860913-chr22_44860968

split

q13.31

ARHGAP8

NM_001017526

44752574

44862784

intron12-intron12

CDS

1077

44860911

44860969

dbVar

chr22:44820754-44869341;chr22:44837184-44861234

0.01

IMH

22:44479419-47655346

0.2479

79.74

-2.62354

0.465679

-1.01906

23779

8.52E-28

0.5199

Cleft lip;Cleft palate;Hypertelorism;Micrognathia;Microphthalmia;cataract

full=3

0/1

8_144279080_144279163_DEL_1

1.44E+08

-82

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:224320:0:0:0:0:0

TGACCACCAAGGGCCATGACCGTCACGGGCCACGACCGCCATGGGCCATGACCCCCATGGGCCTCAAGACCACCACAGGCCAC

790

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-82;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=8;END=144279162;CIPOS=0,8;CIEND=-19,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=425360_1;Best_CCDG_Mismatch_OFP=0.0120482;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.5376;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_8:144279089-144279143;Best_TOPMed_OFP=0.674699;Best_TOPMed_AF=0.549235;Best_TOPMed_Het=67184;Best_TOPMed_HomAlt=39319;Best_TOPMed_PopMax_AF=0.624534;Best_TOPMed_Mismatch_ID=DUP_8:144257901-144309152;Best_TOPMed_Mismatch_OFP=0.00161942;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr8_77f5991f;Best_gnomAD_OFP=0.674699;Best_gnomAD_AF=0.412819;Best_gnomAD_Het=41699;Best_gnomAD_HomAlt=4427;Best_gnomAD_PopMax_AF=0.463041;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr8_4fc86a05;Best_gnomAD_Mismatch_OFP=0.244346;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.5;Best_gnomAD_Mismatch_Het=3;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

1/1:NA:83:0,0:+:780:DEL:DEL00027468:NA:NA:chr8_144279080-chr8_144279163

1/1:NA:82:0,0:+:790:DEL:MantaDEL_224320_0_0_0_0_0:TGACCACCAAGGGCCATGACCGTCACGGGCCACGACCGCCATGGGCCATGACCCCCATGGGCCTCAAGACCACCACAGGCCAC:T:chr8_144279080-chr8_144279162

1/1:NA:55:0,0:+:502:DEL:5409:NA:NA:chr8_144279088-chr8_144279143

split

q24.3

BOP1

NM_015201

1.44E+08

intron2-intron2

CDS

2775

1.44E+08

71.45

0.350937

0.12491

23246

9.28E-02

5.27E-01

full=3

1/1

17_52039252_52049002_DEL_1

52039252

52049002

-9749

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:52948:0:1:0:0:0

1620

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-9749;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=17;END=52049001;CIPOS=0,2;CIEND=0,1;STRANDS=+;Max_AF=0.009991;Max_Het=710;Max_HomAlt=18;Max_PopMax_AF=0.052137;CCDG_Count=1;Best_CCDG_ID=239784;Best_CCDG_OFP=0.999795;Best_CCDG_AF=0.0008206;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=568590;Best_CCDG_Mismatch_OFP=0.000523327;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=0.2957;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0.999795;TOPMed_Count=5;Best_TOPMed_ID=DEL_17:52039255-52049004;Best_TOPMed_OFP=0.999487;Best_TOPMed_AF=0.002648;Best_TOPMed_Het=710;Best_TOPMed_HomAlt=18;Best_TOPMed_PopMax_AF=0.0457731;Best_TOPMed_Mismatch_ID=DUP_17:51966479-52066348;Best_TOPMed_Mismatch_OFP=0.0976259;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_62744;Best_ThousG_OFP=0.999795;Best_ThousG_AF=0.009991;Best_ThousG_Het=62;Best_ThousG_HomAlt=1;Best_ThousG_PopMax_AF=0.052137;Best_ThousG_Mismatch_ID=HGSV_62408;Best_ThousG_Mismatch_OFP=0.000448843;Best_ThousG_Mismatch_SVTYPE=INV;Best_ThousG_Mismatch_AF=0.067926;Best_ThousG_Mismatch_Het=435;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.999795;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr17_7b229558;Best_gnomAD_OFP=0.999795;Best_gnomAD_AF=0.002197;Best_gnomAD_Het=273;Best_gnomAD_HomAlt=2;Best_gnomAD_PopMax_AF=0.046867;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr17_1f0cd36f;Best_gnomAD_Mismatch_OFP=0.0976259;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:9750:19,15:+:1620:DEL:DEL00051442:NA:NA:chr17_52039252-chr17_52049002

0/1:NA:9749:0,0:+:829:DEL:MantaDEL_52948_0_1_0_0_0:NA:NA:chr17_52039252-chr17_52049001

0/1:NA:9747:0,0:+:650:DEL:9547:NA:NA:chr17_52039254-chr17_52049001

split

q21.33

CA10

NM_001082533

51630312

52159801

9751

intron3-intron3

CDS

23316

52039251

52049002

1000g;dbVar;esv3640777

chr17:52039118-52052439;chr17:52039251-52049003;17:52039252-52049003;17:52039252-52049003

0.0496

IMH

17:34039916-62479846;17:34040041-62479166;17:34040143-62479546;17:34040242-62479120;17:34040341-62478867;17:34040432-62479253;17:46268845-67992342;17:46287445-64926623;17:46291987-64922991

0.2957

4.4

1.125011

0.861137

1.183256

-0.11718

1.13949

56934

5.67E-01

9.73E-01

0.4271

Microphthalmia;eye decreased size, abnormal

full=1

0/1

10_18141430_18162954_DUP_1

18141430

18162954

21524

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:37963:0:1:0:0:0

1080

PASS

SUPP=3;SUPP_VEC=111;SVLEN=21524;SVTYPE=DUP;SVMETHOD=SURVIVOR1.0.7;CHR2=10;END=18162954;CIPOS=0,1;CIEND=0,0;STRANDS=-;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=145959;Best_CCDG_Mismatch_OFP=0.00673635;Best_CCDG_Mismatch_SVTYPE=DEL;Best_CCDG_Mismatch_AF=0.000171;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DUP_10:17607298-18187851;Best_TOPMed_OFP=0.0370766;Best_TOPMed_AF=7e-06;Best_TOPMed_Het=2;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=1.25661e-05;Best_TOPMed_Mismatch_ID=DEL_10:18135902-18166700;Best_TOPMed_Mismatch_OFP=0.698864;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_14289;Best_ThousG_Mismatch_OFP=0.00268136;Best_ThousG_Mismatch_SVTYPE=INV;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DUP_chr10_a46e6116;Best_gnomAD_OFP=0.0219146;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=3e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr10_59bf6ec9;Best_gnomAD_Mismatch_OFP=0.115819;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:21523:41,8:-:1080:DUP:DUP00030417:NA:NA:chr10_18141431-chr10_18162954

0/1:NA:21524:0,0:-:470:DUP:MantaDUP_TANDEM_37963_0_1_0_0_0:NA:NA:chr10_18141430-chr10_18162954

0/1:NA:21524:0,0:-:212:DUP:5946:NA:NA:chr10_18141430-chr10_18162954

split

p12.33

CACNB2

XM_047425725

18140423

18518968

21525

intron1-intron2

CDS

573

18141429

18162954

18.41

0.627254

-0.88115

-0.42823

-1.11349

0.425036

Brugada syndrome 1;Brugada syndrome 4;hypertrophic cardiomyopathy;short QT syndrome

Disputed Evidence;Limited

17224476;19358333;20817017;22584458;22840528;25637381;30662450

783

600003

Brugada syndrome 4, 611876 (3) AD

yes

2.67E-06

1.82E-03

full=3

0/1

2_44409095_44409184_DEL_1

44409095

44409184

-88

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:174423:0:0:0:0:0

ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATG

1140

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-88;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=2;END=44409183;CIPOS=0,5;CIEND=-15,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=271444;Best_CCDG_OFP=0.00477493;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=271446_1;Best_CCDG_Mismatch_OFP=0.011236;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.636;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_2:44391632-44410277;Best_TOPMed_OFP=0.00477289;Best_TOPMed_AF=3.2e-05;Best_TOPMed_Het=9;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000107787;Best_TOPMed_Mismatch_ID=INV_2:44403211-44419415;Best_TOPMed_Mismatch_OFP=0.00549179;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_77537;Best_ThousG_OFP=0.775281;Best_ThousG_AF=0.437305;Best_ThousG_Het=1391;Best_ThousG_HomAlt=703;Best_ThousG_PopMax_AF=0.627962;Best_ThousG_Mismatch_ID=HGSV_77475;Best_ThousG_Mismatch_OFP=6.63578e-07;Best_ThousG_Mismatch_SVTYPE=INS;Best_ThousG_Mismatch_AF=0.000468;Best_ThousG_Mismatch_Het=3;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.775281;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr2_ac5169c0;Best_gnomAD_OFP=0.775281;Best_gnomAD_AF=0.424911;Best_gnomAD_Het=38541;Best_gnomAD_HomAlt=6924;Best_gnomAD_PopMax_AF=0.550847;gnomAD_Mismatches=gnomAD-SV_v3_DUP_chr2_a7918d70,gnomAD-SV_v3_DUP_chr2_d33e7116,gnomAD-SV_v3_DUP_chr2_a1ef2047;gnomAD_Mismatches_Count=3;gnomAD_Mismatch_SVTYPEs=DUP;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr2_a1ef2047;Best_gnomAD_Mismatch_OFP=0.828365;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.000226;Best_gnomAD_Mismatch_Het=20;Best_gnomAD_Mismatch_HomAlt=4;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

1/1:NA:89:0,0:+:1140:DEL:DEL00006084:NA:NA:chr2_44409095-chr2_44409184

1/1:NA:88:0,0:+:732:DEL:MantaDEL_174423_0_0_0_0_0:ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATG:A:chr2_44409095-chr2_44409183

1/1:NA:68:0,0:+:699:DEL:1226:NA:NA:chr2_44409100-chr2_44409168

split

p21

CAMKMT

XM_047445879

44361946

44715353

intron3-intron3

CDS

18789

44409094

44409184

dbVar;gnomAD-SV_v3_DUP_chr2_d33e7116

chr2:44405812-44507018;chr2:44409080-44409188

0.0624

dbVar

chr2:44278237-44413378;chr2:44391631-44410269

0.01

IMH

2:21055811-76514955;2:32873521-53185851

0.1623

16.48

-1.41796

-1.07939

-1.18635

-0.0005

-0.70187

79823

1.38E-15

5.15E-13

0.2756

2p21 microdeletion syndrome;Cleft palate;Depressed nasal bridge;Frontal bossing;Micrognathia

full=1

1/1

11_64341843_64341924_DEL_1

64341843

64341924

-80

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:30764:0:1:0:0:0

GGTTGTGGTCTGAGGTCTTGGGCCATCAGTGATGTCACAACCAGATGGCCCAAGACCCCAGACCACAACCCCATGTCTGGT

480

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-80;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=11;END=64341923;CIPOS=0,8;CIEND=0,1;STRANDS=+;Max_AF=0.000519;Max_Het=65;Max_HomAlt=0;Max_PopMax_AF=0.000951;CCDG_Count=0;Best_CCDG_ID=166951;Best_CCDG_OFP=0.00442405;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=166953_2;Best_CCDG_Mismatch_OFP=0.0123457;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.06302;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_11:59466655-66168743;Best_TOPMed_OFP=1.20858e-05;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.26354e-06;Best_TOPMed_Mismatch_ID=DUP_11:60405002-68536600;Best_TOPMed_Mismatch_OFP=9.96114e-06;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_24190;Best_ThousG_Mismatch_OFP=2.06875e-06;Best_ThousG_Mismatch_SVTYPE=INV;Best_ThousG_Mismatch_AF=0.488601;Best_ThousG_Mismatch_Het=3129;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr11_5ab5afbb;Best_gnomAD_OFP=0.901235;Best_gnomAD_AF=0.000519;Best_gnomAD_Het=65;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000951;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr11_4e711591;Best_gnomAD_Mismatch_OFP=0.00309149;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=1.7e-05;Best_gnomAD_Mismatch_Het=0;Best_gnomAD_Mismatch_HomAlt=1;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:81:0,0:+:480:DEL:DEL00035331:NA:NA:chr11_64341843-chr11_64341924

0/1:NA:80:0,0:+:280:DEL:MantaDEL_30764_0_1_0_0_0:GGTTGTGGTCTGAGGTCTTGGGCCATCAGTGATGTCACAACCAGATGGCCCAAGACCCCAGACCACAACCCCATGTCTGGT:G:chr11_64341843-chr11_64341923

0/1:NA:72:0,0:+:197:DEL:6678:NA:NA:chr11_64341851-chr11_64341923

split

q13.1

CCDC88B

NM_032251

64340203

64357534

intron7-intron7

CDS

64341842

64341924

IMH

11:1621661-71538522;11:49193342-89651496;11:49211577-89635120;11:49243027-89597882;11:49358811-89347590;11:49403038-89297530;11:49586833-89037283;11:49629782-88995227;11:49736709-88892563

0.4958

77.95

0.163641

0.700084

0.590085

0.461565

0.989825

283234

1.40E-09

9.29E-04

full=3

0/1

3_112357974_112367723_DUP_1

1.12E+08

9742

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:164788:0:1:0:0:0

881

PASS

SUPP=3;SUPP_VEC=111;SVLEN=9742;SVTYPE=DUP;SVMETHOD=SURVIVOR1.0.7;CHR2=3;END=112367716;CIPOS=0,1;CIEND=0,7;STRANDS=-;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=508907;Best_CCDG_OFP=0.00262431;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=584333;Best_CCDG_Mismatch_OFP=0.00205123;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=6.839e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DUP_3:112266702-112474400;Best_TOPMed_OFP=0.046909;Best_TOPMed_AF=4.7e-05;Best_TOPMed_Het=13;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=8.29431e-05;Best_TOPMed_Mismatch_ID=INV_3:111765091-113399244;Best_TOPMed_Mismatch_OFP=0.0059621;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr3_846bc145;Best_gnomAD_Mismatch_OFP=0.0410551;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=0.000135;Best_gnomAD_Mismatch_Het=17;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=0

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:9741:33,10:-:881:DUP:DUP00010845:NA:NA:chr3_112357975-chr3_112367716

0/1:NA:9742:0,0:-:666:DUP:MantaDUP_TANDEM_164788_0_1_0_0_0:NA:NA:chr3_112357974-chr3_112367716

0/1:NA:9749:0,0:-:155:DUP:2231:NA:NA:chr3_112357974-chr3_112367723

split

q13.2

CD200

NM_001365853

1.12E+08

4839

yes

intron5-txEnd

CDS-3'UTR

3569

1.12E+08

gnomAD-SV_v3_DEL_chr3_9b8d4286

chr3:11110259-145805573

0.0446

IMH

3:30036454-134858252;3:72502419-189537676;3:75447628-125901392

0.239

65.55

0.220641

0.039405

0.154051

-0.07105

0.270677

4345

4.14E-01

1.60E-01

0.1903

Holoprosencephaly;abnormal microglial cell morphology

full=3

0/1

6_118691123_118692764_DEL_1

1.19E+08

-1639

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:127453:1:2:0:0:0

1613

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-1639;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=6;END=118692764;CIPOS=-2,0;CIEND=-9,0;STRANDS=+;Max_AF=0.002853;Max_Het=306;Max_HomAlt=0;Max_PopMax_AF=0.004399;CCDG_Count=0;Best_CCDG_ID=383030;Best_CCDG_OFP=0.04009;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=524510;Best_CCDG_Mismatch_OFP=0.741746;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=0.4692;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_6:118690006-118698985;Best_TOPMed_OFP=0.182608;Best_TOPMed_AF=7.1e-05;Best_TOPMed_Het=20;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000118978;Best_TOPMed_Mismatch_ID=INV_6:118677651-118746246;Best_TOPMed_Mismatch_OFP=0.0239078;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_136958;Best_ThousG_OFP=0.182669;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.000789;Best_ThousG_Mismatch_ID=HGSV_136959;Best_ThousG_Mismatch_OFP=0.741746;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.446284;Best_ThousG_Mismatch_Het=456;Best_ThousG_Mismatch_HomAlt=1201;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr6_730c34b1;Best_gnomAD_OFP=0.811881;Best_gnomAD_AF=0.002853;Best_gnomAD_Het=306;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.004399;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr6_0ee6261a;Best_gnomAD_Mismatch_OFP=0.539753;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.039098;Best_gnomAD_Mismatch_Het=3931;Best_gnomAD_Mismatch_HomAlt=5;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:1632:27,18:+:1613:DEL:DEL00020616:NA:NA:chr6_118691123-chr6_118692755

0/1:NA:1639:0,0:+:579:DEL:MantaDEL_127453_1_2_0_0_0:NA:NA:chr6_118691125-chr6_118692764

0/1:NA:1639:0,0:+:584:DEL:4087:NA:NA:chr6_118691125-chr6_118692764

split

q22.31

CEP85L

NM_001178035

1.18E+08

1.19E+08

1642

intron1-intron1

5'UTR

17271

1.19E+08

CMRI:142_pbsv.SPLIT.DUP.1935;IMH;dbVar

chr6:118470570-118861466;chr6:118563166-118770310;6:118690556-118692765;6:118690557-118692765

0.4692

dbVar

chr6:118563166-118770310;chr6:118690042-118699122;chr6:118690263-118693049

0.01

44.27

-0.87242

-2.53125

-2.47163

-1.75564

-0.84951

lissencephaly 10;lissencephaly due to LIS1 mutation

Definitive;Strong

32097629;32097630;33096394

387119

618865

Lissencephaly 10, 618873 (3) AD

yes

4.54E-09

4.96E-03

0.3527

Microphthalmia;Optic nerve hypoplasia;Posterior-predominant lissencephaly-broad flat pons and medulla-midline crossing defects syndrome

full=1

0/1

2_119659621_119660920_DEL_1

1.2E+08

-1298

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:179317:0:1:0:0:0

1245

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-1298;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=2;END=119660919;CIPOS=0,3;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=279347;Best_CCDG_OFP=0.00104813;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=497353;Best_CCDG_Mismatch_OFP=0.00373295;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_2:119592602-119681700;Best_TOPMed_OFP=0.0145791;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.00010661;Best_TOPMed_Mismatch_ID=DUP_2:119610102-119662000;Best_TOPMed_Mismatch_OFP=0.0250289;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;ThousG_Mismatches=HGSV_81537;ThousG_Mismatches_Count=1;ThousG_Mismatch_SVTYPEs=DUP;Best_ThousG_Mismatch_ID=HGSV_81537;Best_ThousG_Mismatch_OFP=0.916725;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.7297;Best_ThousG_Mismatch_Het=1131;Best_ThousG_Mismatch_HomAlt=1771;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr2_b8d7b14a;Best_gnomAD_OFP=0.00289823;Best_gnomAD_AF=1.6e-05;Best_gnomAD_Het=2;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000161;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_INS_chr2_11e51f62;Best_gnomAD_Mismatch_OFP=0.00623557;Best_gnomAD_Mismatch_SVTYPE=INS;Best_gnomAD_Mismatch_AF=0.000676;Best_gnomAD_Mismatch_Het=81;Best_gnomAD_Mismatch_HomAlt=2;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:1299:21,12:+:1245:DEL:DEL00007394:NA:NA:chr2_119659621-chr2_119660920

0/1:NA:1298:0,0:+:848:DEL:MantaDEL_179317_0_1_0_0_0:NA:NA:chr2_119659621-chr2_119660919

0/1:NA:1295:0,0:+:521:DEL:1472:NA:NA:chr2_119659624-chr2_119660919

split

q14.2

CFAP221

XM_006712353

1.2E+08

703

intron24-txEnd

3'UTR

549

1.2E+08

dbVar

chr2:119496017-119698511;chr2:119607424-119746424

0.01

dbVar;gnomAD-SV_v3_DEL_chr2_8881e883

chr2:106014408-123234450;chr2:119062422-123333424

0.2151

IMH

2:65359567-213949290;2:94555625-132220070

0.3179

primary ciliary dyskinesia

AD;AR

Limited;Moderate;Supportive

31636325[PMID]

200373

full=1

0/1

9_132421610_132421687_DEL_1

1.32E+08

-76

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:213820:0:0:0:0:0

TGAGAATCCTGGGTTCTCATGCTCTGGTTTCTCTTCAAATCGTATAAATCTTTCGCCTTTTACTAAAGATTTCTGTG

1020

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-76;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=9;END=132421686;CIPOS=0,16;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=437382;Best_CCDG_OFP=0.792208;Best_CCDG_AF=0.9596;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=537439;Best_CCDG_Mismatch_OFP=0.00224949;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=0.792208;CCDG_SV_Cov=0.792208;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DUP_9:132104708-132425204;Best_TOPMed_Mismatch_OFP=0.000240251;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=0;Best_ThousG_ID=HGSV_165893;Best_ThousG_OFP=0.792208;Best_ThousG_AF=0.927835;Best_ThousG_Het=424;Best_ThousG_HomAlt=2758;Best_ThousG_PopMax_AF=0.968454;ThousG_SV_Cov=0.792208;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr9_d530eb63;Best_gnomAD_OFP=0.792208;Best_gnomAD_AF=0.731839;Best_gnomAD_Het=33391;Best_gnomAD_HomAlt=29444;Best_gnomAD_PopMax_AF=0.78125;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr9_494359e1;Best_gnomAD_Mismatch_OFP=0.00224949;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=0.792208

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

1/1:NA:77:0,0:+:1020:DEL:DEL00029746:NA:NA:chr9_132421610-chr9_132421687

1/1:NA:76:0,0:+:999:DEL:MantaDEL_213820_0_0_0_0_0:TGAGAATCCTGGGTTCTCATGCTCTGGTTTCTCTTCAAATCGTATAAATCTTTCGCCTTTTACTAAAGATTTCTGTG:T:chr9_132421610-chr9_132421686

1/1:NA:60:0,0:+:827:DEL:5815:NA:NA:chr9_132421626-chr9_132421686

split

q34.13

CFAP77

XM_011518671

1.32E+08

1.33E+08

intron1-intron1

CDS

11143

1.32E+08

IMH

9:65437055-134286391

0.2414

389799

full=3

1/1

8_93405628_93405764_DEL_1

93405628

93405764

-123

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:184904:1:1:0:0:0

TATATATATATATATATATATATATATGTATATATATATATATATGTATATATATATATATATGTATATATATATATATATGTATATATATATATATATATATATGTGTATATATATATATATA

840

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-123;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=8;END=93405764;CIPOS=-13,9;CIEND=-14,0;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=112287_1;Best_CCDG_Mismatch_OFP=0.00806452;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.0006497;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_8:93375834-93553436;Best_TOPMed_OFP=0.000698182;Best_TOPMed_AF=7e-06;Best_TOPMed_Het=2;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000213174;Best_TOPMed_Mismatch_ID=INV_8:93056502-93610923;Best_TOPMed_Mismatch_OFP=0.000223656;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_153347;Best_ThousG_Mismatch_OFP=2.18579e-06;Best_ThousG_Mismatch_SVTYPE=CTX;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr8_4c808af8;Best_gnomAD_OFP=0.172709;Best_gnomAD_AF=0.014802;Best_gnomAD_Het=1343;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.034483;gnomAD_Mismatches=gnomAD-SV_v3_DUP_chr8_25e7e38e;gnomAD_Mismatches_Count=1;gnomAD_Mismatch_SVTYPEs=DUP;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr8_25e7e38e;Best_gnomAD_Mismatch_OFP=0.813172;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.001429;Best_gnomAD_Mismatch_Het=180;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:123:0,0:+:840:DEL:DEL00026665:NA:NA:chr8_93405628-chr8_93405751

0/1:NA:123:0,0:+:632:DEL:MantaDEL_184904_1_1_0_0_0:TATATATATATATATATATATATATATGTATATATATATATATATGTATATATATATATATATGTATATATATATATATATGTATATATATATATATATATATATGTGTATATATATATATATA:TG:chr8_93405641-chr8_93405764

0/1:NA:100:0,0:+:425:DEL:5227:NA:NA:chr8_93405650-chr8_93405750

split

q22.1

CIBAR1-DT

NR_033858

93346466

93700433

137

intron7-intron7

UTR

14404

93405627

93405764

642924

full=3

0/1

5_79750489_79753717_INV_1

79750489

79753717

3228

INV

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaBND:136633:0:1:0:0:0:0

T]chr5:79753717]

1140

PASS

SUPP=3;SUPP_VEC=111;SVLEN=3228;SVTYPE=INV;SVMETHOD=SURVIVOR1.0.7;CHR2=5;END=79753717;CIPOS=0,4;CIEND=0,0;STRANDS=;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=592532;Best_CCDG_OFP=0.000123398;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=359580_1;Best_CCDG_Mismatch_OFP=0.000309693;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.05519;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=INV_5:79227384-80480748;Best_TOPMed_OFP=0.00257626;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.25986e-06;Best_TOPMed_Mismatch_ID=DEL_5:79752602-79756800;Best_TOPMed_Mismatch_OFP=0.0920003;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_123838;Best_ThousG_OFP=9.76245e-05;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0;Best_ThousG_Mismatch_ID=HGSV_124085;Best_ThousG_Mismatch_OFP=0.583906;Best_ThousG_Mismatch_SVTYPE=CPX;Best_ThousG_Mismatch_AF=0.081798;Best_ThousG_Mismatch_Het=478;Best_ThousG_Mismatch_HomAlt=23;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_INV_chr5_29b515bc;Best_gnomAD_OFP=0.000123398;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=3e-05;gnomAD_Mismatches=gnomAD-SV_v3_CPX_chr5_dbd26d18;gnomAD_Mismatches_Count=1;gnomAD_Mismatch_SVTYPEs=CPX;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_CPX_chr5_dbd26d18;Best_gnomAD_Mismatch_OFP=0.938936;Best_gnomAD_Mismatch_SVTYPE=CPX;Best_gnomAD_Mismatch_AF=0.014205;Best_gnomAD_Mismatch_Het=1776;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:3228:28,9::1140:INV:INV00016940:NA:NA:chr5_79750489-chr5_79753717

0/1:NA:3228:0,0::336:INV:MantaBND_136633_0_1_0_0_0_0:NA:NA:chr5_79750489-chr5_79753717

0/1:NA:3224:0,0::260:INV:3323_1:NA:NA:chr5_79750493-chr5_79753717

split

q14.1

CMYA5

NM_153610

79689835

79800222

3229

119

yes

intron5-intron6

CDS

923

79750488

79753717

dbVar

chr5:79531454-79772168;chr5:79672056-79773955

0.01

dbVar

chr5:79531454-79772168;chr5:79672056-79773955

0.01

IMH

5:24758176-102357714;5:40738518-84864090;5:58813595-102383104

0.0576

77.74

-0.42279

0.206259

-0.01032

-0.72954

-2.63571

202333

1.35E-54

3.81E-43

0.377

Holoprosencephaly;abnormal cerebellum morphology

full=NA

0/1

10_123888363_123889122_DEL_1

1.24E+08

-758

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:46419:0:1:0:0:0

GAACCCCTCACTCCCACCTCAGTGCCTCATACATAGCATTGCATCATCCACCCAGTGAAGCAAAGTACAGAAGTTTGCATTAAACACTCCAGGCCACAGTCCAATGTTCCTTCCTATGTAAGTGCCTTCCTAAGATATTCCAAAACAATCCAATGCAGAGATAAGTGCTTCTATTACACCACGAGCAGCATATAGATCAAGCCGCTACTTAAAGTAGAAAAAAAATAATTTTCTCCTAGTGTAGTTTAACTGCACAAAACTGTCACTGATTCCCCTAACTAAGTTCACGCTTAAACCAGTCTTCCCACTTTGGTCCAGGGCAGAGGATTCTGCTGAGCAAACACCAAAATAAAAAAGGACAGGAGTTAAAAATATGAGATAAATGTCACACTTGTCTTGTCATGGTTGGGGAGAGCTCTAAAAAAGCCCCACAGAATTCATTAGAAACACAGCTGACATGGTAGCAGGTCTGCAGGCAGCTGTCCCAACAGGCCTCTGATGTGAGTCTCTAGATCTTCCGAAGACGTGTTTTCAGTATGGGGCTTGGAGATCCCGGTGGATGCCAGGGCTGCGGTGAACTGGGCAATGTGTCCTGCAGGAGCAGAGGCTAGGCACCGAATCAACAGGCTCCCCCATGGCCTGTCTCTACCTGCAAGATGGCCTTCCAAAACCAAATGAGCTTTTTCTTGCAAATTCAGGTTACACTCTGATTTCTCCTCCAGAGACCCCATTCCAAGAGTGGCAAGAGCTGTTTCTCCA

1560

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-758;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=10;END=123889121;CIPOS=0,1;CIEND=0,1;STRANDS=+;Max_AF=3.419e-05;Max_Het=3;Max_HomAlt=0;Max_PopMax_AF=0.000454;CCDG_Count=1;Best_CCDG_ID=156990;Best_CCDG_OFP=0.998682;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;SV_Cov=1;CCDG_SV_Cov=0.998682;TOPMed_Count=0;Best_TOPMed_ID=DEL_10:121934616-128427106;Best_TOPMed_OFP=0.000116904;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.28844e-06;Best_TOPMed_Mismatch_ID=DUP_10:123775202-124006800;Best_TOPMed_Mismatch_OFP=0.0032772;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;ThousG_SV_Cov=0;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr10_028858dd;Best_gnomAD_OFP=0.998682;Best_gnomAD_AF=2.4e-05;Best_gnomAD_Het=3;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000454;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr10_ad8d2382;Best_gnomAD_Mismatch_OFP=0.0484087;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:759:16,13:+:1560:DEL:DEL00033705:NA:NA:chr10_123888363-chr10_123889122

0/1:NA:758:0,0:+:898:DEL:MantaDEL_46419_0_1_0_0_0:GAACCCCTCACTCCCACCTCAGTGCCTCATACATAGCATTGCATCATCCACCCAGTGAAGCAAAGTACAGAAGTTTGCATTAAACACTCCAGGCCACAGTCCAATGTTCCTTCCTATGTAAGTGCCTTCCTAAGATATTCCAAAACAATCCAATGCAGAGATAAGTGCTTCTATTACACCACGAGCAGCATATAGATCAAGCCGCTACTTAAAGTAGAAAAAAAATAATTTTCTCCTAGTGTAGTTTAACTGCACAAAACTGTCACTGATTCCCCTAACTAAGTTCACGCTTAAACCAGTCTTCCCACTTTGGTCCAGGGCAGAGGATTCTGCTGAGCAAACACCAAAATAAAAAAGGACAGGAGTTAAAAATATGAGATAAATGTCACACTTGTCTTGTCATGGTTGGGGAGAGCTCTAAAAAAGCCCCACAGAATTCATTAGAAACACAGCTGACATGGTAGCAGGTCTGCAGGCAGCTGTCCCAACAGGCCTCTGATGTGAGTCTCTAGATCTTCCGAAGACGTGTTTTCAGTATGGGGCTTGGAGATCCCGGTGGATGCCAGGGCTGCGGTGAACTGGGCAATGTGTCCTGCAGGAGCAGAGGCTAGGCACCGAATCAACAGGCTCCCCCATGGCCTGTCTCTACCTGCAAGATGGCCTTCCAAAACCAAATGAGCTTTTTCTTGCAAATTCAGGTTACACTCTGATTTCTCCTCCAGAGACCCCATTCCAAGAGTGGCAAGAGCTGTTTCTCCA:G:chr10_123888363-chr10_123889121

0/1:NA:757:0,0:+:794:DEL:6318:NA:NA:chr10_123888364-chr10_123889121

split

q26.13

CPXM2

NM_198148

1.24E+08

760

intron1-intron1

CDS

2233

1.24E+08

dbVar

chr10:121962383-124521347

0.01

55.19

-0.63744

0.863002

0.269837

1.988612

0.415814

119587

5.49E-13

1.83E-10

full=1

0/1

19_4005348_4159440_DEL_1

4005348

4159440

-154090

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:79083:0:1:0:0:0

1740

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-154090;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=19;END=4159440;CIPOS=-2,0;CIEND=-5,0;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=253950;Best_CCDG_OFP=0.113861;Best_CCDG_AF=6.839e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=490213;Best_CCDG_Mismatch_OFP=0.150976;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=0.735014;CCDG_SV_Cov=0.290815;TOPMed_Count=0;Best_TOPMed_ID=DEL_19:4130566-4146337;Best_TOPMed_OFP=0.102362;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000108719;Best_TOPMed_Mismatch_ID=INV_19:3851264-4364229;Best_TOPMed_Mismatch_OFP=0.300392;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0.400108;ThousG_Count=0;Best_ThousG_ID=HGSV_70074;Best_ThousG_OFP=0.0204879;Best_ThousG_AF=0.000312;Best_ThousG_Het=2;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.00112;Best_ThousG_Mismatch_ID=HGSV_70075;Best_ThousG_Mismatch_OFP=0.148371;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000312;Best_ThousG_Mismatch_Het=2;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.0925492;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr19_5ba69aa0;Best_gnomAD_OFP=0.172119;Best_gnomAD_AF=6.3e-05;Best_gnomAD_Het=8;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000493;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr19_9114b2c5;Best_gnomAD_Mismatch_OFP=0.367091;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=0.733638

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:154087:26,11:+:1740:DEL:DEL00054230:NA:NA:chr19_4005348-chr19_4159435

0/1:NA:154090:0,0:+:999:DEL:MantaDEL_79083_0_1_0_0_0:NA:NA:chr19_4005350-chr19_4159440

0/1:NA:154090:0,0:+:650:DEL:10046:NA:NA:chr19_4005350-chr19_4159440

split

p13.3

CREB3L3

NM_001271996

4153630

4173054

5810

457

yes

txStart-intron3

5'UTR-CDS

223

4153630

4159440

dbVar:nssv18787865

19:4156976-4157315

Hypertriglyceridemia_2

IMH

19:1692676-41507766

0.0103

82.61

-0.25549

-1.46872

-1.15338

0.144667

-0.01045

hypertriglyceridemia;hypertriglyceridemia 1;hypertriglyceridemia 2

Limited;Strong

21666694;24503134;26427795

84699

611998

Hypertriglyceridemia 2, 619324 (3) AD

yes

8.06E-14

1.59E-09

full=5

0/1

19_4005230_4159441_DUP_1

4005230

4159441

154171

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:79083:0:1:1:0:0

999

PASS

SUPP=3;SUPP_VEC=111;SVLEN=154171;SVTYPE=DUP;SVMETHOD=SURVIVOR1.0.7;CHR2=19;END=4159423;CIPOS=-22,1;CIEND=0,18;STRANDS=-;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=490213;Best_CCDG_OFP=0.150896;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=253950;Best_CCDG_Mismatch_OFP=0.113801;Best_CCDG_Mismatch_SVTYPE=DEL;Best_CCDG_Mismatch_AF=6.839e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=0.97591;CCDG_SV_Cov=0.202644;TOPMed_Count=0;Best_TOPMed_ID=DUP_19:4084740-4226078;Best_TOPMed_OFP=0.255974;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.35898e-06;Best_TOPMed_Mismatch_ID=INV_19:3851264-4364229;Best_TOPMed_Mismatch_OFP=0.30055;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0.741834;ThousG_Count=0;Best_ThousG_ID=HGSV_70075;Best_ThousG_OFP=0.14813;Best_ThousG_AF=0.000312;Best_ThousG_Het=2;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.002041;Best_ThousG_Mismatch_ID=HGSV_70074;Best_ThousG_Mismatch_OFP=0.0204771;Best_ThousG_Mismatch_SVTYPE=DEL;Best_ThousG_Mismatch_AF=0.000312;Best_ThousG_Mismatch_Het=2;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.285162;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DUP_chr19_9114b2c5;Best_gnomAD_OFP=0.36671;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=7.9e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr19_5ba69aa0;Best_gnomAD_Mismatch_OFP=0.172029;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=6.3e-05;Best_gnomAD_Mismatch_Het=8;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=0.960771

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:154170:21,8:-:600:DUP:DUP00054229:NA:NA:chr19_4005253-chr19_4159423

0/1:NA:154171:0,0:-:999:DUP:MantaDUP_TANDEM_79083_0_1_1_0_0:NA:NA:chr19_4005252-chr19_4159423

0/1:NA:154211:0,0:-:106:DUP:10045:NA:NA:chr19_4005230-chr19_4159441

split

p13.3

CREB3L3

NM_001271996

4153630

4173054

5811

457

yes

txStart-intron3

5'UTR-CDS

222

4153630

4159441

dbVar:nssv18787865

19:4156976-4157315

Hypertriglyceridemia_2

IMH

19:1692676-41507766

0.0103

82.61

-0.25549

-1.46872

-1.15338

0.144667

-0.01045

hypertriglyceridemia;hypertriglyceridemia 1;hypertriglyceridemia 2

Limited;Strong

21666694;24503134;26427795

84699

611998

Hypertriglyceridemia 2, 619324 (3) AD

yes

8.06E-14

1.59E-09

full=3

0/1

10_66739832_66748834_DEL_1

66739832

66748834

-9001

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:41772:0:1:0:0:0

900

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-9001;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=10;END=66748833;CIPOS=0,4;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=151651;Best_CCDG_OFP=0.152246;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=550410;Best_CCDG_Mismatch_OFP=0.00023818;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_10:66743635-66747408;Best_TOPMed_OFP=0.419351;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000108861;Best_TOPMed_Mismatch_ID=INV_10:66737797-66745382;Best_TOPMed_Mismatch_OFP=0.451163;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_17158;Best_ThousG_OFP=0.141815;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.000832;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr10_ae68f6a5;Best_gnomAD_OFP=0.573931;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=1.7e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr10_bb431596;Best_gnomAD_Mismatch_OFP=0.113538;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:9002:19,11:+:900:DEL:DEL00032380:NA:NA:chr10_66739832-chr10_66748834

0/1:NA:9001:0,0:+:408:DEL:MantaDEL_41772_0_1_0_0_0:NA:NA:chr10_66739832-chr10_66748833

0/1:NA:8997:0,0:+:389:DEL:6102:NA:NA:chr10_66739836-chr10_66748833

split

q21.3

CTNNA3

XM_017016157

65912522

66838602

9003

intron3-intron3

CDS

17429

66739831

66748834

dbVar;gnomAD-SV_v3_DEL_chr10_a13546d2;gnomAD-SV_v3_DEL_chr10_e433cf8f;gnomAD-SV_v3_DEL_chr10_f70efaa2

chr10:37996824-76847693;chr10:53764413-94620402;chr10:59459006-109812369;chr10:66401619-66756961;chr10:66507333-66750567;chr10:66558659-66899003;chr10:66627986-66764657;chr10:66653518-66833431;chr10:66689895-66832247;chr10:66691061-66754539

0.3941

2.58

-2.62354

-1.83693

-2.47163

-0.81711

-2.50548

arrhythmogenic right ventricular cardiomyopathy;arrhythmogenic right ventricular dysplasia 13

Limited

21254927;23136403;28202948;28416588;30847666;32880476

29119

607667

Arrhythmogenic right ventricular dysplasia 13, 615616 (3) AD

yes

1.02E-12

6.54E-08

full=1

0/1

1_46934266_46938413_DEL_1

46934266

46938413

-4146

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:192794:0:1:0:0:0

368

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-4146;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=1;END=46938412;CIPOS=0,4;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=456535;Best_CCDG_Mismatch_OFP=0.0351945;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=INV_1:46904533-46976957;Best_TOPMed_Mismatch_OFP=0.0572584;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=1.4e-05;Best_TOPMed_Mismatch_Het=4;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_3133;Best_ThousG_Mismatch_OFP=0.0351945;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000312;Best_ThousG_Mismatch_Het=0;Best_ThousG_Mismatch_HomAlt=1;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr1_c9a27eb5;Best_gnomAD_OFP=0.0505233;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=1.7e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr1_536cca67;Best_gnomAD_Mismatch_OFP=0.0351945;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:4147:15,10:+:364:DEL:DEL00002018:NA:NA:chr1_46934266-chr1_46938413

0/1:NA:4146:0,0:+:333:DEL:MantaDEL_192794_0_1_0_0_0:NA:NA:chr1_46934266-chr1_46938412

0/1:NA:4142:0,0:+:368:DEL:402:NA:NA:chr1_46934270-chr1_46938412

split

p33

CYP4A11

NM_000778

46929187

46941476

4148

803

yes

intron1-exon8

CDS

46934265

46938413

dbVar

chr1:46851047-46968877;chr1:46897535-46950292;chr1:46906324-47107665

0.01

gnomAD-SV_v3_DEL_chr1_cf5f2df8

chr1:13203398-167621949

0.1676

IMH

1:7601938-50381771;1:10187873-186857210;1:16798094-234784887;1:31594523-94732184;1:36241392-73134343;1:41598779-54316740;1:46855517-47110532;1:46855922-47110120;1:46928737-47150547

0.4698

80.74

1.525402

-1.04546

1579

1.09E-24

1.57E-15

full=3

0/1

7_158845413_158849948_DEL_1

1.59E+08

-4534

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:117616:0:1:0:0:0

840

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-4534;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=7;END=158849947;CIPOS=0,5;CIEND=0,1;STRANDS=+;Max_AF=0.000468;Max_Het=3;Max_HomAlt=0;Max_PopMax_AF=0.002496;CCDG_Count=0;Best_CCDG_Mismatch_ID=531469;Best_CCDG_Mismatch_OFP=0.0204096;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=6.839e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_7:158840783-158851228;Best_TOPMed_OFP=0.434096;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.00010879;TOPMed_Mismatches=INV_7:158845422-158849948;TOPMed_Mismatches_Count=1;TOPMed_Mismatch_SVTYPEs=INV;Best_TOPMed_Mismatch_ID=INV_7:158845422-158849948;Best_TOPMed_Mismatch_OFP=0.998015;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=3.9e-05;Best_TOPMed_Mismatch_Het=11;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_150660;Best_ThousG_OFP=0.998897;Best_ThousG_AF=0.000468;Best_ThousG_Het=3;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.002496;Best_ThousG_Mismatch_ID=HGSV_150654;Best_ThousG_Mismatch_OFP=0.00957005;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000312;Best_ThousG_Mismatch_Het=2;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.998897;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr7_be27f839;Best_gnomAD_OFP=0.998897;Best_gnomAD_AF=2.4e-05;Best_gnomAD_Het=3;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000682;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr7_f232bfce;Best_gnomAD_Mismatch_OFP=0.0346691;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:4535:24,11:+:840:DEL:DEL00025162:NA:NA:chr7_158845413-chr7_158849948

0/1:NA:4534:0,0:+:527:DEL:MantaDEL_117616_0_1_0_0_0:NA:NA:chr7_158845413-chr7_158849947

0/1:NA:4529:0,0:+:401:DEL:4931:NA:NA:chr7_158845418-chr7_158849947

split

q36.3

DYNC2I1

NM_001350914

1.59E+08

4536

intron1-intron1

5'UTR

5914

1.59E+08

dbVar

chr7:158644451-159005913;chr7:158779308-159164309;chr7:158804459-158851414;chr7:158827353-158934388

0.01

dbVar

chr7:158815335-158864408

0.01

Jeune syndrome;short rib-polydactyly syndrome, Verma-Naumoff type;short-rib thoracic dysplasia 8 with or without polydactyly

Strong;Supportive

23910462;23910462[PMID];26874042;28454995;29068549;29271569;9068549

55112

615462

Short-rib thoracic dysplasia 8 with or without polydactyly, 615503 (3) AR

0.6436

Cleft lip;Cleft palate;Cleft upper lip;Micrognathia;Short rib-polydactyly syndrome, Verma-Naumoff type

full=3

0/1

7_158840077_158850185_INV_1

1.59E+08

10108

INV

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaBND:117616:2:3:0:0:0:1

A]chr7:158850185]

984

PASS

SUPP=3;SUPP_VEC=111;SVLEN=10108;SVTYPE=INV;SVMETHOD=SURVIVOR1.0.7;CHR2=7;END=158850185;CIPOS=0,4;CIEND=0,0;STRANDS=;Max_AF=3.9e-05;Max_Het=11;Max_HomAlt=0;Max_PopMax_AF=0.00120297;CCDG_Count=0;Best_CCDG_Mismatch_ID=531469;Best_CCDG_Mismatch_OFP=0.0454953;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=6.839e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=1;Best_TOPMed_ID=INV_7:158840078-158850185;Best_TOPMed_OFP=1;Best_TOPMed_AF=3.9e-05;Best_TOPMed_Het=11;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.00120297;TOPMed_Mismatches=DEL_7:158840783-158851228;TOPMed_Mismatches_Count=1;TOPMed_Mismatch_SVTYPEs=DEL;Best_TOPMed_Mismatch_ID=DEL_7:158840783-158851228;Best_TOPMed_Mismatch_OFP=0.837386;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_150659;Best_ThousG_Mismatch_OFP=0.479591;Best_ThousG_Mismatch_SVTYPE=DEL;Best_ThousG_Mismatch_AF=0.000468;Best_ThousG_Mismatch_Het=3;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;gnomAD_Mismatches=gnomAD-SV_v3_DEL_chr7_700d536c;gnomAD_Mismatches_Count=1;gnomAD_Mismatch_SVTYPEs=DEL;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr7_700d536c;Best_gnomAD_Mismatch_OFP=0.837706;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=0

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:10108:24,7::984:INV:INV00025160:NA:NA:chr7_158840077-chr7_158850185

0/1:NA:10108:0,0::585:INV:MantaBND_117616_2_3_0_0_0_1:NA:NA:chr7_158840077-chr7_158850185

0/1:NA:10104:0,0::317:INV:4932_1:NA:NA:chr7_158840081-chr7_158850185

split

q36.3

DYNC2I1

NM_001350914

1.59E+08

10109

intron1-intron1

5'UTR

578

1.59E+08

dbVar

chr7:158644451-159005913;chr7:158779308-159164309;chr7:158804459-158851414;chr7:158827353-158934388

0.01

dbVar

chr7:158815335-158864408

0.01

Jeune syndrome;short rib-polydactyly syndrome, Verma-Naumoff type;short-rib thoracic dysplasia 8 with or without polydactyly

Strong;Supportive

23910462;23910462[PMID];26874042;28454995;29068549;29271569;9068549

55112

615462

Short-rib thoracic dysplasia 8 with or without polydactyly, 615503 (3) AR

0.6436

Cleft lip;Cleft palate;Cleft upper lip;Micrognathia;Short rib-polydactyly syndrome, Verma-Naumoff type

full=NA

0/1

10_92864682_92873535_DEL_1

92864682

92873535

-8852

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:43772:0:1:0:0:0

1080

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-8852;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=10;END=92873534;CIPOS=0,5;CIEND=0,1;STRANDS=+;Max_AF=0.003122;Max_Het=133;Max_HomAlt=5;Max_PopMax_AF=0.0202;CCDG_Count=1;Best_CCDG_ID=154088;Best_CCDG_OFP=0.999435;Best_CCDG_AF=0.00106;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=550410;Best_CCDG_Mismatch_OFP=0.000234237;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0.999435;TOPMed_Count=2;Best_TOPMed_ID=DEL_10:92864688-92873540;Best_TOPMed_OFP=0.998758;Best_TOPMed_AF=0.000507;Best_TOPMed_Het=133;Best_TOPMed_HomAlt=5;Best_TOPMed_PopMax_AF=0.0151186;Best_TOPMed_Mismatch_ID=DUP_10:92834902-92875100;Best_TOPMed_Mismatch_OFP=0.220224;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0.999435;ThousG_Count=1;Best_ThousG_ID=HGSV_18630;Best_ThousG_OFP=0.959779;Best_ThousG_AF=0.003122;Best_ThousG_Het=20;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.016639;Best_ThousG_Mismatch_ID=HGSV_18631;Best_ThousG_Mismatch_OFP=0.00587372;Best_ThousG_Mismatch_SVTYPE=INS;Best_ThousG_Mismatch_AF=0.001093;Best_ThousG_Mismatch_Het=7;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr10_3841b527;Best_gnomAD_OFP=0.986737;Best_gnomAD_AF=0.000722;Best_gnomAD_Het=89;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.0202;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr10_3d69cad9;Best_gnomAD_Mismatch_OFP=0.092979;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:8853:17,9:+:1080:DEL:DEL00032978:NA:NA:chr10_92864682-chr10_92873535

0/1:NA:8852:0,0:+:485:DEL:MantaDEL_43772_0_1_0_0_0:NA:NA:chr10_92864682-chr10_92873534

0/1:NA:8847:0,0:+:392:DEL:6204:NA:NA:chr10_92864687-chr10_92873534

split

q23.33

EXOC6

XM_017016347

92872843

93059490

692

yes

txStart-intron1

5'UTR-CDS

223

92872843

92873535

1000g;dbVar;gnomAD-SV_v3_DEL_chr10_244783f4;gnomAD-SV_v3_DEL_chr10_e433cf8f;gnomAD-SV_v3_DEL_chr10_f048c376;gnomAD-SV_v3_DEL_chr10_f70efaa2

chr10:53764413-94620402;chr10:59459006-109812369;chr10:90655870-109812371;chr10:90661220-109812370;chr10:92864611-92873535;10:92864612-92873535

0.4959

7.76

0.185137

0.111528

0.181862

-0.397

0.598347

54536

2.44E-07

2.82E-02

full=3

0/1

6_5606319_5609855_DEL_1

5606319

5609855

-3517

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:39071:0:1:0:0:0

954

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-3517;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=6;END=5609855;CIPOS=-19,3;CIEND=-3,0;STRANDS=+;Max_AF=0.005464;Max_Het=170;Max_HomAlt=7;Max_PopMax_AF=0.029118;CCDG_Count=0;Best_CCDG_Mismatch_ID=369898_2;Best_CCDG_Mismatch_OFP=0.000284252;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.001094;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=2;Best_TOPMed_ID=DEL_6:5606321-5609856;Best_TOPMed_OFP=0.994628;Best_TOPMed_AF=0.000633;Best_TOPMed_Het=170;Best_TOPMed_HomAlt=4;Best_TOPMed_PopMax_AF=0.0172301;Best_TOPMed_Mismatch_ID=INV_6:5606188-5607137;Best_TOPMed_Mismatch_OFP=0.191295;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=1.1e-05;Best_TOPMed_Mismatch_Het=3;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_130286;Best_ThousG_OFP=0.994628;Best_ThousG_AF=0.005464;Best_ThousG_Het=21;Best_ThousG_HomAlt=7;Best_ThousG_PopMax_AF=0.029118;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr6_3bb97935;Best_gnomAD_OFP=0.994628;Best_gnomAD_AF=0.000864;Best_gnomAD_Het=101;Best_gnomAD_HomAlt=4;Best_gnomAD_PopMax_AF=0.021108;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr6_ce5e12be;Best_gnomAD_Mismatch_OFP=0.0118053;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:3511:18,10:+:954:DEL:DEL00018600:NA:NA:chr6_5606341-chr6_5609852

0/1:NA:3517:0,0:+:416:DEL:MantaDEL_39071_0_1_0_0_0:NA:NA:chr6_5606338-chr6_5609855

0/1:NA:3536:0,0:+:332:DEL:3665:NA:NA:chr6_5606319-chr6_5609855

split

p25.1

FARS2

XM_047418086

5249933

5771583

3537

intron5-intron5

CDS

3313

5606318

5609855

dbVar

chr6:5578125-5645911

0.01

dbVar

chr6:5562842-5641064;chr6:5606319-5609855

0.01

44.7

-2.62354

-0.67047

-1.79433

-0.69919

0.096804

Leigh syndrome;combined oxidative phosphorylation defect type 14;hereditary spastic paraplegia 77

Limited;Moderate;Strong;Supportive

22499341;22499341[PMID];22833457;25851414;26553276;26553276[PMID];27549011;27652284;29126765

10667

611592

Combined oxidative phosphorylation deficiency 14, 614946 (3) AR;Spastic paraplegia 77, AR, 617046 (3) AR

yes

9.30E-09

4.54E-06

0.409

Autosomal recessive spastic paraplegia type 77;Cleft palate;Macrodontia of permanent maxillary central incisor;Micrognathia;Retrognathia

full=1

0/1

10_13652960_13653018_DEL_1

13652960

13653018

-57

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:37558:0:0:0:0:0

ACAGAGGGCAGAGCTGGAATTCCAGCTCCCTCCAGCTGTCAGACTTTGGGCCAGGCAC

720

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-57;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=10;END=13653017;CIPOS=0,0;CIEND=0,1;STRANDS=+;Max_AF=0.00921;Max_Het=374;Max_HomAlt=11;Max_PopMax_AF=0.049085;CCDG_Count=0;Best_CCDG_Mismatch_ID=145531_1;Best_CCDG_Mismatch_OFP=0.0172414;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.001368;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=1;Best_TOPMed_ID=DEL_10:13652961-13653017;Best_TOPMed_OFP=1;Best_TOPMed_AF=0.001071;Best_TOPMed_Het=257;Best_TOPMed_HomAlt=6;Best_TOPMed_PopMax_AF=0.0312274;Best_TOPMed_Mismatch_ID=DUP_10:13580086-13654763;Best_TOPMed_Mismatch_OFP=0.000776657;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=1.4e-05;Best_TOPMed_Mismatch_Het=4;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_14079;Best_ThousG_OFP=1;Best_ThousG_AF=0.00921;Best_ThousG_Het=39;Best_ThousG_HomAlt=10;Best_ThousG_PopMax_AF=0.049085;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr10_2288408b;Best_gnomAD_OFP=0.865672;Best_gnomAD_AF=0.003142;Best_gnomAD_Het=374;Best_gnomAD_HomAlt=11;Best_gnomAD_PopMax_AF=0.034968;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr10_f8fe9e87;Best_gnomAD_Mismatch_OFP=0.000776657;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:58:0,0:+:720:DEL:DEL00030300:NA:NA:chr10_13652960-chr10_13653018

0/1:NA:57:0,0:+:660:DEL:MantaDEL_37558_0_0_0_0_0:ACAGAGGGCAGAGCTGGAATTCCAGCTCCCTCCAGCTGTCAGACTTTGGGCCAGGCAC:A:chr10_13652960-chr10_13653017

0/1:NA:57:0,0:+:293:DEL:5923:NA:NA:chr10_13652960-chr10_13653017

split

p13

FRMD4A

NM_001318338

13643705

13707567

intron12-intron12

CDS

985

13652959

13653018

dbVar

chr10:13543727-13697859;chr10:13580085-13654763

0.01

21.52

0.79038

-0.06336

0.267812

-0.26748

3.274066

severe intellectual disability-corpus callosum agenesis-facial dysmorphism-cerebellar ataxia syndrome

Limited;Strong;Supportive

25388005;25388005[PMID];30214071;34869127

55691

616305

?Corpus callosum, agenesis of, with facial anomalies and cerebellar ataxia, 616819 (3) AR

yes

1.0000e

1.00E+00

0.4303

Cleft lip;Severe intellectual disability-corpus callosum agenesis-facial dysmorphism-cerebellar ataxia syndrome;Thick lower lip vermilion

Cleft lip;Cleft palate;Hypertelorism;Micrognathia;Microphthalmia;abnormal retina blood vessel morphology

full=3

0/1

14_66758452_66758602_DEL_1

66758452

66758602

-149

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:75072:0:1:0:0:0

TCAGAGGCTTGTCTAAGGATCCCCAGTAAAAGGGAGCCATCGTTTGAAGCTACAGTTGCGTGACCATTTTGAGTTTGATGGCCTGAAGGCGAGAAGAGAGAAACTGGGTTATTAGAAGACATGTATCAAAATGAAAAAAGGGGGTAAGGA

840

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-149;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=14;END=66758601;CIPOS=0,3;CIEND=0,1;STRANDS=+;Max_AF=0.000624;Max_Het=27;Max_HomAlt=0;Max_PopMax_AF=0.00411;CCDG_Count=1;Best_CCDG_ID=206074;Best_CCDG_OFP=0.98;Best_CCDG_AF=0.0003419;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=562107;Best_CCDG_Mismatch_OFP=4.203e-06;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_14:66756635-66760354;Best_TOPMed_OFP=0.0403117;Best_TOPMed_AF=8.9e-05;Best_TOPMed_Het=25;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000319966;Best_TOPMed_Mismatch_ID=DUP_14:66721655-66768709;Best_TOPMed_Mismatch_OFP=0.00318769;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_46304;Best_ThousG_OFP=0.98;Best_ThousG_AF=0.000624;Best_ThousG_Het=4;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.003328;ThousG_SV_Cov=0.98;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr14_21c34aba;Best_gnomAD_OFP=0.98;Best_gnomAD_AF=0.000215;Best_gnomAD_Het=27;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.00411;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_INV_chr14_53e4a3ab;Best_gnomAD_Mismatch_OFP=3.31211e-05;Best_gnomAD_Mismatch_SVTYPE=INV;Best_gnomAD_Mismatch_AF=2.4e-05;Best_gnomAD_Mismatch_Het=3;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:150:0,0:+:840:DEL:DEL00042430:NA:NA:chr14_66758452-chr14_66758602

0/1:NA:149:0,0:+:585:DEL:MantaDEL_75072_0_1_0_0_0:TCAGAGGCTTGTCTAAGGATCCCCAGTAAAAGGGAGCCATCGTTTGAAGCTACAGTTGCGTGACCATTTTGAGTTTGATGGCCTGAAGGCGAGAAGAGAGAAACTGGGTTATTAGAAGACATGTATCAAAATGAAAAAAGGGGGTAAGGA:T:chr14_66758452-chr14_66758601

0/1:NA:146:0,0:+:353:DEL:8086:NA:NA:chr14_66758455-chr14_66758601

split

q23.3

GPHN

NM_001024218

66508146

67181803

151

intron2-intron2

CDS

17861

66758451

66758602

gnomAD-SV_v3_DEL_chr14_040215df;gnomAD-SV_v3_DEL_chr14_aa7bf92b

chr14:41140072-69277618;chr14:56471274-99420950

0.633

IMH

14:23629193-97505158

0.4022

2.69

0.037021

-0.55458

-0.32602

0.35526

3.981971

hereditary hyperekplexia;sulfite oxidase deficiency due to molybdenum cofactor deficiency type C

AD;AR

Limited;Moderate;Strong;Supportive

11095995;12684523;20301437[PMID];22040219;9812897

10243

603930

Molybdenum cofactor deficiency C, 615501 (3) AR

yes

1.00E+00

0.4913

Cleft lip;Cleft palate;Holoprosencephaly;Hypertelorism;Micrognathia;Microphthalmia;abnormal motor neuron morphology;abnormal retina inner plexiform layer morphology

full=3

0/1

3_7562320_7562538_DEL_1

7562320

7562538

-217

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:157633:0:1:0:0:0

GTGAAGTAATAGTTCACTTTCCCCCTTATATTTTTTTAAAAAGAAAAAAAAAATACTAGTTTTAATTGACTATTACCCCTCTAAAATACTCTCAAATATAGAGTCATATTTGGTTTTTCTGTAACTCCATTAATTGACCTCACAGAAGTTAAGTGAGTCGATCAAGATGATCTAGCCAGAATTGAGAGCGTTTGCAACCCAGTTCATGTTCTATAAGT

900

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-217;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=3;END=7562537;CIPOS=0,1;CIEND=0,1;STRANDS=+;Max_AF=0.000312;Max_Het=24;Max_HomAlt=0;Max_PopMax_AF=0.003191;CCDG_Count=1;Best_CCDG_ID=311214;Best_CCDG_OFP=0.995413;Best_CCDG_AF=0.0002393;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=505309;Best_CCDG_Mismatch_OFP=0.00318746;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0.995413;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DUP_3:7509306-7783201;Best_TOPMed_Mismatch_OFP=0.00079592;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=1;Best_ThousG_ID=HGSV_97735;Best_ThousG_OFP=0.995413;Best_ThousG_AF=0.000312;Best_ThousG_Het=2;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.001664;Best_ThousG_Mismatch_ID=HGSV_97728;Best_ThousG_Mismatch_OFP=0.000861827;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000312;Best_ThousG_Mismatch_Het=2;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.995413;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr3_6696a17a;Best_gnomAD_OFP=0.889908;Best_gnomAD_AF=0.000191;Best_gnomAD_Het=24;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.003191;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr3_bfde11c2;Best_gnomAD_Mismatch_OFP=0.000433586;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:218:0,0:+:900:DEL:DEL00009225:NA:NA:chr3_7562320-chr3_7562538

0/1:NA:217:0,0:+:574:DEL:MantaDEL_157633_0_1_0_0_0:GTGAAGTAATAGTTCACTTTCCCCCTTATATTTTTTTAAAAAGAAAAAAAAAATACTAGTTTTAATTGACTATTACCCCTCTAAAATACTCTCAAATATAGAGTCATATTTGGTTTTTCTGTAACTCCATTAATTGACCTCACAGAAGTTAAGTGAGTCGATCAAGATGATCTAGCCAGAATTGAGAGCGTTTGCAACCCAGTTCATGTTCTATAAGT:G:chr3_7562320-chr3_7562537

0/1:NA:216:0,0:+:407:DEL:1877:NA:NA:chr3_7562321-chr3_7562537

split

p26.1

GRM7

XM_047448053

6861114

7680295

219

intron7-intron7

CDS

15883

7562319

7562538

dbVar

chr3:7413097-7915880;chr3:7507741-7629043;chr3:7509066-7752803

0.01

dbVar

chr3:2977315-7774313

0.01

8.74

0.251415

3.075868

neurodevelopmental disorder with seizures, hypotonia, and brain imaging abnormalities

Moderate;Strong

27435318;28097321;32286009

2917

604101

Neurodevelopmental disorder with seizures, hypotonia, and brain abnormalities, 618922 (3) AR

yes

9.99E-01

0.5649

Cleft lip;Cleft palate;Early infantile epileptic encephalopathy;Micrognathia;Short finger

full=3

0/1

11_113935087_113935461_DEL_1

1.14E+08

-373

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:34525:0:0:0:0:0

TATTATTTGTAGTTACATGTCACTTTCCTTCACCCTAAATGTTAATTCGTCAACAGCAGCTGAAGGTTTTCTATATACCATCTCCATTTTAATTATGATGAACAGAGACAGAAGATTGTCTAATGGAGGGGAGGCTTCCCTGGATCTCAGAGCCATGGTCCAGTTCCTCTGCTCTCCTCACTGCCATGCTTCCCCCCGGGTACGTTTTGAAGTGGAAGTGTGCTGGAGGCAGGTGCAATTTGATTTCATGCTCTTGGAACTTTTCCATGGGTCCTTTTGCCCCGGGGGTGGACGTGGGTTATCTAGCAGGGCTGGCCTCTGCCCTGGTCCTCAGGAGCAGAGTAGGGAGAGAATCCTGAGTAGAGTCACAGATC

611

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-373;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=11;END=113935460;CIPOS=0,2;CIEND=0,1;STRANDS=+;Max_AF=0.0028;Max_Het=614;Max_HomAlt=0;Max_PopMax_AF=0.00483092;CCDG_Count=0;Best_CCDG_Mismatch_ID=468820;Best_CCDG_Mismatch_OFP=0.563571;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=0.1058;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=1;Best_TOPMed_ID=DEL_11:113935090-113935460;Best_TOPMed_OFP=0.994652;Best_TOPMed_AF=0.0028;Best_TOPMed_Het=614;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.00483092;Best_TOPMed_Mismatch_ID=INV_11:107936486-114400629;Best_TOPMed_Mismatch_OFP=5.78576e-05;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0.994652;ThousG_Count=0;Best_ThousG_ID=HGSV_27620;Best_ThousG_OFP=4.5051e-05;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.000789;Best_ThousG_Mismatch_ID=HGSV_28027;Best_ThousG_Mismatch_OFP=0.563571;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.102124;Best_ThousG_Mismatch_Het=336;Best_ThousG_Mismatch_HomAlt=159;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr11_15837620;Best_gnomAD_OFP=1.9578e-05;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000248;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr11_8701e58a;Best_gnomAD_Mismatch_OFP=8.59435e-05;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.066172;Best_gnomAD_Mismatch_Het=7511;Best_gnomAD_Mismatch_HomAlt=169;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:374:0,0:+:540:DEL:DEL00036329:NA:NA:chr11_113935087-chr11_113935461

0/1:NA:373:0,0:+:611:DEL:MantaDEL_34525_0_0_0_0_0:TATTATTTGTAGTTACATGTCACTTTCCTTCACCCTAAATGTTAATTCGTCAACAGCAGCTGAAGGTTTTCTATATACCATCTCCATTTTAATTATGATGAACAGAGACAGAAGATTGTCTAATGGAGGGGAGGCTTCCCTGGATCTCAGAGCCATGGTCCAGTTCCTCTGCTCTCCTCACTGCCATGCTTCCCCCCGGGTACGTTTTGAAGTGGAAGTGTGCTGGAGGCAGGTGCAATTTGATTTCATGCTCTTGGAACTTTTCCATGGGTCCTTTTGCCCCGGGGGTGGACGTGGGTTATCTAGCAGGGCTGGCCTCTGCCCTGGTCCTCAGGAGCAGAGTAGGGAGAGAATCCTGAGTAGAGTCACAGATC:T:chr11_113935087-chr11_113935460

0/1:NA:371:0,0:+:401:DEL:6861:NA:NA:chr11_113935089-chr11_113935460

split

q23.2

HTR3B

XM_024448767

1.14E+08

375

intron6-intron6

CDS

1993

1.14E+08

57.7

-0.74871

0.590207

0.068695

0.432545

-0.26425

9177

2.48E-07

6.15E-07

full=3

0/1

1_228180857_228185000_DEL_1

2.28E+08

-4142

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:203946:0:1:0:0:0

1214

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-4142;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=1;END=228184999;CIPOS=0,3;CIEND=0,1;STRANDS=+;Max_AF=0.000781;Max_Het=129;Max_HomAlt=1;Max_PopMax_AF=0.00534468;CCDG_Count=0;Best_CCDG_Mismatch_ID=141197_1;Best_CCDG_Mismatch_OFP=0.000241371;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.007283;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=1;Best_TOPMed_ID=DEL_1:228180861-228185003;Best_TOPMed_OFP=0.998311;Best_TOPMed_AF=0.000467;Best_TOPMed_Het=129;Best_TOPMed_HomAlt=1;Best_TOPMed_PopMax_AF=0.00534468;Best_TOPMed_Mismatch_ID=DUP_1:228142774-228211680;Best_TOPMed_Mismatch_OFP=0.0601236;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_11644;Best_ThousG_OFP=0.998073;Best_ThousG_AF=0.000781;Best_ThousG_Het=5;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.003328;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr1_491b7c9a;Best_gnomAD_OFP=0.976662;Best_gnomAD_AF=0.000365;Best_gnomAD_Het=44;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.003631;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr1_4733695d;Best_gnomAD_Mismatch_OFP=0.0240871;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:4143:16,11:+:1214:DEL:DEL00004747:NA:NA:chr1_228180857-chr1_228185000

0/1:NA:4142:0,0:+:375:DEL:MantaDEL_203946_0_1_0_0_0:NA:NA:chr1_228180857-chr1_228184999

0/1:NA:4139:0,0:+:596:DEL:959:NA:NA:chr1_228180860-chr1_228184999

split

q42.13

IBA57

NM_001010867

2.28E+08

1401

exon3-txEnd

3'UTR

5735

2.28E+08

dbVar

chr1:228180819-228184966;chr1:228180831-228184999

0.01

IMH

1:16798094-234784887;1:107555343-232824950;1:208408863-234126540

0.3106

80.91

0.234203

0.61881

0.672301

0.547812

0.716851

hereditary spastic paraplegia 74;multiple mitochondrial dysfunctions syndrome 3

Limited;Strong;Supportive

23462291;23462291[PMID];25609768;25609768[PMID];2569768;25971455;27785568;28671726

200205

615316

?Spastic paraplegia 74, AR, 616451 (3) AR;Multiple mitochondrial dysfunctions syndrome 3, 615330 (3) AR

yes

8.39E-03

8.30E-02

0.4683

Cleft palate;High palate;Micrognathia;Multiple mitochondrial dysfunctions syndrome 3;Retrognathia

full=3

0/1

X_105056165_105057819_DUP_1

1.05E+08

1651

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:5078:0:1:0:0:0

1680

PASS

SUPP=3;SUPP_VEC=111;SVLEN=1651;SVTYPE=DUP;SVMETHOD=SURVIVOR1.0.7;CHR2=X;END=105057816;CIPOS=0,1;CIEND=0,3;STRANDS=-;Max_AF=0.000218878;Max_Het=17;Max_HomAlt=2;Max_PopMax_AF=0.00763914;CCDG_Count=0;Best_CCDG_Mismatch_ID=449704_1;Best_CCDG_Mismatch_OFP=0.000605327;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.0003077;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DUP_23:105010354-105059267;Best_TOPMed_OFP=0.0337729;Best_TOPMed_AF=9e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=1.64107e-05;Best_TOPMed_Mismatch_ID=DEL_23:105051214-105069228;Best_TOPMed_Mismatch_OFP=0.0916963;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=5e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_170862;Best_ThousG_Mismatch_OFP=0.000605327;Best_ThousG_Mismatch_SVTYPE=INS;Best_ThousG_Mismatch_AF=0.0025;Best_ThousG_Mismatch_Het=0;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DUP_chrX_d04d6449;Best_gnomAD_OFP=0.998187;Best_gnomAD_AF=0.000218878;Best_gnomAD_Het=17;Best_gnomAD_HomAlt=2;Best_gnomAD_PopMax_AF=0.00763914;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chrX_b5294bd1;Best_gnomAD_Mismatch_OFP=0.618644;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=0.000145946;Best_gnomAD_Mismatch_Het=13;Best_gnomAD_Mismatch_HomAlt=1;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:1650:7,20:-:1680:DUP:DUP00063615:NA:NA:chrX_105056166-chrX_105057816

0/1:NA:1651:0,0:-:999:DUP:MantaDUP_TANDEM_5078_0_1_0_0_0:NA:NA:chrX_105056165-chrX_105057816

1/1:NA:1654:0,0:-:534:DUP:11517:NA:NA:chrX_105056165-chrX_105057819

split

q22.3

IL1RAPL2

NM_017416

1.05E+08

1.06E+08

1655

intron2-intron2

CDS

137655

1.05E+08

dbVar

chrX:105035005-105106372

0.01

gnomAD-SV_v3_DEL_chrX_25f0d36f;gnomAD-SV_v3_DEL_chrX_a8ba77a6

chrX:85568529-142769920;chrX:101187696-118298467

0.4905

IMH

X:101070962-130555575;X:101432821-114762040

0.59

4.12

0.303567

1.985591

26280

9.84E-01

9.73E-01

full=3

1/1

X_105056492_105057815_DEL_1

1.05E+08

-1323

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:5078:0:1:1:0:0

742

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-1323;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=X;END=105057815;CIPOS=0,0;CIEND=-8,0;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=449704_2;Best_CCDG_Mismatch_OFP=0.000755287;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.0003077;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_23:105051214-105069228;Best_TOPMed_OFP=0.0734902;Best_TOPMed_AF=5e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000139373;Best_TOPMed_Mismatch_ID=DUP_23:105010354-105059267;Best_TOPMed_Mismatch_OFP=0.0270674;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=9e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_170862;Best_ThousG_Mismatch_OFP=0.000755287;Best_ThousG_Mismatch_SVTYPE=INS;Best_ThousG_Mismatch_AF=0.0025;Best_ThousG_Mismatch_Het=0;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chrX_b5294bd1;Best_gnomAD_OFP=0.771903;Best_gnomAD_AF=0.000145946;Best_gnomAD_Het=13;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.00511135;gnomAD_Mismatches=gnomAD-SV_v3_DUP_chrX_d04d6449;gnomAD_Mismatches_Count=1;gnomAD_Mismatch_SVTYPEs=DUP;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chrX_d04d6449;Best_gnomAD_Mismatch_OFP=0.8;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.000218878;Best_gnomAD_Mismatch_Het=17;Best_gnomAD_Mismatch_HomAlt=2;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:1315:6,10:+:742:DEL:DEL00063616:NA:NA:chrX_105056492-chrX_105057807

0/1:NA:1323:0,0:+:734:DEL:MantaDEL_5078_0_1_1_0_0:NA:NA:chrX_105056492-chrX_105057815

0/1:NA:1323:0,0:+:488:DEL:11518:NA:NA:chrX_105056492-chrX_105057815

split

q22.3

IL1RAPL2

NM_017416

1.05E+08

1.06E+08

1324

intron2-intron2

CDS

137659

1.05E+08

dbVar

chrX:105035005-105106372

0.01

gnomAD-SV_v3_DEL_chrX_25f0d36f;gnomAD-SV_v3_DEL_chrX_a8ba77a6

chrX:85568529-142769920;chrX:101187696-118298467

0.4905

IMH

X:101070962-130555575;X:101432821-114762040

0.59

4.12

0.303567

1.985591

26280

9.84E-01

9.73E-01

full=3

0/1

12_118350_118652_DEL_1

118350

118652

-301

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:14387:0:1:0:0:0

TTCTGCCCGTCTGAGATCACCATATTGATTCAAAGAAAGGAGGGAAAAGAAGTGTTTTAGAAAGGGCTAAAAATCTTGAGGGGACGTGACGCATGTTGTTAGCTTTTGTCTAGAAAATGCTTCATAGCTTTGTCCCAGAAGAGCTTTAAGAATGGCTGGCAGAGTCTGGGATAATCTAGTGCAATTGGCCAGGCCCTCTGGAGGAGTCTTCATACCCAAGGAGTCCATCAGCCTTCAAAATGCTCCTGGTAGAGTCTCTAGTAATTACTGTGCTAGCCATTGCCGAGATAGGAGAACAGCCC

540

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-301;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=12;END=118651;CIPOS=0,2;CIEND=0,1;STRANDS=+;Max_AF=0.006244;Max_Het=28;Max_HomAlt=6;Max_PopMax_AF=0.02579;CCDG_Count=0;Best_CCDG_Mismatch_ID=174164_1;Best_CCDG_Mismatch_OFP=0.00331126;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.004035;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_12:105734-121528;Best_TOPMed_OFP=0.0191188;Best_TOPMed_AF=7e-06;Best_TOPMed_Het=2;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=1.25214e-05;Best_TOPMed_Mismatch_ID=INV_12:109574-130409;Best_TOPMed_Mismatch_OFP=0.0144934;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_29233;Best_ThousG_OFP=0.993378;Best_ThousG_AF=0.006244;Best_ThousG_Het=28;Best_ThousG_HomAlt=6;Best_ThousG_PopMax_AF=0.02579;Best_ThousG_Mismatch_ID=HGSV_29232;Best_ThousG_Mismatch_OFP=0.00221494;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.001093;Best_ThousG_Mismatch_Het=7;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr12_ca8579db;Best_gnomAD_OFP=0.464615;Best_gnomAD_AF=0.002994;Best_gnomAD_Het=376;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.0108;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr12_d0d84cd3;Best_gnomAD_Mismatch_OFP=0.00578821;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=1.6e-05;Best_gnomAD_Mismatch_Het=2;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:302:0,0:+:540:DEL:DEL00036695:NA:NA:chr12_118350-chr12_118652

0/1:NA:301:0,0:+:328:DEL:MantaDEL_14387_0_1_0_0_0:TTCTGCCCGTCTGAGATCACCATATTGATTCAAAGAAAGGAGGGAAAAGAAGTGTTTTAGAAAGGGCTAAAAATCTTGAGGGGACGTGACGCATGTTGTTAGCTTTTGTCTAGAAAATGCTTCATAGCTTTGTCCCAGAAGAGCTTTAAGAATGGCTGGCAGAGTCTGGGATAATCTAGTGCAATTGGCCAGGCCCTCTGGAGGAGTCTTCATACCCAAGGAGTCCATCAGCCTTCAAAATGCTCCTGGTAGAGTCTCTAGTAATTACTGTGCTAGCCATTGCCGAGATAGGAGAACAGCCC:T:chr12_118350-chr12_118651

0/1:NA:299:0,0:+:326:DEL:6921:NA:NA:chr12_118352-chr12_118651

split

p13.33

IQSEC3

XM_047428865

66766

171330

303

intron2-intron2

CDS

6980

118349

118652

dbVar

chr12:45740-204934;chr12:72834-118834;chr12:114421-232803;chr12:115648-162429

0.01

dbVar

chr12:115648-162429

0.01

56.71

2.479006

3.288811

440073

3.87E-03

9.25E-01

0.4858

Cleft lip;Cleft palate;Hypertelorism;Micrognathia;Microphthalmia;decreased total retina thickness

full=1

0/1

7_31547158_31552382_INV_1

31547158

31552382

5224

INV

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaBND:107320:0:2:0:0:0:1

[chr7:31552382[T

1860

PASS

SUPP=3;SUPP_VEC=111;SVLEN=5224;SVTYPE=INV;SVMETHOD=SURVIVOR1.0.7;CHR2=7;END=31552382;CIPOS=0,0;CIEND=0,0;STRANDS=;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=599604;Best_CCDG_OFP=0.627368;Best_CCDG_AF=0.1509;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=393327;Best_CCDG_Mismatch_OFP=0.323062;Best_CCDG_Mismatch_SVTYPE=DEL;Best_CCDG_Mismatch_AF=0.1649;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=INV_7:31547416-31550692;Best_TOPMed_OFP=0.627368;Best_TOPMed_AF=0.164089;Best_TOPMed_Het=35249;Best_TOPMed_HomAlt=4452;Best_TOPMed_PopMax_AF=0.318713;Best_TOPMed_Mismatch_ID=DEL_7:31539302-31551300;Best_TOPMed_Mismatch_OFP=0.273755;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=0.000166;Best_TOPMed_Mismatch_Het=43;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_142363;Best_ThousG_OFP=0.00333769;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.00056;ThousG_Mismatches=HGSV_142371;ThousG_Mismatches_Count=1;ThousG_Mismatch_SVTYPEs=CPX;Best_ThousG_Mismatch_ID=HGSV_142371;Best_ThousG_Mismatch_OFP=0.999617;Best_ThousG_Mismatch_SVTYPE=CPX;Best_ThousG_Mismatch_AF=0.175773;Best_ThousG_Mismatch_Het=856;Best_ThousG_Mismatch_HomAlt=135;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_INV_chr7_30ab2e39;Best_gnomAD_OFP=0.00333769;Best_gnomAD_AF=1.6e-05;Best_gnomAD_Het=0;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=5.9e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr7_eb25a3d2;Best_gnomAD_Mismatch_OFP=0.522166;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:5224:18,14:--:1860:INV:INV00022053:NA:NA:chr7_31547158-chr7_31552382

0/1:NA:5224:0,0::851:INV:MantaBND_107320_0_2_0_0_0_1:NA:NA:chr7_31547158-chr7_31552382

0/1:NA:5224:0,0:--:707:INV:4351_1:NA:NA:chr7_31547158-chr7_31552382

split

p14.3

ITPRID1

NM_001257967

31514089

31656504

5225

intron1-intron2

5'UTR

619

31547157

31552382

gnomAD-SV_v3_DEL_chr7_f5bb684d

chr7:26936102-36716780

0.0533

1000g;IMH

7:23851402-66061756;7:29684534-32729958;7:31547152-31552405

0.391

223075

full=NA

0/1

6_36476339_36476763_DEL_1

36476339

36476763

-423

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:121876:0:1:0:0:0

TGATCACACTAATTTATTGAATTCTAGGCTAAATAGAATCCAGCCATTCAAATATATGTGTATTTGAACATATAAATTCACAGTGAACCATTTTTTTTTTTTTTTTTTTAAGACAGAGTCTCACTCTGTCACCAAGGCTGGAGGGCAGTGGTGCAATCTCGGCTCACTGCAACCTCCACCTCCCGGGTTCAAGCAATTCTCGTGCCTCAGCCTCCCAAGTAGCTGGGATCACAGGTGTGTGCCACCACACCCGGCAAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCACGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCGTGATCCGCCCACCTTAGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGTGCCTGGCCACAGCGAACCACTTTTTAATTAGAACCAAACCTGT

TTTTAA

600

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-423;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=6;END=36476762;CIPOS=0,7;CIEND=0,1;STRANDS=+;Max_AF=0.000175;Max_Het=20;Max_HomAlt=1;Max_PopMax_AF=0.001923;CCDG_Count=0;Best_CCDG_ID=374925;Best_CCDG_OFP=0.0373634;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=595637;Best_CCDG_Mismatch_OFP=0.119041;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_6:36474415-36478946;Best_TOPMed_OFP=0.0935363;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.26088e-06;Best_TOPMed_Mismatch_ID=DUP_6:36465002-36492500;Best_TOPMed_Mismatch_OFP=0.0154182;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=0.000155;Best_TOPMed_Mismatch_Het=41;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;ThousG_SV_Cov=0;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr6_035dfea3;Best_gnomAD_OFP=1;Best_gnomAD_AF=0.000175;Best_gnomAD_Het=20;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.001923;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_CPX_chr6_cd4299ce;Best_gnomAD_Mismatch_OFP=0.400378;Best_gnomAD_Mismatch_SVTYPE=CPX;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:417:15,2:+:600:DEL:DEL00019390:NA:NA:chr6_36476346-chr6_36476763

0/1:NA:423:0,0:+:275:DEL:MantaDEL_121876_0_1_0_0_0:TGATCACACTAATTTATTGAATTCTAGGCTAAATAGAATCCAGCCATTCAAATATATGTGTATTTGAACATATAAATTCACAGTGAACCATTTTTTTTTTTTTTTTTTTAAGACAGAGTCTCACTCTGTCACCAAGGCTGGAGGGCAGTGGTGCAATCTCGGCTCACTGCAACCTCCACCTCCCGGGTTCAAGCAATTCTCGTGCCTCAGCCTCCCAAGTAGCTGGGATCACAGGTGTGTGCCACCACACCCGGCAAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCACGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCGTGATCCGCCCACCTTAGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGTGCCTGGCCACAGCGAACCACTTTTTAATTAGAACCAAACCTGT:TTTTAA:chr6_36476339-chr6_36476762

0/1:NA:423:0,0:+:299:DEL:3823:NA:NA:chr6_36476339-chr6_36476762

split

p21.31

KCTD20

XM_047418378

36442999

36484824

425

intron3-intron3

CDS

1276

36476338

36476763

dgv1761e212

6:36476140-36486595

0.01

42.66

0.013891

1.195528

0.837954

0.449161

1.083038

222658

9.43E-04

3.99E-01

full=1

0/1

6_61568977_61569054_DEL_1

61568977

61569054

-76

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:123588:0:0:0:0:0

AGTGGGCATATGGGGAAGTGTGAGGTCCAAAAGCCATGCTTGCTTTCTTGGAAGGGAAGCTCATGGCATGGGGCAGG

999

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-76;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=6;END=61569053;CIPOS=0,2;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=377597_2;Best_CCDG_Mismatch_OFP=0.012987;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.5879;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;TOPMed_SV_Cov=0;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_132575;Best_ThousG_Mismatch_OFP=2.5552e-06;Best_ThousG_Mismatch_SVTYPE=CPX;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr6_3ece45c4;Best_gnomAD_OFP=4.3123e-06;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=3e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_CPX_chr6_63da49e2;Best_gnomAD_Mismatch_OFP=1.55211e-06;Best_gnomAD_Mismatch_SVTYPE=CPX;Best_gnomAD_Mismatch_AF=2.4e-05;Best_gnomAD_Mismatch_Het=3;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

1/1:NA:77:0,0:+:780:DEL:DEL00019859:NA:NA:chr6_61568977-chr6_61569054

1/1:NA:76:0,0:+:999:DEL:MantaDEL_123588_0_0_0_0_0:AGTGGGCATATGGGGAAGTGTGAGGTCCAAAAGCCATGCTTGCTTTCTTGGAAGGGAAGCTCATGGCATGGGGCAGG:A:chr6_61568977-chr6_61569053

1/1:NA:74:0,0:+:649:DEL:3909:NA:NA:chr6_61568979-chr6_61569053

split

q11.1

KHDRBS2

NR_146870

61542669

62286225

intron14-intron14

UTR

22533

61568976

61569054

dbVar

chr6:61468685-62211095;chr6:61539594-61702095;chr6:61539985-61604664

0.01

IMH

6:38040936-64295998;6:47589331-73036081

0.2088

11.27

-2.14059

-0.63655

202559

3.85E-02

1.43E-01

0.3426

Holoprosencephaly;tau protein deposits

full=3

1/1

3_160519499_160519819_DEL_1

1.61E+08

-319

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:167979:0:1:0:0:0

TAAAAAAAATAGGCGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAAATACAAAAAATTAGCCGGGCGCGGTGGTGGGCGCCTGTAGTCCCAGCTACTGGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGTGCCACTGCAGTCCGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAA

720

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-319;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=3;END=160519818;CIPOS=0,13;CIEND=0,1;STRANDS=+;Max_AF=0.002822;Max_Het=353;Max_HomAlt=1;Max_PopMax_AF=0.005784;CCDG_Count=0;CCDG_Mismatches=327029;CCDG_Mismatches_Count=1;CCDG_Mismatch_SVTYPEs=MEI;Best_CCDG_Mismatch_ID=327029;Best_CCDG_Mismatch_OFP=0.959375;Best_CCDG_Mismatch_SVTYPE=MEI;Best_CCDG_Mismatch_AF=0.0003761;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DUP_3:160478802-160535100;Best_TOPMed_Mismatch_OFP=0.00568384;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=3.6e-05;Best_TOPMed_Mismatch_Het=10;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=1;Best_ThousG_ID=HGSV_105866;Best_ThousG_OFP=0.959375;Best_ThousG_AF=0.000781;Best_ThousG_Het=5;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.00416;ThousG_SV_Cov=0.959375;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr3_e32466a0;Best_gnomAD_OFP=0.895185;Best_gnomAD_AF=0.002822;Best_gnomAD_Het=353;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.005784;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr3_0ec68f91;Best_gnomAD_Mismatch_OFP=0.015436;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8.7e-05;Best_gnomAD_Mismatch_Het=9;Best_gnomAD_Mismatch_HomAlt=1;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:320:0,0:+:720:DEL:DEL00011547:NA:NA:chr3_160519499-chr3_160519819

0/1:NA:319:0,0:+:539:DEL:MantaDEL_167979_0_1_0_0_0:TAAAAAAAATAGGCGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAAATACAAAAAATTAGCCGGGCGCGGTGGTGGGCGCCTGTAGTCCCAGCTACTGGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAAGCGGAGCTTGCAGTGAGCCGAGATTGTGCCACTGCAGTCCGCAGTCCGGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAA:T:chr3_160519499-chr3_160519818

0/1:NA:306:0,0:+:509:DEL:2379:NA:NA:chr3_160519512-chr3_160519818

split

q25.33

KPNA4

NM_002268

1.6E+08

1.61E+08

321

intron11-intron11

CDS

1959

1.61E+08

IMH

3:72502419-189537676;3:152031051-176727053;3:152031060-176727190

0.1058

12.34

1.049593

0.011461

0.436278

0.176904

2.94291

3840

1.00E+00

9.98E-01

full=3

0/1

22_33237876_33238156_DEL_1

33237876

33238156

-279

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:94356:0:1:0:0:0

AAATAAATGTGCATAACGCACGGGAGTACAGTATGGTAAAGGAAAGGGAGTGGAGGCTGACATCACATTCAGAGGCTGTATTTTAAGATGAAAGGTAACATATATGTAGTTTGTCTCAAAGTTATATCTTGAGACCAGGATGGGGACGAGGAAAGGGGACAGAAGAAAAAGGTTTCAAATGCAGTTTGAGGCTCAGCTGCTAAGCTGCTGGTTACAATAATAATAAATTGGAAACAACAACCAAAAAAGCTGTTTAGAGTTTTTAAAGGAGCACAAATAT

900

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-279;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=22;END=33238155;CIPOS=0,2;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=306905;Best_CCDG_OFP=0.00124581;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DUP_22:33131875-33262184;Best_TOPMed_Mismatch_OFP=0.00214871;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr22_b967dc51;Best_gnomAD_OFP=0.00200649;Best_gnomAD_AF=1.6e-05;Best_gnomAD_Het=2;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000159;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr22_38e9d68d;Best_gnomAD_Mismatch_OFP=0.00214871;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=1.6e-05;Best_gnomAD_Mismatch_Het=2;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:280:0,0:+:900:DEL:DEL00061816:NA:NA:chr22_33237876-chr22_33238156

0/1:NA:279:0,0:+:753:DEL:MantaDEL_94356_0_1_0_0_0:AAATAAATGTGCATAACGCACGGGAGTACAGTATGGTAAAGGAAAGGGAGTGGAGGCTGACATCACATTCAGAGGCTGTATTTTAAGATGAAAGGTAACATATATGTAGTTTGTCTCAAAGTTATATCTTGAGACCAGGATGGGGACGAGGAAAGGGGACAGAAGAAAAAGGTTTCAAATGCAGTTTGAGGCTCAGCTGCTAAGCTGCTGGTTACAATAATAATAAATTGGAAACAACAACCAAAAAAGCTGTTTAGAGTTTTTAAAGGAGCACAAATAT:A:chr22_33237876-chr22_33238155

0/1:NA:277:0,0:+:827:DEL:11292:NA:NA:chr22_33237878-chr22_33238155

split

q12.3

LARGE1

XR_007067993

33066662

33920476

281

intron14-intron14

UTR

45045

33237875

33238156

congenital muscular dystrophy with intellectual disability;muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A6;muscular dystrophy-dystroglycanopathy type B6;muscular dystrophy-dystroglycanopathy, type A

Definitive;Strong;Supportive

12966029;17436019;19067344;19299310;21248746;21397493[PMID];21727005[PMID]_19299310[PMID]

9215

603590

Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 6, 613154 (3) AR;Muscular dystrophy-dystroglycanopathy (congenital with impaired intellectual development), type B, 6, 608840 (3) AR

0.7369

Cleft lip;Cleft palate;Microphthalmia;Walker-Warburg syndrome

Cleft lip;Cleft palate;Holoprosencephaly;Hypertelorism;Micrognathia;Microphthalmia;abnormal myelination;abnormal tongue morphology

full=3

0/1

11_1894044_1915726_DEL_1

1894044

1915726

-21681

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:25948:0:1:0:0:0

830

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-21681;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=11;END=1915725;CIPOS=0,3;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=159323;Best_CCDG_OFP=0.312102;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=551838;Best_CCDG_Mismatch_OFP=0.000310112;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=0.01792;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0.341389;TOPMed_Count=0;Best_TOPMed_ID=DEL_11:1905428-1912864;Best_TOPMed_OFP=0.34305;Best_TOPMed_AF=1.8e-05;Best_TOPMed_Het=5;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=3.13138e-05;Best_TOPMed_Mismatch_ID=INV_11:1707647-1896713;Best_TOPMed_Mismatch_OFP=0.00173902;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=2.9e-05;Best_TOPMed_Mismatch_Het=8;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_21180;Best_ThousG_OFP=0.018633;Best_ThousG_AF=0.005781;Best_ThousG_Het=37;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.01636;Best_ThousG_Mismatch_ID=HGSV_21179;Best_ThousG_Mismatch_OFP=0.331427;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.018633;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr11_0a7bb213;Best_gnomAD_OFP=0.34305;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=1.7e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr11_5791e2d7;Best_gnomAD_Mismatch_OFP=0.330274;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=1.6e-05;Best_gnomAD_Mismatch_Het=2;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=0.620976

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

1/1:NA:21679:0,0:+:600:DEL:DEL00033993:NA:NA:chr11_1894047-chr11_1915726

1/1:NA:21681:0,0:+:830:DEL:MantaDEL_25948_0_1_0_0_0:NA:NA:chr11_1894044-chr11_1915725

1/1:NA:21681:0,0:+:827:DEL:6377:NA:NA:chr11_1894044-chr11_1915725

split

p15.5

LINC01150

NR_120534

1896758

1908359

11601

txStart-txEnd

UTR

1896758

1908359

1000g;CMRI:0_pbsv.DEL.123_duplicate4;DDD:34791;HI40:ISCA-46652;HPRC:pbsv.DEL.895;dbVar;esv2666901;esv3625119

chr11:1894005-1915726;11:1894006-1915726;11:1894006-1915726;11:1894016-1915772;11:1894020-1915779;11:1894044-1915722;chr11:1894044-1915722;11:1894045-1915726

0.9522

IMH

11:1621661-71538522

0.0179

1.02E+08

full=1

1/1

3_109455011_109455111_DEL_1

1.09E+08

-99

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:164604:0:1:0:0:0

TTGTGAAAGACCTGACTCTGAGGCAGAGTTCTTCGGTGGATTCAACCACCTCCCACCAGGTCCCTCCCACAACACGTGGGAATTCAAGATGAGATTTGGG

523

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-99;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=3;END=109455110;CIPOS=0,2;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=322619;Best_CCDG_OFP=0.00047242;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=508909;Best_CCDG_Mismatch_OFP=0.00323572;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=0.000171;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_3:109369440-109465112;Best_TOPMed_OFP=0.00104522;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.28228e-06;Best_TOPMed_Mismatch_ID=DUP_3:109424903-109455806;Best_TOPMed_Mismatch_OFP=0.00323572;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=0.000229;Best_TOPMed_Mismatch_Het=59;Best_TOPMed_Mismatch_HomAlt=2;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_103179;Best_ThousG_Mismatch_OFP=0.00323572;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000468;Best_ThousG_Mismatch_Het=3;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr3_646c3991;Best_gnomAD_OFP=0.00104523;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=1.7e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr3_444bdf92;Best_gnomAD_Mismatch_OFP=0.00323572;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.000159;Best_gnomAD_Mismatch_Het=20;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:100:0,0:+:420:DEL:DEL00010828:NA:NA:chr3_109455011-chr3_109455111

0/1:NA:99:0,0:+:523:DEL:MantaDEL_164604_0_1_0_0_0:TTGTGAAAGACCTGACTCTGAGGCAGAGTTCTTCGGTGGATTCAACCACCTCCCACCAGGTCCCTCCCACAACACGTGGGAATTCAAGATGAGATTTGGG:T:chr3_109455011-chr3_109455110

0/1:NA:97:0,0:+:293:DEL:2228:NA:NA:chr3_109455013-chr3_109455110

split

q13.13

LINC01205

NR_109841

1.09E+08

101

intron2-intron2

UTR

4771

1.09E+08

dbVar

chr3:109424902-109455806

0.01

dbVar;gnomAD-SV_v3_DEL_chr3_9b8d4286

chr3:11110259-145805573;chr3:108633893-111492183;chr3:109441411-109471369;chr3:109453096-109716138

0.0446

IMH

3:30036454-134858252;3:72502419-189537676;3:75447628-125901392

0.239

401082

full=1

0/1

1_185620013_185620102_DEL_1

1.86E+08

-88

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:200913:0:1:0:0:0

AATGTGTGTATATATATATGGAATCTTCATATATGTGTATATATATATATACACATATATGAAGATTCCATATATATATACACACACAT

239

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-88;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=1;END=185620101;CIPOS=0,14;CIEND=0,1;STRANDS=+;Max_AF=4.8e-05;Max_Het=6;Max_HomAlt=0;Max_PopMax_AF=0.000247;CCDG_Count=0;Best_CCDG_ID=137217;Best_CCDG_OFP=0.00985931;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=137220_1;Best_CCDG_Mismatch_OFP=0.011236;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.06291;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_1:185617022-185620071;Best_TOPMed_OFP=0.0128195;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.26786e-06;Best_TOPMed_Mismatch_ID=INV_1:183856810-187909288;Best_TOPMed_Mismatch_OFP=2.19619e-05;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0.662921;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_9278;Best_ThousG_Mismatch_OFP=0.418323;Best_ThousG_Mismatch_SVTYPE=INS;Best_ThousG_Mismatch_AF=0.000625;Best_ThousG_Mismatch_Het=4;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=2;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr1_91caac2e;Best_gnomAD_OFP=0.842697;Best_gnomAD_AF=3.3e-05;Best_gnomAD_Het=4;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=5.1e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_INS_chr1_5eaa9906;Best_gnomAD_Mismatch_OFP=0.494382;Best_gnomAD_Mismatch_SVTYPE=INS;Best_gnomAD_Mismatch_AF=0.004189;Best_gnomAD_Mismatch_Het=524;Best_gnomAD_Mismatch_HomAlt=2;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:89:0,0:+:239:DEL:DEL00004115:NA:NA:chr1_185620013-chr1_185620102

0/1:NA:88:0,0:+:139:DEL:MantaDEL_200913_0_1_0_0_0:AATGTGTGTATATATATATGGAATCTTCATATATGTGTATATATATATATACACATATATGAAGATTCCATATATATATACACACACAT:A:chr1_185620013-chr1_185620101

0/1:NA:74:0,0:+:83:DEL:818:NA:NA:chr1_185620027-chr1_185620101

split

q25.3

LINC01350

NR_110793

1.86E+08

intron2-intron2

UTR

6389

1.86E+08

gnomAD-SV_v3_DEL_chr1_339fd21d

chr1:168349020-187167586

0.9262

IMH

1:10187873-186857210;1:16798094-234784887;1:68663392-188869781;1:107555343-232824950

0.4698

1.02E+08

full=1

0/1

12_127057469_127058489_DEL_1

1.27E+08

-1019

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:24988:0:1:0:0:0

1208

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-1019;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=12;END=127058488;CIPOS=0,0;CIEND=0,1;STRANDS=+;Max_AF=0.002342;Max_Het=26;Max_HomAlt=6;Max_PopMax_AF=0.011111;CCDG_Count=1;Best_CCDG_ID=189451;Best_CCDG_OFP=1;Best_CCDG_AF=0.0002052;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=473555;Best_CCDG_Mismatch_OFP=0.000673294;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_12:127053980-127059275;Best_TOPMed_OFP=0.192562;Best_TOPMed_AF=1.8e-05;Best_TOPMed_Het=5;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000319829;Best_TOPMed_Mismatch_ID=DUP_12:127022996-127106412;Best_TOPMed_Mismatch_OFP=0.0122276;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=1.1e-05;Best_TOPMed_Mismatch_Het=3;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_36909;Best_ThousG_OFP=1;Best_ThousG_AF=0.002342;Best_ThousG_Het=11;Best_ThousG_HomAlt=2;Best_ThousG_PopMax_AF=0.011111;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr12_1208cb5d;Best_gnomAD_OFP=1;Best_gnomAD_AF=0.000301;Best_gnomAD_Het=26;Best_gnomAD_HomAlt=6;Best_gnomAD_PopMax_AF=0.005673;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr12_ba1f336a;Best_gnomAD_Mismatch_OFP=0.0122276;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:1020:18,10:+:1208:DEL:DEL00039909:NA:NA:chr12_127057469-chr12_127058489

0/1:NA:1019:0,0:+:738:DEL:MantaDEL_24988_0_1_0_0_0:NA:NA:chr12_127057469-chr12_127058488

0/1:NA:1019:0,0:+:638:DEL:7506:NA:NA:chr12_127057469-chr12_127058488

split

q24.32

LINC02405

NR_104646

1.27E+08

1021

intron1-intron1

UTR

1597

1.27E+08

1000g;dbVar;esv3631095

chr12:126267752-127405141;chr12:126945957-127328431;12:126945958-127328431;12:126945958-127328431

0.2423

dbVar

chr12:126929324-127229788;chr12:126945957-127328431;chr12:127051823-127065815;chr12:127053979-127059273

0.01

1.02E+08

full=1

0/1

4_32069419_32072988_DUP_1

32069419

32072988

3567

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:146148:0:4:0:3:0

780

PASS

SUPP=3;SUPP_VEC=111;SVLEN=3567;SVTYPE=DUP;SVMETHOD=SURVIVOR1.0.7;CHR2=4;END=32072986;CIPOS=0,1;CIEND=0,2;STRANDS=-;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=335440_2;Best_CCDG_Mismatch_OFP=0.000280269;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.0769;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DUP_4:32067402-32083700;Best_TOPMed_OFP=0.218896;Best_TOPMed_AF=1.8e-05;Best_TOPMed_Het=5;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=3.15235e-05;Best_TOPMed_Mismatch_ID=DEL_4:32071446-32071490;Best_TOPMed_Mismatch_OFP=0.0128924;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=0.733614;Best_TOPMed_Mismatch_Het=49055;Best_TOPMed_Mismatch_HomAlt=74776;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_110436;Best_ThousG_OFP=0.0746085;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.000832;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DUP_chr4_3dfbb6eb;Best_gnomAD_OFP=0.775484;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=1.7e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr4_169d334c;Best_gnomAD_Mismatch_OFP=0.342667;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:3566:23,5:-:780:DUP:DUP00012709:NA:NA:chr4_32069420-chr4_32072986

0/1:NA:3567:0,0:-:234:DUP:MantaDUP_TANDEM_146148_0_4_0_3_0:NA:NA:chr4_32069419-chr4_32072986

0/1:NA:3569:0,0:-:179:DUP:2628:NA:NA:chr4_32069419-chr4_32072988

split

p15.1

LINC02506

NR_125936

31997378

32155406

3570

intron1-intron1

UTR

71596

32069418

32072988

dbVar;gnomAD-SV_v3_DEL_chr4_6939d627

chr4:22150396-36380550;chr4:31682402-32265926;chr4:31692223-32398776

0.0703

IMH

4:1330317-92330038;4:4772332-76608755;4:21291890-139485605;4:21757282-83521389

0.0791

1.03E+08

full=3

0/1

5_96989313_96989413_DEL_1

96989313

96989413

-100

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:137680:0:1:0:0:0

TTATATATAATATATAATTATATATAATATATAATATATTATATATTATATATAATTATATATTATATATTATATACAATATATTATATATTATATATAAT

840

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-100;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=5;END=96989413;CIPOS=0,6;CIEND=-18,0;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=360884;Best_CCDG_OFP=0.712871;Best_CCDG_AF=0.5915;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=518287;Best_CCDG_Mismatch_OFP=0.00013066;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_5:94767306-97708544;Best_TOPMed_OFP=3.43393e-05;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.26991e-06;Best_TOPMed_Mismatch_ID=DUP_5:96412204-97185198;Best_TOPMed_Mismatch_OFP=0.00013066;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_125011;Best_ThousG_OFP=0.712871;Best_ThousG_AF=0.543035;Best_ThousG_Het=1813;Best_ThousG_HomAlt=797;Best_ThousG_PopMax_AF=0.588296;Best_ThousG_Mismatch_ID=HGSV_123838;Best_ThousG_Mismatch_OFP=3.0536e-06;Best_ThousG_Mismatch_SVTYPE=INV;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.712871;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr5_10bc6569;Best_gnomAD_OFP=0.712871;Best_gnomAD_AF=0.464419;Best_gnomAD_Het=36288;Best_gnomAD_HomAlt=8294;Best_gnomAD_PopMax_AF=0.557355;gnomAD_Mismatches=gnomAD-SV_v3_DUP_chr5_e1bfdcf7,gnomAD-SV_v3_DUP_chr5_d71655ea;gnomAD_Mismatches_Count=2;gnomAD_Mismatch_SVTYPEs=DUP;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr5_d71655ea;Best_gnomAD_Mismatch_OFP=0.942132;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.00069;Best_gnomAD_Mismatch_Het=75;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:99:0,0:+:840:DEL:DEL00017100:NA:NA:chr5_96989313-chr5_96989412

0/1:NA:100:0,0:+:569:DEL:MantaDEL_137680_0_1_0_0_0:TTATATATAATATATAATTATATATAATATATAATATATTATATATTATATATAATTATATATTATATATTATATACAATATATTATATATTATATATAAT:TA:chr5_96989313-chr5_96989413

0/1:NA:76:0,0:+:137:DEL:3366:NA:NA:chr5_96989319-chr5_96989395

split

q15

LNPEP

NM_005575

96936079

97037513

101

intron4-intron4

CDS

2642

96989312

96989413

IMH

5:96989258-96989487

0.5915

IMH

5:24758176-102357714;5:58813595-102383104;5:85192778-162907706;5:96855635-159536527

0.5229

30.65

-0.25318

1.308589

0.738283

-1.2897

0.496385

4012

1.00E+00

9.98E-01

full=1

0/1

14_64893668_64896823_DEL_1

64893668

64896823

-3154

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:2676:14:16:0:0:0

1980

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-3154;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=14;END=64896822;CIPOS=0,10;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=85670_2;Best_CCDG_Mismatch_OFP=0.000316957;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=6.839e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_14:64884040-64901316;Best_TOPMed_OFP=0.182602;Best_TOPMed_AF=2e-05;Best_TOPMed_Het=5;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000365586;Best_TOPMed_Mismatch_ID=DUP_14:64880628-64904139;Best_TOPMed_Mismatch_OFP=0.134181;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr14_e5ca311d;Best_gnomAD_OFP=0.182623;Best_gnomAD_AF=3.2e-05;Best_gnomAD_Het=4;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=6.8e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr14_55ea796c;Best_gnomAD_Mismatch_OFP=0.62143;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.025569;Best_gnomAD_Mismatch_Het=2157;Best_gnomAD_Mismatch_HomAlt=97;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:3155:9,16:+:1980:DEL:DEL00042387:NA:NA:chr14_64893668-chr14_64896823

0/1:NA:3154:0,0:+:999:DEL:MantaDEL_2676_14_16_0_0_0:NA:NA:chr14_64893668-chr14_64896822

0/1:NA:3144:0,0:+:968:DEL:8075:NA:NA:chr14_64893678-chr14_64896822

split

q23.3

LOC105370534

XR_943942

64880880

64902128

3156

intron1-intron1

UTR

5248

64893667

64896823

gnomAD-SV_v3_DUP_chr14_55ea796c

chr14:64892637-64897713

0.0539

dbVar;gnomAD-SV_v3_DEL_chr14_040215df;gnomAD-SV_v3_DEL_chr14_aa7bf92b

chr14:41140072-69277618;chr14:56471274-99420950;chr14:64884041-64901316

0.633

IMH

14:23629193-97505158

0.4022

-1

full=1

0/1

19_9516280_9516365_DEL_1

9516280

9516365

-84

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:80093:0:1:0:0:0

CAGTGGCCAGGCATGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGTTGGATCACCTGAGGCTGGGAGTTTG

399

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-84;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=19;END=9516364;CIPOS=0,2;CIEND=0,1;STRANDS=+;Max_AF=0.005932;Max_Het=90;Max_HomAlt=13;Max_PopMax_AF=0.031614;CCDG_Count=0;Best_CCDG_Mismatch_ID=255366_1;Best_CCDG_Mismatch_OFP=0.0117647;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.001641;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_19:9515494-9519966;Best_TOPMed_OFP=0.0189987;Best_TOPMed_AF=7e-06;Best_TOPMed_Het=2;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=2.40125e-05;Best_TOPMed_Mismatch_ID=INV_19:9514942-9524335;Best_TOPMed_Mismatch_OFP=0.00904737;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=1.8e-05;Best_TOPMed_Mismatch_Het=5;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_70656;Best_ThousG_OFP=0.976471;Best_ThousG_AF=0.005932;Best_ThousG_Het=34;Best_ThousG_HomAlt=2;Best_ThousG_PopMax_AF=0.031614;ThousG_SV_Cov=0.976471;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr19_6613b8a4;Best_gnomAD_OFP=0.976471;Best_gnomAD_AF=0.000921;Best_gnomAD_Het=90;Best_gnomAD_HomAlt=13;Best_gnomAD_PopMax_AF=0.026232;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_CPX_chr19_66bc3b95;Best_gnomAD_Mismatch_OFP=1.04375e-05;Best_gnomAD_Mismatch_SVTYPE=CPX;Best_gnomAD_Mismatch_AF=0.000158;Best_gnomAD_Mismatch_Het=5;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:85:0,0:+:399:DEL:DEL00054768:NA:NA:chr19_9516280-chr19_9516365

0/1:NA:84:0,0:+:398:DEL:MantaDEL_80093_0_1_0_0_0:CAGTGGCCAGGCATGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGTTGGATCACCTGAGGCTGGGAGTTTG:C:chr19_9516280-chr19_9516364

0/1:NA:82:0,0:+:212:DEL:10163:NA:NA:chr19_9516282-chr19_9516364

split

p13.2

LOC105372268

XR_001753862

9507807

9520840

intron1-intron1

UTR

1625

9516279

9516365

dbVar

chr19:9504987-9533322

0.01

IMH

19:1692676-41507766

0.0103

-1

full=1

0/1

20_17303439_17303526_DEL_1

17303439

17303526

-84

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:97657:0:1:0:0:0

AATATATATTATATTAAATATAATATATATTATATATAATATATATTATATTTAATATAATATATATTATATATAATATAATATA

415

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-84;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=20;END=17303526;CIPOS=-3,9;CIEND=-10,0;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=293077;Best_CCDG_OFP=0.0182639;Best_CCDG_AF=0.0001026;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=293079_1;Best_CCDG_Mismatch_OFP=0.0117647;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.227;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DUP_20:17274064-17318502;Best_TOPMed_Mismatch_OFP=0.00191269;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_89585;Best_ThousG_Mismatch_OFP=0.000140685;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr20_94becb03;Best_gnomAD_OFP=0.729412;Best_gnomAD_AF=0.04733;Best_gnomAD_Het=4091;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.166667;gnomAD_Mismatches=gnomAD-SV_v3_DUP_chr20_91afbc86;gnomAD_Mismatches_Count=1;gnomAD_Mismatch_SVTYPEs=DUP;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr20_91afbc86;Best_gnomAD_Mismatch_OFP=0.835294;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.036155;Best_gnomAD_Mismatch_Het=4531;Best_gnomAD_Mismatch_HomAlt=9;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:83:0,0:+:415:DEL:DEL00058353:NA:NA:chr20_17303439-chr20_17303522

0/1:NA:84:0,0:+:385:DEL:MantaDEL_97657_0_1_0_0_0:AATATATATTATATTAAATATAATATATATTATATATAATATATATTATATTTAATATAATATATATTATATATAATATAATATA:AT:chr20_17303442-chr20_17303526

0/1:NA:65:0,0:+:68:DEL:10795:NA:NA:chr20_17303451-chr20_17303516

split

p12.1

LOC105372546

XR_007067540

17232476

17326898

intron2-intron2

UTR

21685

17303438

17303526

dbVar

chr20:17301743-17309639

0.01

-1

full=3

0/1

22_44860912_44860969_DEL_1

44860912

44860969

-56

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:95612:0:1:0:0:0

TTGGAGAATGTCACTTCTTGGTTTTACAACAATTTTTTTTCTCCCTGTTGCTTGACA

653

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:57:0,0:+:653:DEL:DEL00062432:NA:NA:chr22_44860912-chr22_44860969

1/1:NA:56:0,0:+:486:DEL:MantaDEL_95612_0_1_0_0_0:TTGGAGAATGTCACTTCTTGGTTTTACAACAATTTTTTTTCTCCCTGTTGCTTGACA:T:chr22_44860912-chr22_44860968

0/1:NA:55:0,0:+:272:DEL:11382:NA:NA:chr22_44860913-chr22_44860968

split

q13.31

LOC105373062

XR_938302

44859455

44864239

intron3-intron3

UTR

1428

44860911

44860969

dbVar

chr22:44820754-44869341;chr22:44837184-44861234

0.01

IMH

22:44479419-47655346

0.2479

-1

full=3

0/1

X_33781588_33785512_DEL_1

33781588

33785512

-3923

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:2903:0:1:0:0:0

1315

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-3923;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=X;END=33785511;CIPOS=0,3;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=539821;Best_CCDG_Mismatch_OFP=0.0146633;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DUP_23:33748407-33870946;Best_TOPMed_Mismatch_OFP=0.0320219;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=9e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=0;Best_ThousG_ID=HGSV_168273;Best_ThousG_OFP=0.00554321;Best_ThousG_AF=0.002185;Best_ThousG_Het=14;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.005521;Best_ThousG_Mismatch_ID=HGSV_168277;Best_ThousG_Mismatch_OFP=0.0140504;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000312;Best_ThousG_Mismatch_Het=0;Best_ThousG_Mismatch_HomAlt=1;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chrX_2bdd080e;Best_gnomAD_OFP=0.219512;Best_gnomAD_AF=9.38057e-05;Best_gnomAD_Het=9;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000116722;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chrX_fb572db6;Best_gnomAD_Mismatch_OFP=0.0211519;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=1.04225e-05;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

1/1:NA:3924:0,13:+:1315:DEL:DEL00063126:NA:NA:chrX_33781588-chrX_33785512

1/1:NA:3923:0,0:+:873:DEL:MantaDEL_2903_0_1_0_0_0:NA:NA:chrX_33781588-chrX_33785511

1/1:NA:3920:0,0:+:827:DEL:11464:NA:NA:chrX_33781591-chrX_33785511

split

p21.1

LOC105373153

XR_950542

33726365

34077114

3925

intron1-intron1

UTR

54952

33781587

33785512

dbVar

chrX:33602583-34344183

0.01

dbVar

chrX:33721460-33821194;chrX:33769575-33787450

0.01

-1

full=1

1/1

4_19649216_19650455_DEL_1

19649216

19650455

-1238

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:145217:0:1:0:0:0

1560

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-1238;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=4;END=19650454;CIPOS=0,1;CIEND=0,1;STRANDS=+;Max_AF=4.8e-05;Max_Het=6;Max_HomAlt=0;Max_PopMax_AF=0.001362;CCDG_Count=1;Best_CCDG_ID=334245;Best_CCDG_OFP=0.999193;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=586428;Best_CCDG_Mismatch_OFP=2.6142e-05;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_4:19649081-19653066;Best_TOPMed_OFP=0.31076;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=1.19849e-05;Best_TOPMed_Mismatch_ID=DUP_4:19295396-20168361;Best_TOPMed_Mismatch_OFP=0.0014193;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_109700;Best_ThousG_OFP=0.0104568;Best_ThousG_AF=0.000312;Best_ThousG_Het=2;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.002041;Best_ThousG_Mismatch_ID=HGSV_109703;Best_ThousG_Mismatch_OFP=8.25469e-05;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr4_c18c8389;Best_gnomAD_OFP=0.999193;Best_gnomAD_AF=4.8e-05;Best_gnomAD_Het=6;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.001362;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr4_5a32eae1;Best_gnomAD_Mismatch_OFP=0.206466;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:1239:20,17:+:1560:DEL:DEL00012561:NA:NA:chr4_19649216-chr4_19650455

0/1:NA:1238:0,0:+:881:DEL:MantaDEL_145217_0_1_0_0_0:NA:NA:chr4_19649216-chr4_19650454

0/1:NA:1237:0,0:+:722:DEL:2587:NA:NA:chr4_19649217-chr4_19650454

split

p15.31

LOC105374511

NR_188378

19455417

19937562

1240

intron1-intron1

UTR

193563

19649215

19650455

dbVar

chr4:19081377-19733377;chr4:19561981-19730035;chr4:19609252-19655172;chr4:19634532-19727318

0.01

IMH

4:1330317-92330038;4:4772332-76608755

0.0791

-1

full=1

0/1

6_43418273_43418352_DEL_1

43418273

43418352

-75

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:7791:8:8:0:0:0

AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAGAAAGAAAGAAAG

ATA

553

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-75;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=6;END=43418352;CIPOS=-4,0;CIEND=-7,0;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=375664_2;Best_CCDG_Mismatch_OFP=0.0131579;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.6983;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DUP_6:43339402-43752100;Best_TOPMed_Mismatch_OFP=0.000184153;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=0;Best_ThousG_ID=HGSV_132721;Best_ThousG_OFP=0.449045;Best_ThousG_AF=0.512644;Best_ThousG_Het=2786;Best_ThousG_HomAlt=249;Best_ThousG_PopMax_AF=0.571795;Best_ThousG_Mismatch_ID=HGSV_132722;Best_ThousG_Mismatch_OFP=0.0444079;Best_ThousG_Mismatch_SVTYPE=INS;Best_ThousG_Mismatch_AF=0.055626;Best_ThousG_Mismatch_Het=348;Best_ThousG_Mismatch_HomAlt=1;ThousG_SV_Cov=0.776316;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr6_cc44a6bc;Best_gnomAD_OFP=0.459888;Best_gnomAD_AF=0.49725;Best_gnomAD_Het=48660;Best_gnomAD_HomAlt=3694;Best_gnomAD_PopMax_AF=0.569136;gnomAD_Mismatches=gnomAD-SV_v3_DUP_chr6_7545c21e;gnomAD_Mismatches_Count=1;gnomAD_Mismatch_SVTYPEs=DUP;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr6_7545c21e;Best_gnomAD_Mismatch_OFP=0.818876;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=1.6e-05;Best_gnomAD_Mismatch_Het=2;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

1/1:NA:69:0,0:+:461:DEL:DEL00019591:NA:NA:chr6_43418276-chr6_43418345

1/1:NA:75:0,0:+:553:DEL:MantaDEL_7791_8_8_0_0_0:AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAGAAAGAAAGAAAG:ATA:chr6_43418277-chr6_43418352

1/1:NA:79:0,0:+:472:DEL:3852:NA:NA:chr6_43418273-chr6_43418352

split

p21.1

LOC105375065

XR_001744123

43391172

43424730

intron4-intron4

UTR

831

43418272

43418352

dbVar

chr6:43418240-43418352

0.01

IMH

6:38040936-64295998

0.0991

-1

full=1

1/1

8_48780211_48783201_DEL_1

48780211

48783201

-2989

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:218300:0:1:0:0:0

1680

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-2989;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=8;END=48783200;CIPOS=0,2;CIEND=0,1;STRANDS=+;Max_AF=0.00843;Max_Het=349;Max_HomAlt=26;Max_PopMax_AF=0.046754;CCDG_Count=1;Best_CCDG_ID=415954;Best_CCDG_OFP=0.999331;Best_CCDG_AF=0.002188;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=603900;Best_CCDG_Mismatch_OFP=4.07356e-05;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=0.0006839;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0.999331;TOPMed_Count=1;Best_TOPMed_ID=DEL_8:48780214-48783203;Best_TOPMed_OFP=0.998329;Best_TOPMed_AF=0.001281;Best_TOPMed_Het=349;Best_TOPMed_HomAlt=6;Best_TOPMed_PopMax_AF=0.0363676;Best_TOPMed_Mismatch_ID=DUP_8:48722331-48892732;Best_TOPMed_Mismatch_OFP=0.0175466;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0.999331;ThousG_Count=1;Best_ThousG_ID=HGSV_153702;Best_ThousG_OFP=0.999331;Best_ThousG_AF=0.00843;Best_ThousG_Het=50;Best_ThousG_HomAlt=2;Best_ThousG_PopMax_AF=0.044925;Best_ThousG_Mismatch_ID=HGSV_153347;Best_ThousG_Mismatch_OFP=5.27058e-05;Best_ThousG_Mismatch_SVTYPE=CTX;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.999331;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr8_30e467c1;Best_gnomAD_OFP=0.999331;Best_gnomAD_AF=0.001745;Best_gnomAD_Het=168;Best_gnomAD_HomAlt=26;Best_gnomAD_PopMax_AF=0.046754;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr8_aab752ee;Best_gnomAD_Mismatch_OFP=0.0175466;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:2990:23,12:+:1680:DEL:DEL00026148:NA:NA:chr8_48780211-chr8_48783201

0/1:NA:2989:0,0:+:985:DEL:MantaDEL_218300_0_1_0_0_0:NA:NA:chr8_48780211-chr8_48783200

0/1:NA:2987:0,0:+:725:DEL:5120:NA:NA:chr8_48780213-chr8_48783200

split

q11.21

LOC105375825

XR_001745894

48780607

48828577

2594

txStart-intron1

UTR

166

48780607

48783201

dbVar

chr8:48708380-49699549

0.01

1000g;dbVar

chr8:48779934-48783395;chr8:48780157-48783358;8:48780158-48783358

0.0419

-1

full=1

0/1

9_7209820_7212300_DEL_1

7209820

7212300

-2479

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:206240:0:1:0:0:0

780

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-2479;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=9;END=7212299;CIPOS=0,3;CIEND=0,1;STRANDS=+;Max_AF=0.000468;Max_Het=34;Max_HomAlt=2;Max_PopMax_AF=0.002951;CCDG_Count=1;Best_CCDG_ID=426586;Best_CCDG_OFP=0.99879;Best_CCDG_AF=0.0001368;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=1;Best_TOPMed_ID=DEL_9:7209824-7212299;Best_TOPMed_OFP=0.99879;Best_TOPMed_AF=0.000121;Best_TOPMed_Het=34;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.00291545;Best_TOPMed_Mismatch_ID=DUP_9:6991180-7215651;Best_TOPMed_Mismatch_OFP=0.0110481;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=1.1e-05;Best_TOPMed_Mismatch_Het=3;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_159767;Best_ThousG_OFP=0.99879;Best_ThousG_AF=0.000468;Best_ThousG_Het=1;Best_ThousG_HomAlt=1;Best_ThousG_PopMax_AF=0.002496;ThousG_SV_Cov=0.99879;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr9_1d907117;Best_gnomAD_OFP=0.995584;Best_gnomAD_AF=0.000127;Best_gnomAD_Het=12;Best_gnomAD_HomAlt=2;Best_gnomAD_PopMax_AF=0.002951;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr9_d8f0accb;Best_gnomAD_Mismatch_OFP=0.0110481;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:2480:17,6:+:780:DEL:DEL00027669:NA:NA:chr9_7209820-chr9_7212300

0/1:NA:2479:0,0:+:322:DEL:MantaDEL_206240_0_1_0_0_0:NA:NA:chr9_7209820-chr9_7212299

0/1:NA:2476:0,0:+:197:DEL:5450:NA:NA:chr9_7209823-chr9_7212299

split

p24.1

LOC105375969

XR_007061413

7202335

7210505

686

exon3-txEnd

UTR

903

7209819

7210505

-1

full=3

0/1

10_2581858_2636673_DUP_1

2581858

2636673

54815

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:36455:0:1:0:0:0

660

PASS

SUPP=3;SUPP_VEC=111;SVLEN=54815;SVTYPE=DUP;SVMETHOD=SURVIVOR1.0.7;CHR2=10;END=2636673;CIPOS=0,1;CIEND=0,0;STRANDS=-;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=461358;Best_CCDG_OFP=0.390488;Best_CCDG_AF=6.839e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=144152;Best_CCDG_Mismatch_OFP=0.21979;Best_CCDG_Mismatch_SVTYPE=DEL;Best_CCDG_Mismatch_AF=6.839e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DUP_10:2600430-2645536;Best_TOPMed_OFP=0.531294;Best_TOPMed_AF=1.1e-05;Best_TOPMed_Het=3;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=3.61185e-05;Best_TOPMed_Mismatch_ID=DEL_10:2542693-2659833;Best_TOPMed_Mismatch_OFP=0.467945;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_13339;Best_ThousG_OFP=0.0167112;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.000855;Best_ThousG_Mismatch_ID=HGSV_13340;Best_ThousG_Mismatch_OFP=0.221651;Best_ThousG_Mismatch_SVTYPE=CPX;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.417615;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DUP_chr10_e1dac703;Best_gnomAD_OFP=0.531294;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=3e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_CPX_chr10_d7e99c97;Best_gnomAD_Mismatch_OFP=0.221195;Best_gnomAD_Mismatch_SVTYPE=CPX;Best_gnomAD_Mismatch_AF=4.8e-05;Best_gnomAD_Mismatch_Het=6;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:54814:22,3:-:660:DUP:DUP00030026:NA:NA:chr10_2581859-chr10_2636673

0/1:NA:54815:0,0:-:530:DUP:MantaDUP_TANDEM_36455_0_1_0_0_0:NA:NA:chr10_2581858-chr10_2636673

0/1:NA:54815:0,0:-:122:DUP:5867:NA:NA:chr10_2581858-chr10_2636673

split

p15.3

LOC105376350

NR_188171

2501852

2618741

36884

intron4-txEnd

UTR

11592

2581857

2618741

dbVar

chr10:2357805-2763808;chr10:2460844-3257750

0.01

dbVar

chr10:2505807-3017808

0.01

-1

full=3

0/1

10_2580097_2636532_DEL_1

2580097

2636532

-56434

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:36411:0:1:0:0:0

1260

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-56434;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=10;END=2636531;CIPOS=0,1;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=144152;Best_CCDG_OFP=0.213485;Best_CCDG_AF=6.839e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=461358;Best_CCDG_Mismatch_OFP=0.379286;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=6.839e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0.415522;TOPMed_Count=0;Best_TOPMed_ID=DEL_10:2542693-2659833;Best_TOPMed_OFP=0.481766;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.00010879;Best_TOPMed_Mismatch_ID=DUP_10:2600430-2645536;Best_TOPMed_Mismatch_OFP=0.512017;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=1.1e-05;Best_TOPMed_Mismatch_Het=3;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_13341;Best_ThousG_OFP=0.213502;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0;Best_ThousG_Mismatch_ID=HGSV_13340;Best_ThousG_Mismatch_OFP=0.215292;Best_ThousG_Mismatch_SVTYPE=CPX;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.508869;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr10_e348455b;Best_gnomAD_OFP=0.198069;Best_gnomAD_AF=0.000325;Best_gnomAD_Het=41;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.001572;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr10_e1dac703;Best_gnomAD_Mismatch_OFP=0.512017;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:56435:30,13:+:1260:DEL:DEL00030025:NA:NA:chr10_2580097-chr10_2636532

0/1:NA:56434:0,0:+:779:DEL:MantaDEL_36411_0_1_0_0_0:NA:NA:chr10_2580097-chr10_2636531

0/1:NA:56433:0,0:+:479:DEL:5866:NA:NA:chr10_2580098-chr10_2636531

split

p15.3

LOC105376350

NR_188171

2501852

2618741

38645

intron4-txEnd

UTR

9831

2580096

2618741

dbVar

chr10:2357805-2763808;chr10:2460844-3257750

0.01

dbVar

chr10:2505807-3017808

0.01

-1

full=1

0/1

1_19035733_19044940_DEL_1

19035733

19044940

-9206

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:189990:0:1:0:0:0

720

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-9206;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=1;END=19044939;CIPOS=0,2;CIEND=0,1;STRANDS=+;Max_AF=0.004527;Max_Het=162;Max_HomAlt=2;Max_PopMax_AF=0.023295;CCDG_Count=0;Best_CCDG_ID=122441;Best_CCDG_OFP=0.031339;Best_CCDG_AF=0.0003078;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=543252;Best_CCDG_Mismatch_OFP=0.000215224;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=0.01679;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0.0326925;TOPMed_Count=2;Best_TOPMed_ID=DEL_1:19035736-19044942;Best_TOPMed_OFP=0.999457;Best_TOPMed_AF=0.000589;Best_TOPMed_Het=162;Best_TOPMed_HomAlt=2;Best_TOPMed_PopMax_AF=0.0173014;Best_TOPMed_Mismatch_ID=DUP_1:18981802-19060600;Best_TOPMed_Mismatch_OFP=0.11684;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=1e-05;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_1365;Best_ThousG_OFP=0.999783;Best_ThousG_AF=0.004527;Best_ThousG_Het=29;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.023295;ThousG_SV_Cov=0.999783;gnomAD_Count=2;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr1_f6c129cb;Best_gnomAD_OFP=0.998264;Best_gnomAD_AF=5.6e-05;Best_gnomAD_Het=7;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.001589;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_INS_chr1_d65cf9e9;Best_gnomAD_Mismatch_OFP=0.0016292;Best_gnomAD_Mismatch_SVTYPE=INS;Best_gnomAD_Mismatch_AF=0.000841;Best_gnomAD_Mismatch_Het=106;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:9207:12,7:+:720:DEL:DEL00000764:NA:NA:chr1_19035733-chr1_19044940

0/1:NA:9206:0,0:+:318:DEL:MantaDEL_189990_0_1_0_0_0:NA:NA:chr1_19035733-chr1_19044939

0/1:NA:9204:0,0:+:275:DEL:150:NA:NA:chr1_19035735-chr1_19044939

split

p36.13

LOC105376815

XR_947015

18970477

19051428

9208

intron1-intron1

UTR

5937

19035732

19044940

1000g;dbVar;gnomAD-SV_v3_DEL_chr1_cf5f2df8

chr1:13203398-167621949;chr1:19035658-19045037;1:19035659-19045037

0.1676

IMH

1:7601938-50381771;1:10187873-186857210;1:16798094-234784887

0.4698

-1

full=1

0/1

14_48882017_49020572_DUP_1

48882017

49020572

138551

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:73635:0:1:0:0:0

2007

PASS

SUPP=3;SUPP_VEC=111;SVLEN=138551;SVTYPE=DUP;SVMETHOD=SURVIVOR1.0.7;CHR2=14;END=49020572;CIPOS=-4,0;CIEND=0,0;STRANDS=-;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=477632;Best_CCDG_OFP=0.0752779;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=204462;Best_CCDG_Mismatch_OFP=0.493609;Best_CCDG_Mismatch_SVTYPE=DEL;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0.282233;TOPMed_Count=0;Best_TOPMed_ID=DUP_14:48916068-48955171;Best_TOPMed_OFP=0.282241;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=7.29714e-05;Best_TOPMed_Mismatch_ID=DEL_14:48939002-49018200;Best_TOPMed_Mismatch_OFP=0.571627;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=0.000811;Best_TOPMed_Mismatch_Het=206;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_45304;Best_ThousG_Mismatch_OFP=0.168825;Best_ThousG_Mismatch_SVTYPE=DEL;Best_ThousG_Mismatch_AF=0.000312;Best_ThousG_Mismatch_Het=2;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DUP_chr14_cae0226a;Best_gnomAD_OFP=0.282241;Best_gnomAD_AF=2.4e-05;Best_gnomAD_Het=3;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000493;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr14_0e69a72e;Best_gnomAD_Mismatch_OFP=0.493609;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=4e-05;Best_gnomAD_Mismatch_Het=5;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:138555:18,18:-:2007:DUP:DUP00042067:NA:NA:chr14_48882017-chr14_49020572

0/1:NA:138551:0,0:-:999:DUP:MantaDUP_TANDEM_73635_0_1_0_0_0:NA:NA:chr14_48882021-chr14_49020572

1/1:NA:138551:0,0:-:658:DUP:8005:NA:NA:chr14_48882021-chr14_49020572

split

q21.3

LOC105378178

XR_007064152

48393998

49288023

138556

intron4-intron4

UTR

49219

48882016

49020572

dbVar

chr14:48646756-49611813

0.01

dbVar;gnomAD-SV_v3_DEL_chr14_040215df

chr14:41140072-69277618;chr14:48768510-49049201

0.0745

IMH

14:23629193-97505158;14:46648665-62759566;14:46648974-62759579

0.4022

-1

full=3

1/1

1_185620013_185620102_DEL_1

1.86E+08

-88

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:200913:0:1:0:0:0

AATGTGTGTATATATATATGGAATCTTCATATATGTGTATATATATATATACACATATATGAAGATTCCATATATATATACACACACAT

239

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:89:0,0:+:239:DEL:DEL00004115:NA:NA:chr1_185620013-chr1_185620102

0/1:NA:88:0,0:+:139:DEL:MantaDEL_200913_0_1_0_0_0:AATGTGTGTATATATATATGGAATCTTCATATATGTGTATATATATATATACACATATATGAAGATTCCATATATATATACACACACAT:A:chr1_185620013-chr1_185620101

0/1:NA:74:0,0:+:83:DEL:818:NA:NA:chr1_185620027-chr1_185620101

split

q25.3

LOC107985239

XR_001738340

1.85E+08

1.86E+08

intron1-intron1

UTR

59346

1.86E+08

gnomAD-SV_v3_DEL_chr1_339fd21d

chr1:168349020-187167586

0.9262

IMH

1:10187873-186857210;1:16798094-234784887;1:68663392-188869781;1:107555343-232824950

0.4698

-1

full=1

0/1

4_58562829_58569632_DUP_1

58562829

58569632

6800

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:148111:0:1:1:1:0

1440

PASS

SUPP=3;SUPP_VEC=111;SVLEN=6800;SVTYPE=DUP;SVMETHOD=SURVIVOR1.0.7;CHR2=4;END=58569632;CIPOS=-3,0;CIEND=-1,0;STRANDS=-;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=586980;Best_CCDG_Mismatch_OFP=0.000206405;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=0.004513;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DUP_4:58560946-58570336;Best_TOPMed_OFP=0.724127;Best_TOPMed_AF=7e-06;Best_TOPMed_Het=0;Best_TOPMed_HomAlt=1;Best_TOPMed_PopMax_AF=0.000218007;Best_TOPMed_Mismatch_ID=INV_4:57645482-58575877;Best_TOPMed_Mismatch_OFP=0.00730978;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_111856;Best_ThousG_OFP=0.0024321;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.000855;Best_ThousG_Mismatch_ID=HGSV_111855;Best_ThousG_Mismatch_OFP=0.000147037;Best_ThousG_Mismatch_SVTYPE=INS;Best_ThousG_Mismatch_AF=0.15029;Best_ThousG_Mismatch_Het=0;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.169534;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DUP_chr4_41308de1;Best_gnomAD_OFP=0.0382297;Best_gnomAD_AF=0.030721;Best_gnomAD_Het=1874;Best_gnomAD_HomAlt=276;Best_gnomAD_PopMax_AF=0.162393;gnomAD_Mismatches=gnomAD-SV_v3_DEL_chr4_a828013e;gnomAD_Mismatches_Count=1;gnomAD_Mismatch_SVTYPEs=DEL;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr4_a828013e;Best_gnomAD_Mismatch_OFP=0.843692;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=1.6e-05;Best_gnomAD_Mismatch_Het=2;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:6802:25,13:-:1440:DUP:DUP00014346:NA:NA:chr4_58562829-chr4_58569631

0/1:NA:6800:0,0:-:780:DUP:MantaDUP_TANDEM_148111_0_1_1_1_0:NA:NA:chr4_58562832-chr4_58569632

1/1:NA:6800:0,0:-:305:DUP:2704:NA:NA:chr4_58562832-chr4_58569632

split

q13.1

LOC107986228

XR_001741512

58567286

58590243

2346

txStart-intron1

UTR

1952

58567286

58569632

dbVar

chr4:57322428-61871079

0.01

IMH

4:1330317-92330038;4:4772332-76608755;4:21291890-139485605;4:21757282-83521389;4:32217847-78249129;4:41369891-94869199

0.1882

-1

full=3

1/1

4_58562830_58569374_DEL_1

58562830

58569374

-6543

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:148111:0:1:0:0:0

1680

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-6543;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=4;END=58569373;CIPOS=0,4;CIEND=0,1;STRANDS=+;Max_AF=1.6e-05;Max_Het=2;Max_HomAlt=0;Max_PopMax_AF=0.000247;CCDG_Count=0;Best_CCDG_Mismatch_ID=586980;Best_CCDG_Mismatch_OFP=0.000198605;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=0.004513;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_4:58042412-59020458;Best_TOPMed_OFP=0.00669088;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.26025e-06;Best_TOPMed_Mismatch_ID=DUP_4:58560946-58570336;Best_TOPMed_Mismatch_OFP=0.696763;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=0;Best_TOPMed_Mismatch_HomAlt=1;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_111856;Best_ThousG_Mismatch_OFP=0.00151959;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr4_a828013e;Best_gnomAD_OFP=0.81181;Best_gnomAD_AF=1.6e-05;Best_gnomAD_Het=2;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000247;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr4_e4405b6f;Best_gnomAD_Mismatch_OFP=0.0265892;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.083682;Best_gnomAD_Mismatch_Het=9593;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:6544:26,17:+:1680:DEL:DEL00014347:NA:NA:chr4_58562830-chr4_58569374

0/1:NA:6543:0,0:+:754:DEL:MantaDEL_148111_0_1_0_0_0:NA:NA:chr4_58562830-chr4_58569373

0/1:NA:6539:0,0:+:737:DEL:2703:NA:NA:chr4_58562834-chr4_58569373

split

q13.1

LOC107986228

XR_001741512

58567286

58590243

2088

txStart-intron1

UTR

1694

58567286

58569374

dbVar

chr4:57322428-61871079

0.01

IMH

4:1330317-92330038;4:4772332-76608755;4:21291890-139485605;4:21757282-83521389;4:32217847-78249129;4:41369891-94869199

0.1882

-1

full=3

0/1

6_169981355_169981464_DEL_1

1.7E+08

-108

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:131153:0:1:0:0:0

GTCACTGAACCTGGAGGGGGCTCAGGGTCCTCACTGCTCACTGAACCTGGAGGGGGCTCAGGATCCTCACTGCTCACTGAGGCTGGAGGGGGCTCAGGGTCCTCAAAGC

240

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-108;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=6;END=169981463;CIPOS=0,40;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=388275;Best_CCDG_OFP=0.633027;Best_CCDG_AF=0.2137;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_6:169981396-169981504;Best_TOPMed_OFP=0.397081;Best_TOPMed_AF=0.176012;Best_TOPMed_Het=39469;Best_TOPMed_HomAlt=188;Best_TOPMed_PopMax_AF=0.409962;Best_TOPMed_Mismatch_ID=INV_6:169946302-169997872;Best_TOPMed_Mismatch_OFP=0.00211355;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_139953;Best_ThousG_OFP=0.633027;Best_ThousG_AF=0.306588;Best_ThousG_Het=1332;Best_ThousG_HomAlt=316;Best_ThousG_PopMax_AF=0.54188;Best_ThousG_Mismatch_ID=HGSV_139951;Best_ThousG_Mismatch_OFP=0.00939979;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.633027;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr6_773e44d8;Best_gnomAD_OFP=0.201479;Best_gnomAD_AF=0.168424;Best_gnomAD_Het=20073;Best_gnomAD_HomAlt=535;Best_gnomAD_PopMax_AF=0.449405;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_INS_chr6_0cc115b6;Best_gnomAD_Mismatch_OFP=0.550459;Best_gnomAD_Mismatch_SVTYPE=INS;Best_gnomAD_Mismatch_AF=0.062465;Best_gnomAD_Mismatch_Het=5871;Best_gnomAD_Mismatch_HomAlt=2;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:109:0,0:+:240:DEL:DEL00021316:NA:NA:chr6_169981355-chr6_169981464

0/1:NA:108:0,0:+:227:DEL:MantaDEL_131153_0_1_0_0_0:GTCACTGAACCTGGAGGGGGCTCAGGGTCCTCACTGCTCACTGAACCTGGAGGGGGCTCAGGATCCTCACTGCTCACTGAGGCTGGAGGGGGCTCAGGGTCCTCAAAGC:G:chr6_169981355-chr6_169981463

0/1:NA:68:0,0:+:86:DEL:4219:NA:NA:chr6_169981395-chr6_169981463

split

q27

LOC107986675

XR_001744484

1.7E+08

110

exon2-exon2

UTR

1609

1.7E+08

-1

full=3

0/1

9_110267689_110275007_DUP_1

1.1E+08

7316

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:211865:1:2:0:0:0

480

PASS

SUPP=3;SUPP_VEC=111;SVLEN=7316;SVTYPE=DUP;SVMETHOD=SURVIVOR1.0.7;CHR2=9;END=110275005;CIPOS=0,1;CIEND=0,2;STRANDS=-;Max_AF=8e-06;Max_Het=1;Max_HomAlt=0;Max_PopMax_AF=0.000229;CCDG_Count=0;Best_CCDG_Mismatch_ID=434989;Best_CCDG_Mismatch_OFP=0.554245;Best_CCDG_Mismatch_SVTYPE=DEL;Best_CCDG_Mismatch_AF=0.1392;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DEL_9:110266596-110270066;Best_TOPMed_Mismatch_OFP=0.222593;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=0;Best_ThousG_ID=HGSV_164584;Best_ThousG_OFP=0.0261064;Best_ThousG_AF=0.265436;Best_ThousG_Het=808;Best_ThousG_HomAlt=430;Best_ThousG_PopMax_AF=0.613074;Best_ThousG_Mismatch_ID=HGSV_164582;Best_ThousG_Mismatch_OFP=2.5337e-08;Best_ThousG_Mismatch_SVTYPE=CPX;Best_ThousG_Mismatch_AF=0.228224;Best_ThousG_Mismatch_Het=1136;Best_ThousG_Mismatch_HomAlt=163;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DUP_chr9_e71fd71d;Best_gnomAD_OFP=0.820145;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000229;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr9_72a68986;Best_gnomAD_Mismatch_OFP=0.56303;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=8.2e-05;Best_gnomAD_Mismatch_Het=10;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:7315:21,2:-:480:DUP:DUP00029046:NA:NA:chr9_110267690-chr9_110275005

0/1:NA:7316:0,0:-:344:DUP:MantaDUP_TANDEM_211865_1_2_0_0_0:NA:NA:chr9_110267689-chr9_110275005

0/1:NA:7318:0,0:-:110:DUP:5706:NA:NA:chr9_110267689-chr9_110275007

split

q31.3

LOC107987114

XR_001746890

1.1E+08

7319

intron1-intron2

UTR

2249

1.1E+08

dbVar

chr9:110129325-110304387

0.01

IMH

9:65437055-134286391;9:80897170-125694547;9:89671548-130954998

0.4714

-1

full=3

0/1

9_110765848_110766057_DEL_1

1.11E+08

-208

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:211911:0:1:0:0:0

ACAGGTGTGAGCCACCACACTCAGCCAAAGCAATCCATTTTTATGCTTAGGTTCAATGAAGTATGAACAGCTGTGTAGAAATATGATTAGACACAAAGGGTATGATCTAATGCTAACAGGCTGAGTGGGGAAACTAGCCCATCCTGCTTGTTCAGATTTTTCTCAGCCCCTCTGTGCAGCACTCACTCCTCCCAGGCAAGAGGTAGGAT

325

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-208;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=9;END=110766056;CIPOS=0,1;CIEND=0,1;STRANDS=+;Max_AF=0.0003419;Max_Het=30;Max_HomAlt=1;Max_PopMax_AF=0.003636;CCDG_Count=1;Best_CCDG_ID=435033;Best_CCDG_OFP=0.995215;Best_CCDG_AF=0.0003419;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=608311;Best_CCDG_Mismatch_OFP=7.767e-06;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0.995215;TOPMed_Count=1;Best_TOPMed_ID=DEL_9:110765850-110766056;Best_TOPMed_OFP=0.995215;Best_TOPMed_AF=0.000123;Best_TOPMed_Het=30;Best_TOPMed_HomAlt=1;Best_TOPMed_PopMax_AF=0.00344418;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_164623;Best_ThousG_OFP=0.995215;Best_ThousG_AF=0.000312;Best_ThousG_Het=2;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.001664;ThousG_SV_Cov=0.995215;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr9_c7517a2c;Best_gnomAD_OFP=0.995215;Best_gnomAD_AF=0.000127;Best_gnomAD_Het=14;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.003636;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr9_005c44cc;Best_gnomAD_Mismatch_OFP=0.000567588;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=1.6e-05;Best_gnomAD_Mismatch_Het=2;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:209:0,0:+:145:DEL:DEL00029056:NA:NA:chr9_110765848-chr9_110766057

0/1:NA:208:0,0:+:325:DEL:MantaDEL_211911_0_1_0_0_0:ACAGGTGTGAGCCACCACACTCAGCCAAAGCAATCCATTTTTATGCTTAGGTTCAATGAAGTATGAACAGCTGTGTAGAAATATGATTAGACACAAAGGGTATGATCTAATGCTAACAGGCTGAGTGGGGAAACTAGCCCATCCTGCTTGTTCAGATTTTTCTCAGCCCCTCTGTGCAGCACTCACTCCTCCCAGGCAAGAGGTAGGAT:A:chr9_110765848-chr9_110766056

0/1:NA:207:0,0:+:185:DEL:5707:NA:NA:chr9_110765849-chr9_110766056

split

q31.3

LOC107987115

XR_001746892

1.11E+08

210

intron2-intron2

UTR

1010

1.11E+08

IMH

9:65437055-134286391;9:80897170-125694547;9:89671548-130954998

0.4714

-1

full=3

0/1

4_9677435_9677500_DEL_1

9677435

9677500

-64

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:144537:0:1:0:0:0

CATCGATACTGTCATGAACTGGTTCACCTAGGAAGACTTTGACTTTGTGACTCTGTGCTACAGAG

624

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-64;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=4;END=9677499;CIPOS=0,1;CIEND=0,1;STRANDS=+;Max_AF=0.000781;Max_Het=67;Max_HomAlt=1;Max_PopMax_AF=0.005102;CCDG_Count=0;Best_CCDG_ID=333250;Best_CCDG_OFP=0.0093633;Best_CCDG_AF=0.0001026;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=333251_1;Best_CCDG_Mismatch_OFP=0.0153846;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.0007864;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_4:9676028-9683014;Best_TOPMed_OFP=0.00930166;Best_TOPMed_AF=7.8e-05;Best_TOPMed_Het=22;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000239527;Best_TOPMed_Mismatch_ID=INV_4:9552055-9715383;Best_TOPMed_Mismatch_OFP=0.000397967;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_109152;Best_ThousG_OFP=0.984615;Best_ThousG_AF=0.000781;Best_ThousG_Het=5;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.003419;Best_ThousG_Mismatch_ID=HGSV_109100;Best_ThousG_Mismatch_OFP=0.000133584;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000312;Best_ThousG_Mismatch_Het=2;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr4_864b8b7d;Best_gnomAD_OFP=0.90022;Best_gnomAD_AF=0.000548;Best_gnomAD_Het=67;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.005102;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr4_522a85bf;Best_gnomAD_Mismatch_OFP=0.000836045;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:65:0,0:+:386:DEL:DEL00012463:NA:NA:chr4_9677435-chr4_9677500

0/1:NA:64:0,0:+:624:DEL:MantaDEL_144537_0_1_0_0_0:CATCGATACTGTCATGAACTGGTTCACCTAGGAAGACTTTGACTTTGTGACTCTGTGCTACAGAG:C:chr4_9677435-chr4_9677499

0/1:NA:63:0,0:+:353:DEL:2565:NA:NA:chr4_9677436-chr4_9677499

split

p16.1

LOC124900660

XR_007058018

9659024

9687076

exon3-exon3

UTR

124

9677434

9677500

dbVar

chr4:9634602-9716386

0.01

dbVar

chr4:9675966-9682958;chr4:9676050-9682991

0.01

IMH

4:1330317-92330038;4:2821273-17704603;4:4772332-76608755

0.0791

-1

full=1

0/1

4_58562829_58569632_DUP_1

58562829

58569632

6800

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:148111:0:1:1:1:0

1440

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:6802:25,13:-:1440:DUP:DUP00014346:NA:NA:chr4_58562829-chr4_58569631

0/1:NA:6800:0,0:-:780:DUP:MantaDUP_TANDEM_148111_0_1_1_1_0:NA:NA:chr4_58562832-chr4_58569632

1/1:NA:6800:0,0:-:305:DUP:2704:NA:NA:chr4_58562832-chr4_58569632

split

q13.1

LOC124900833

XR_007058424

58562164

58565212

2384

txStart-intron2

UTR

509

58562828

58565212

dbVar

chr4:57322428-61871079

0.01

IMH

4:1330317-92330038;4:4772332-76608755;4:21291890-139485605;4:21757282-83521389;4:32217847-78249129;4:41369891-94869199

0.1882

-1

full=3

1/1

4_58562830_58569374_DEL_1

58562830

58569374

-6543

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:148111:0:1:0:0:0

1680

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:6544:26,17:+:1680:DEL:DEL00014347:NA:NA:chr4_58562830-chr4_58569374

0/1:NA:6543:0,0:+:754:DEL:MantaDEL_148111_0_1_0_0_0:NA:NA:chr4_58562830-chr4_58569373

0/1:NA:6539:0,0:+:737:DEL:2703:NA:NA:chr4_58562834-chr4_58569373

split

q13.1

LOC124900833

XR_007058424

58562164

58565212

2383

txStart-intron2

UTR

510

58562829

58565212

dbVar

chr4:57322428-61871079

0.01

IMH

4:1330317-92330038;4:4772332-76608755;4:21291890-139485605;4:21757282-83521389;4:32217847-78249129;4:41369891-94869199

0.1882

-1

full=3

0/1

9_110267689_110275007_DUP_1

1.1E+08

7316

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:211865:1:2:0:0:0

480

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:7315:21,2:-:480:DUP:DUP00029046:NA:NA:chr9_110267690-chr9_110275005

0/1:NA:7316:0,0:-:344:DUP:MantaDUP_TANDEM_211865_1_2_0_0_0:NA:NA:chr9_110267689-chr9_110275005

0/1:NA:7318:0,0:-:110:DUP:5706:NA:NA:chr9_110267689-chr9_110275007

split

q31.3

LOC124902246

XR_007061729

1.1E+08

1101

txStart-intron1

UTR

296

1.1E+08

dbVar

chr9:110129325-110304387

0.01

IMH

9:65437055-134286391;9:80897170-125694547;9:89671548-130954998

0.4714

-1

full=3

0/1

1_238530121_238538212_DUP_1

2.39E+08

8091

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:204825:0:1:2:0:0

2280

PASS

SUPP=3;SUPP_VEC=111;SVLEN=8091;SVTYPE=DUP;SVMETHOD=SURVIVOR1.0.7;CHR2=1;END=238538212;CIPOS=0,1;CIEND=0,0;STRANDS=-;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=460872;Best_CCDG_OFP=0.00656401;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=142309;Best_CCDG_Mismatch_OFP=0.0403346;Best_CCDG_Mismatch_SVTYPE=DEL;Best_CCDG_Mismatch_AF=3.42e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DUP_1:238488419-238615184;Best_TOPMed_OFP=0.0638336;Best_TOPMed_AF=0.000178;Best_TOPMed_Het=48;Best_TOPMed_HomAlt=1;Best_TOPMed_PopMax_AF=0.000296026;Best_TOPMed_Mismatch_ID=DEL_1:238534402-238541900;Best_TOPMed_Mismatch_OFP=0.239436;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_12298;Best_ThousG_OFP=0.0638336;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.00102;ThousG_Mismatches=HGSV_12303;ThousG_Mismatches_Count=1;ThousG_Mismatch_SVTYPEs=DEL;Best_ThousG_Mismatch_ID=HGSV_12303;Best_ThousG_Mismatch_OFP=0.967364;Best_ThousG_Mismatch_SVTYPE=DEL;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DUP_chr1_cd345c39;Best_gnomAD_OFP=0.0638336;Best_gnomAD_AF=0.000254;Best_gnomAD_Het=30;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.000636;gnomAD_Mismatches=gnomAD-SV_v3_DEL_chr1_ea98a6f7;gnomAD_Mismatches_Count=1;gnomAD_Mismatch_SVTYPEs=DEL;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr1_ea98a6f7;Best_gnomAD_Mismatch_OFP=0.921782;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=0.000135;Best_gnomAD_Mismatch_Het=17;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:8090:36,21:-:2280:DUP:DUP00004939:NA:NA:chr1_238530122-chr1_238538212

0/1:NA:8091:0,0:-:999:DUP:MantaDUP_TANDEM_204825_0_1_2_0_0:NA:NA:chr1_238530121-chr1_238538212

1/1:NA:8091:0,0:-:503:DUP:1012:NA:NA:chr1_238530121-chr1_238538212

split

q43

LOC124904565

XR_007066966

2.39E+08

4764

txStart-intron1

UTR

4700

2.39E+08

dbVar

chr1:237600877-238691725;chr1:238021699-238768700;chr1:238488418-238615188;chr1:238498219-238566226

0.01

-1

full=3

1/1

1_238530104_238537891_DEL_1

2.39E+08

-7786

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:204825:0:1:0:0:0

1080

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-7786;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=1;END=238537890;CIPOS=0,4;CIEND=0,1;STRANDS=+;Max_AF=0.000156;Max_Het=17;Max_HomAlt=0;Max_PopMax_AF=0.00056;CCDG_Count=0;Best_CCDG_ID=142309;Best_CCDG_OFP=0.0388143;Best_CCDG_AF=3.42e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=460872;Best_CCDG_Mismatch_OFP=0.0063166;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_1:238534402-238541900;Best_TOPMed_OFP=0.208554;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.2626e-06;Best_TOPMed_Mismatch_ID=DUP_1:238488419-238615184;Best_TOPMed_Mismatch_OFP=0.0614277;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=0.000178;Best_TOPMed_Mismatch_Het=48;Best_TOPMed_Mismatch_HomAlt=1;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_12303;Best_ThousG_OFP=0.930903;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.00056;Best_ThousG_Mismatch_ID=HGSV_12298;Best_ThousG_Mismatch_OFP=0.0614277;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr1_ea98a6f7;Best_gnomAD_OFP=0.962245;Best_gnomAD_AF=0.000135;Best_gnomAD_Het=17;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000385;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr1_cd345c39;Best_gnomAD_Mismatch_OFP=0.0614277;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.000254;Best_gnomAD_Mismatch_Het=30;Best_gnomAD_Mismatch_HomAlt=1;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:7787:33,8:+:1080:DEL:DEL00004938:NA:NA:chr1_238530104-chr1_238537891

0/1:NA:7786:0,0:+:445:DEL:MantaDEL_204825_0_1_0_0_0:NA:NA:chr1_238530104-chr1_238537890

0/1:NA:7782:0,0:+:299:DEL:1011:NA:NA:chr1_238530108-chr1_238537890

split

q43

LOC124904565

XR_007066966

2.39E+08

4443

txStart-intron1

UTR

4379

2.39E+08

dbVar

chr1:237600877-238691725;chr1:238021699-238768700;chr1:238488418-238615188;chr1:238498219-238566226

0.01

-1

full=3

0/1

2_44409095_44409184_DEL_1

44409095

44409184

-88

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:174423:0:0:0:0:0

ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATG

1140

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

1/1:NA:89:0,0:+:1140:DEL:DEL00006084:NA:NA:chr2_44409095-chr2_44409184

1/1:NA:88:0,0:+:732:DEL:MantaDEL_174423_0_0_0_0_0:ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATG:A:chr2_44409095-chr2_44409183

1/1:NA:68:0,0:+:699:DEL:1226:NA:NA:chr2_44409100-chr2_44409168

split

p21

LOC124907759

XR_007086304

44401132

44421913

intron1-intron1

UTR

2828

44409094

44409184

dbVar;gnomAD-SV_v3_DUP_chr2_d33e7116

chr2:44405812-44507018;chr2:44409080-44409188

0.0624

dbVar

chr2:44278237-44413378;chr2:44391631-44410269

0.01

IMH

2:21055811-76514955;2:32873521-53185851

0.1623

-1

full=1

1/1

9_110998042_111009830_DEL_1

1.11E+08

-11787

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:211928:0:1:0:0:0

1103

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-11787;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=9;END=111009829;CIPOS=0,6;CIEND=0,1;STRANDS=+;Max_AF=0.000312;Max_Het=19;Max_HomAlt=1;Max_PopMax_AF=0.0021777;CCDG_Count=1;Best_CCDG_ID=435050;Best_CCDG_OFP=0.999491;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=608311;Best_CCDG_Mismatch_OFP=0.000438074;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0.999491;TOPMed_Count=1;Best_TOPMed_ID=DEL_9:110998049-111009829;Best_TOPMed_OFP=0.999491;Best_TOPMed_AF=7.4e-05;Best_TOPMed_Het=19;Best_TOPMed_HomAlt=1;Best_TOPMed_PopMax_AF=0.0021777;Best_TOPMed_Mismatch_ID=DUP_9:111002802-111008800;Best_TOPMed_Mismatch_OFP=0.508992;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0.999491;ThousG_Count=1;Best_ThousG_ID=HGSV_164637;Best_ThousG_OFP=0.999491;Best_ThousG_AF=0.000312;Best_ThousG_Het=2;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.001664;ThousG_SV_Cov=0.999491;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr9_7139caaf;Best_gnomAD_OFP=0.999491;Best_gnomAD_AF=3.2e-05;Best_gnomAD_Het=4;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000681;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_INS_chr9_6fd63941;Best_gnomAD_Mismatch_OFP=0.00398711;Best_gnomAD_Mismatch_SVTYPE=INS;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:11788:19,7:+:1103:DEL:DEL00029057:NA:NA:chr9_110998042-chr9_111009830

0/1:NA:11787:0,0:+:498:DEL:MantaDEL_211928_0_1_0_0_0:NA:NA:chr9_110998042-chr9_111009829

0/1:NA:11781:0,0:+:368:DEL:5708:NA:NA:chr9_110998048-chr9_111009829

split

q31.3

LPAR1

XM_047422903

1.11E+08

11789

intron3-intron4

5'UTR

629

1.11E+08

IMH

9:65437055-134286391;9:80897170-125694547;9:89671548-130954998

0.4714

11.39

0.873443

1.061705

1.264533

-0.79036

2.571295

1902

1.86E-01

1.42E-03

0.9511

Cleft lip;Cleft palate;Hypertelorism;Micrognathia;Microphthalmia;long incisors;ocular hypertelorism;short snout

Meckel's cartilage deformed, abnormal;Micrognathia

full=3

0/1

10_19237576_19237674_DEL_1

19237576

19237674

-97

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:38088:0:0:0:2:0

AATTATAATTATATAATTATATAATTATAATTATAATTATATAATTATATAATTATAATTATATATAAATTATTATAATTATATATAAATTATATAAT

480

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-97;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=10;END=19237673;CIPOS=0,0;CIEND=-10,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=146122;Best_CCDG_OFP=0.022192;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=146123_1;Best_CCDG_Mismatch_OFP=0.0102041;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.06837;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_10:19227120-19238593;Best_TOPMed_OFP=0.00854031;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.26339e-06;Best_TOPMed_Mismatch_ID=INV_10:19224623-19248206;Best_TOPMed_Mismatch_OFP=0.00415518;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=0.0001;Best_TOPMed_Mismatch_Het=28;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_14412;Best_ThousG_OFP=0.00363988;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0;Best_ThousG_Mismatch_ID=HGSV_14289;Best_ThousG_Mismatch_OFP=1.22078e-05;Best_ThousG_Mismatch_SVTYPE=INV;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr10_8222a499;Best_gnomAD_OFP=0.52973;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000227;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr10_3dd3b75f;Best_gnomAD_Mismatch_OFP=0.000489772;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=1.6e-05;Best_gnomAD_Mismatch_Het=2;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:98:0,0:+:480:DEL:DEL00030447:NA:NA:chr10_19237576-chr10_19237674

0/1:NA:97:0,0:+:251:DEL:MantaDEL_38088_0_0_0_2_0:AATTATAATTATATAATTATATAATTATAATTATAATTATATAATTATATAATTATAATTATATATAAATTATTATAATTATATATAAATTATATAAT:A:chr10_19237576-chr10_19237673

0/1:NA:87:0,0:+:200:DEL:5951:NA:NA:chr10_19237576-chr10_19237663

split

p12.31

MALRD1

XM_047425168

19046926

19287047

intron19-intron19

CDS

20009

19237575

19237674

dbVar

chr10:19093771-19584071;chr10:19223342-19249473;chr10:19224621-19255405

0.01

72.62

340895

9.38E-21

0.7305

Cleft lip;Cleft palate;Hypertelorism;Micrognathia;Microphthalmia;abnormal eye morphology;anophthalmia

full=3

0/1

10_19473089_19473179_DEL_1

19473089

19473179

-89

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:38069:0:1:0:0:0

GAAATGTGAAAGCTTGTTCATAACCTCACTTTATCCTCAACTTAAATTTTGAGGATAAATTGAGGTTATGAACAAGCTTTCACATTTCTT

240

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-89;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=10;END=19473178;CIPOS=0,10;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=146150;Best_CCDG_OFP=0.00583733;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=146153_2;Best_CCDG_Mismatch_OFP=0.0111111;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.2654;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_10:19470114-19478623;Best_TOPMed_OFP=0.0105746;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.26205e-06;Best_TOPMed_Mismatch_ID=DUP_10:19321083-19476602;Best_TOPMed_Mismatch_OFP=0.0005787;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_14289;Best_ThousG_Mismatch_OFP=1.12113e-05;Best_ThousG_Mismatch_SVTYPE=INV;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr10_d0388585;Best_gnomAD_OFP=0.243902;Best_gnomAD_AF=0.00067;Best_gnomAD_Het=84;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.001188;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr10_006be9e5;Best_gnomAD_Mismatch_OFP=0.000304053;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:90:0,0:+:240:DEL:DEL00030450:NA:NA:chr10_19473089-chr10_19473179

0/1:NA:89:0,0:+:164:DEL:MantaDEL_38069_0_1_0_0_0:GAAATGTGAAAGCTTGTTCATAACCTCACTTTATCCTCAACTTAAATTTTGAGGATAAATTGAGGTTATGAACAAGCTTTCACATTTCTT:G:chr10_19473089-chr10_19473178

0/1:NA:79:0,0:+:47:DEL:5952:NA:NA:chr10_19473099-chr10_19473178

split

p12.31

MALRD1

XM_047425167

19046926

19567592

intron30-intron30

CDS

18337

19473088

19473179

dbVar

chr10:19093771-19584071;chr10:19355571-19822382

0.01

72.62

340895

9.38E-21

0.7305

Cleft lip;Cleft palate;Hypertelorism;Micrognathia;Microphthalmia;abnormal eye morphology;anophthalmia

full=3

0/1

19_4005348_4159440_DEL_1

4005348

4159440

-154090

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:79083:0:1:0:0:0

1740

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:154087:26,11:+:1740:DEL:DEL00054230:NA:NA:chr19_4005348-chr19_4159435

0/1:NA:154090:0,0:+:999:DEL:MantaDEL_79083_0_1_0_0_0:NA:NA:chr19_4005350-chr19_4159440

0/1:NA:154090:0,0:+:650:DEL:10046:NA:NA:chr19_4005350-chr19_4159440

split

p13.3

MAP2K2

NM_030662

4090320

4124122

33802

1203

100

txStart-txEnd

5'UTR-3'UTR

4090320

4124122

Cardiofaciocutaneous syndrome 4, 615280 (3) AD

morbid:MAP2K2

19:4090321-4124122

Cardio-facio-cutaneous_syndrome;Cardiofaciocutaneous_syndrome_1;Cardiofaciocutaneous_syndrome_4;Castleman-Kojima_disease;Gastric_adenocarcinoma;Malignant_melanoma_of_skin;Melanoma;Noonan_syndrome;Noonan_syndrome_1;Pancreatic_adenocarcinoma;RASopathy;Smith-Magenis_Syndrome-like;Squamous_cell_carcinoma_of_the_head_and_neck

IMH

19:1692676-41507766

0.0103

38.94

0.37913

0.438659

0.549595

-1.31922

1.476321

Noonan syndrome;cardiofaciocutaneous syndrome;cardiofaciocutaneous syndrome 1;cardiofaciocutaneous syndrome 4;neurofibromatosis-Noonan syndrome

Definitive;Limited;Strong;Supportive

16439621;18042262;20301365[PMID]_16825433[PMID];20358587;21396583;23379592;24311457[PMID]

5605

601263

Cardiofaciocutaneous syndrome 4, 615280 (3) AD

yes

9.67E-01

8.63E-01

0.6168

Cardiofaciocutaneous syndrome;Cleft lip;Cleft palate;High palate;Hypertelorism;Hypoplasia of the zygomatic bone;Micrognathia;Submucous cleft hard palate

full=5

0/1

19_4005230_4159441_DUP_1

4005230

4159441

154171

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:79083:0:1:1:0:0

999

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:154170:21,8:-:600:DUP:DUP00054229:NA:NA:chr19_4005253-chr19_4159423

0/1:NA:154171:0,0:-:999:DUP:MantaDUP_TANDEM_79083_0_1_1_0_0:NA:NA:chr19_4005252-chr19_4159423

0/1:NA:154211:0,0:-:106:DUP:10045:NA:NA:chr19_4005230-chr19_4159441

split

p13.3

MAP2K2

NM_030662

4090320

4124122

33802

1203

100

txStart-txEnd

5'UTR-3'UTR

4090320

4124122

Cardiofaciocutaneous syndrome 4, 615280 (3) AD

morbid:MAP2K2

19:4090321-4124122

IMH

19:1692676-41507766

0.0103

38.94

0.37913

0.438659

0.549595

-1.31922

1.476321

Noonan syndrome;cardiofaciocutaneous syndrome;cardiofaciocutaneous syndrome 1;cardiofaciocutaneous syndrome 4;neurofibromatosis-Noonan syndrome

Definitive;Limited;Strong;Supportive

16439621;18042262;20301365[PMID]_16825433[PMID];20358587;21396583;23379592;24311457[PMID]

5605

601263

Cardiofaciocutaneous syndrome 4, 615280 (3) AD

yes

9.67E-01

8.63E-01

0.6168

Cardiofaciocutaneous syndrome;Cleft lip;Cleft palate;High palate;Hypertelorism;Hypoplasia of the zygomatic bone;Micrognathia;Submucous cleft hard palate

full=3

0/1

15_99687009_99687107_DEL_1

99687009

99687107

-97

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:71235:0:1:0:0:0

CTGCCTCCTGGGCTCACCTCAGCCTCCTTAGTTTCTGGGACTACAGGTGCACACCACCATGTCCTATTAATTTTTCTTTTTTTTTTTTTTTTTTTTTT

602

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-97;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=15;END=99687106;CIPOS=0,1;CIEND=0,1;STRANDS=+;Max_AF=0.000156;Max_Het=8;Max_HomAlt=0;Max_PopMax_AF=0.000832;CCDG_Count=0;Best_CCDG_Mismatch_ID=481461;Best_CCDG_Mismatch_OFP=0.000322503;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_15:93794810-100070222;Best_TOPMed_OFP=1.56165e-05;Best_TOPMed_AF=5.4e-05;Best_TOPMed_Het=13;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000244559;Best_TOPMed_Mismatch_ID=INV_15:99320521-99873567;Best_TOPMed_Mismatch_OFP=0.0001772;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_53719;Best_ThousG_OFP=0.989796;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.000832;ThousG_SV_Cov=0.989796;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr15_589928e5;Best_gnomAD_OFP=0.979696;Best_gnomAD_AF=6.4e-05;Best_gnomAD_Het=8;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000454;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr15_c71511db;Best_gnomAD_Mismatch_OFP=0.000322503;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=1.6e-05;Best_gnomAD_Mismatch_Het=2;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:98:0,0:+:480:DEL:DEL00045486:NA:NA:chr15_99687009-chr15_99687107

0/1:NA:97:0,0:+:602:DEL:MantaDEL_71235_0_1_0_0_0:CTGCCTCCTGGGCTCACCTCAGCCTCCTTAGTTTCTGGGACTACAGGTGCACACCACCATGTCCTATTAATTTTTCTTTTTTTTTTTTTTTTTTTTTT:C:chr15_99687009-chr15_99687106

0/1:NA:96:0,0:+:284:DEL:8640:NA:NA:chr15_99687010-chr15_99687106

split

q26.3

MEF2A

NM_001352617

99565416

99716488

intron7-intron7

CDS

3133

99687008

99687107

dbVar

chr15:99437793-99780795;chr15:99645280-99949158

0.01

IMH

15:52285432-100775019

0.2918

6.04

0.108002

-0.74081

-0.49525

-0.919

0.53855

4205

600660

(Coronary artery disease, AD, 1), 608320 (3) AD

yes

9.87E-01

7.37E-01

full=3

0/1

11_64341843_64341924_DEL_1

64341843

64341924

-80

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:30764:0:1:0:0:0

GGTTGTGGTCTGAGGTCTTGGGCCATCAGTGATGTCACAACCAGATGGCCCAAGACCCCAGACCACAACCCCATGTCTGGT

480

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:81:0,0:+:480:DEL:DEL00035331:NA:NA:chr11_64341843-chr11_64341924

0/1:NA:80:0,0:+:280:DEL:MantaDEL_30764_0_1_0_0_0:GGTTGTGGTCTGAGGTCTTGGGCCATCAGTGATGTCACAACCAGATGGCCCAAGACCCCAGACCACAACCCCATGTCTGGT:G:chr11_64341843-chr11_64341923

0/1:NA:72:0,0:+:197:DEL:6678:NA:NA:chr11_64341851-chr11_64341923

split

q13.1

MIR7155

NR_106977

64341848

64341904

txStart-txEnd

UTR

64341848

64341904

IMH

11:1621661-71538522;11:49193342-89651496;11:49211577-89635120;11:49243027-89597882;11:49358811-89347590;11:49403038-89297530;11:49586833-89037283;11:49629782-88995227;11:49736709-88892563

0.4958

1.02E+08

full=3

0/1

12_123221910_123222409_DEL_1

1.23E+08

-498

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:24599:0:1:2:0:0

TTATAGATTTGGGTAAGAAAGTATATTAAACATCATATTTTTATGACTGTTACAAGAATATCATGTTTCAAAATATGATGAGATATTATTCTAAAGATAATGTGATACTTTATCTTTAGTTTATAAACAAAATTGAGGCTGGTGGCCAGGCACAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCAGATCACAAGGTCAGGAGCTCAAGACCAGCTTGGCCAACACGGTGAAACTCTGACTCTACTAAAAATTAGCCAGACACGGTGGTGCGCATCTGTAATTCCAGCTACTCAGGAGTCTGAGGCAGGAGAATTTCTTGAACCCAGGAGGCAGAGGTTGCAGTCAGCTAAAATCATGTCACTGCACGCCAGCCTGGGTGACAGAGTGAGACCTTGTCTCAAAAAAAAAAAAAAAAATTGATATAACGTATTGTTTTTTCTTACAAATATAAAAAAGGATGCTGGGTGTGGTGGCTCACGCCTG

1072

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-498;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=12;END=123222408;CIPOS=0,2;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=188912;Best_CCDG_OFP=0.0898775;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=473454;Best_CCDG_Mismatch_OFP=0.00533964;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DUP_12:123175345-123268795;Best_TOPMed_Mismatch_OFP=0.00533964;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=1.8e-05;Best_TOPMed_Mismatch_Het=5;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_36639;Best_ThousG_Mismatch_OFP=0.0314054;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.001249;Best_ThousG_Mismatch_Het=8;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr12_41af712a;Best_gnomAD_OFP=0.268201;Best_gnomAD_AF=4e-05;Best_gnomAD_Het=5;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000643;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr12_c72d7304;Best_gnomAD_Mismatch_OFP=0.0314054;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=3.2e-05;Best_gnomAD_Mismatch_Het=4;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:499:17,5:+:1072:DEL:DEL00039773:NA:NA:chr12_123221910-chr12_123222409

0/1:NA:498:0,0:+:970:DEL:MantaDEL_24599_0_1_2_0_0:TTATAGATTTGGGTAAGAAAGTATATTAAACATCATATTTTTATGACTGTTACAAGAATATCATGTTTCAAAATATGATGAGATATTATTCTAAAGATAATGTGATACTTTATCTTTAGTTTATAAACAAAATTGAGGCTGGTGGCCAGGCACAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCAGATCACAAGGTCAGGAGCTCAAGACCAGCTTGGCCAACACGGTGAAACTCTGACTCTACTAAAAATTAGCCAGACACGGTGGTGCGCATCTGTAATTCCAGCTACTCAGGAGTCTGAGGCAGGAGAATTTCTTGAACCCAGGAGGCAGAGGTTGCAGTCAGCTAAAATCATGTCACTGCACGCCAGCCTGGGTGACAGAGTGAGACCTTGTCTCAAAAAAAAAAAAAAAAATTGATATAACGTATTGTTTTTTCTTACAAATATAAAAAAGGATGCTGGGTGTGGTGGCTCACGCCTG:T:chr12_123221910-chr12_123222408

0/1:NA:496:0,0:+:719:DEL:7478:NA:NA:chr12_123221912-chr12_123222408

split

q24.31

MPHOSPH9

XM_047428063

1.23E+08

500

intron3-intron3

CDS

1.23E+08

dbVar

chr12:123076425-123304379;chr12:123175344-123268795

0.01

47.37

-0.39718

-0.88773

-0.67925

1.085043

-0.1163

10198

1.66E-10

7.60E-04

full=3

0/1

13_29375409_29375645_DEL_1

29375409

29375645

-218

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:8169:0:0:0:0:1

TTACTTACTTTTAATGGCAAAAACCGCAATTACTTACTTTTAATGGCAACAACCGCAATTACTTACTTTTAATGGCAAAAACCGCAATCACCTTTGCACCAGCCTACTATATATATATATATATATATACGTGTATATATATATATATACGTATATATATATATACATATATATATATACGTATATATATATATATATACGTATATATATATATATATA

TCACCTTTGCACCAACCTAC

999

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-218;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=13;END=29375627;CIPOS=0,126;CIEND=0,18;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=31451_1;Best_CCDG_Mismatch_OFP=0.00456621;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.1431;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DUP_13:29193402-29635100;Best_TOPMed_Mismatch_OFP=0.000495812;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=5.2e-05;Best_TOPMed_Mismatch_Het=14;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr13_807ad7b8;Best_gnomAD_OFP=0.58451;Best_gnomAD_AF=0.00012;Best_gnomAD_Het=15;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000952;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_BND_chr13_95491615;Best_gnomAD_Mismatch_OFP=0.00456621;Best_gnomAD_Mismatch_SVTYPE=BND;Best_gnomAD_Mismatch_AF=0.007648;Best_gnomAD_Mismatch_Het=871;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

1/1:NA:111:0,0:+:449:DEL:DEL00040360:NA:NA:chr13_29375534-chr13_29375645

1/1:NA:218:0,0:+:999:DEL:MantaDEL_8169_0_0_0_0_1:TTACTTACTTTTAATGGCAAAAACCGCAATTACTTACTTTTAATGGCAACAACCGCAATTACTTACTTTTAATGGCAAAAACCGCAATCACCTTTGCACCAGCCTACTATATATATATATATATATATACGTGTATATATATATATATACGTATATATATATATACATATATATATATACGTATATATATATATATATACGTATATATATATATATATA:TCACCTTTGCACCAACCTAC:chr13_29375409-chr13_29375627

1/1:NA:109:0,0:+:531:DEL:7674:NA:NA:chr13_29375535-chr13_29375644

split

q12.3

MTUS2

NM_001384605

28819962

29505947

237

intron8-intron8

CDS

15935

29375408

29375645

47.5

2.149185

0.994348

1.333913

-1.65367

-1.4549

23281

7.95E-01

3.31E-01

full=3

1/1

9_110765848_110766057_DEL_1

1.11E+08

-208

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:211911:0:1:0:0:0

325

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:209:0,0:+:145:DEL:DEL00029056:NA:NA:chr9_110765848-chr9_110766057

0/1:NA:207:0,0:+:185:DEL:5707:NA:NA:chr9_110765849-chr9_110766056

split

q31.3

MUSK

NM_001166280

1.11E+08

210

intron9-intron9

CDS

3639

1.11E+08

IMH

9:65437055-134286391;9:80897170-125694547;9:89671548-130954998

0.4714

6.69

-2.62354

-0.96266

-2.19452

0.604569

0.165293

congenital myasthenic syndrome 9;fetal akinesia deformation sequence 1;postsynaptic congenital myasthenic syndrome

Strong;Supportive

15496425;19949040;20301347[PMID];20371544;24122059;25537362;25612909;25612909[PMID]_25537362[PMID];25695962;25900532;32253145;8653786

4593

601296

Fetal akinesia deformation sequence 1, 208150 (3) AR;Myasthenic syndrome, congenital, 9, associated with acetylcholine receptor deficiency, 616325 (3) AR

yes

4.25E-08

8.17E-05

0.7065

Cleft lip;Cleft palate;Fetal akinesia deformation sequence 1;Hypertelorism;Micrognathia

Holoprosencephaly;abnormal innervation

Holoprosencephaly;spinal cord motor neuron differentiation process quality, abnormal

full=3

0/1

11_19982066_19983779_DEL_1

19982066

19983779

-1712

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:27470:0:1:0:0:0

1260

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-1712;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=11;END=19983778;CIPOS=0,3;CIEND=0,1;STRANDS=+;Max_AF=0.002966;Max_Het=51;Max_HomAlt=2;Max_PopMax_AF=0.015807;CCDG_Count=0;Best_CCDG_ID=161160;Best_CCDG_OFP=0.0656246;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=161162_1;Best_CCDG_Mismatch_OFP=0.000583771;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.0003761;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_11:19971227-19997332;Best_TOPMed_OFP=0.0656146;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.26049e-06;Best_TOPMed_Mismatch_ID=INV_11:16966271-21356221;Best_TOPMed_Mismatch_OFP=0.000390209;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=1.1e-05;Best_TOPMed_Mismatch_Het=3;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_22181;Best_ThousG_OFP=1;Best_ThousG_AF=0.002966;Best_ThousG_Het=17;Best_ThousG_HomAlt=1;Best_ThousG_PopMax_AF=0.015807;Best_ThousG_Mismatch_ID=HGSV_21984;Best_ThousG_Mismatch_OFP=0.000401453;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr11_753e4dc0;Best_gnomAD_OFP=0.940176;Best_gnomAD_AF=0.000436;Best_gnomAD_Het=51;Best_gnomAD_HomAlt=2;Best_gnomAD_PopMax_AF=0.012483;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr11_949f9834;Best_gnomAD_Mismatch_OFP=0.00482213;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:1710:24,12:+:1260:DEL:DEL00034364:NA:NA:chr11_19982069-chr11_19983779

0/1:NA:1712:0,0:+:598:DEL:MantaDEL_27470_0_1_0_0_0:NA:NA:chr11_19982066-chr11_19983778

0/1:NA:1712:0,0:+:464:DEL:6447:NA:NA:chr11_19982066-chr11_19983778

split

p15.1

NAV2

NM_001111018

19345235

20121601

1714

intron11-intron11

CDS

345

19982065

19983779

1000g;dbVar;gnomAD-SV_v3_DEL_chr11_f71dd9b5

chr11:8142635-35706287;chr11:19981743-19984278;chr11:19982013-19983809;11:19982014-19983809

0.048

IMH

11:1621661-71538522

0.0179

4.74

1.246539

0.869153

1.12478

-0.79706

1.145418

89797

1.00E+00

9.98E-01

0.4815

Cleft lip;Cleft palate;Holoprosencephaly;Hypertelorism;Micrognathia;Microphthalmia;abnormal olfaction;abnormal optic nerve morphology

full=3

0/1

2_205740722_205740786_DEL_1

2.06E+08

-63

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:185092:0:1:0:0:0

TTCAACTCTCTGCAAACAGCATGACTGCACCACATGACCTTCCCAGAAAGACTGGCTCAAGGAC

600

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-63;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=2;END=205740785;CIPOS=0,4;CIEND=0,1;STRANDS=+;Max_AF=0.000781;Max_Het=22;Max_HomAlt=0;Max_PopMax_AF=0.004781;CCDG_Count=0;Best_CCDG_Mismatch_ID=286657_1;Best_CCDG_Mismatch_OFP=0.015625;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.000171;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;TOPMed_SV_Cov=0;ThousG_Count=1;Best_ThousG_ID=HGSV_86223;Best_ThousG_OFP=0.9375;Best_ThousG_AF=0.000781;Best_ThousG_Het=5;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.00416;Best_ThousG_Mismatch_ID=HGSV_83331;Best_ThousG_Mismatch_OFP=8.01915e-07;Best_ThousG_Mismatch_SVTYPE=CPX;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0.9375;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr2_05698c28;Best_gnomAD_OFP=0.9375;Best_gnomAD_AF=0.000175;Best_gnomAD_Het=22;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.004781;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr2_6713af26;Best_gnomAD_Mismatch_OFP=0.00914155;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=1.6e-05;Best_gnomAD_Mismatch_Het=2;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:64:0,0:+:600:DEL:DEL00008477:NA:NA:chr2_205740722-chr2_205740786

0/1:NA:63:0,0:+:495:DEL:MantaDEL_185092_0_1_0_0_0:TTCAACTCTCTGCAAACAGCATGACTGCACCACATGACCTTCCCAGAAAGACTGGCTCAAGGAC:T:chr2_205740722-chr2_205740785

0/1:NA:59:0,0:+:233:DEL:1732:NA:NA:chr2_205740726-chr2_205740785

split

q33.3

NRP2

NM_201264

2.06E+08

intron8-intron8

CDS

2.06E+08

dbVar

chr2:204935496-205936029

0.01

gnomAD-SV_v3_DEL_chr2_d8522047

chr2:148424217-233186659

0.0146

IMH

2:65359567-213949290;2:121478683-234514775;2:136890294-221566955;2:198679776-209089296

0.3179

3.46

-0.16967

1.072076

0.636235

0.439149

1.349211

4753

8.07E-04

1.71E-03

0.584

Cleft lip;Cleft palate;Holoprosencephaly;Hypertelorism;Micrognathia;Microphthalmia;abnormal vomeronasal sensory neuron morphology;abnormal vomeronasal sensory neuron physiology;hydrocephaly

full=3

0/1

11_55597948_55678392_INV_1

55597948

55678392

80444

INV

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaBND:29968:0:1:0:0:0:0

A]chr11:55678392]

704

PASS

SUPP=3;SUPP_VEC=111;SVLEN=80444;SVTYPE=INV;SVMETHOD=SURVIVOR1.0.7;CHR2=11;END=55678392;CIPOS=0,4;CIEND=0,0;STRANDS=;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=554066;Best_CCDG_OFP=0.139484;Best_CCDG_AF=0.005471;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=165830;Best_CCDG_Mismatch_OFP=0.356791;Best_CCDG_Mismatch_SVTYPE=DEL;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;TOPMed_SV_Cov=0;ThousG_Count=0;Best_ThousG_ID=HGSV_24190;Best_ThousG_OFP=0.00205457;Best_ThousG_AF=0.488601;Best_ThousG_Het=3129;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_INV_chr11_19a01d73;Best_gnomAD_OFP=0.00148313;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=1.7e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_CPX_chr11_66eeb635;Best_gnomAD_Mismatch_OFP=0.00209769;Best_gnomAD_Mismatch_SVTYPE=CPX;Best_gnomAD_Mismatch_AF=0.310979;Best_gnomAD_Mismatch_Het=36260;Best_gnomAD_Mismatch_HomAlt=1476;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:80444:19,8::704:INV:INV00035040:NA:NA:chr11_55597948-chr11_55678392

0/1:NA:80444:0,0::563:INV:MantaBND_29968_0_1_0_0_0_0:NA:NA:chr11_55597948-chr11_55678392

0/1:NA:80440:0,0::173:INV:6621_1:NA:NA:chr11_55597952-chr11_55678392

split

q11

OR4C11

NM_001004700

55602359

55607645

5286

933

txStart-txEnd

5'UTR-3'UTR

55602359

55607645

DDD:35907;dbVar;dgv144n27;dgv369e212;nsv517440

11:55572904-55836936;11:55592738-55693312;11:55593807-55706749;11:55595852-55686087;chr11:55597674-55664124;chr11:55600896-55659493

0.4343

1000g;DDD:35907;DDD:35910;HI40:ISCA-46458;dbVar;dgv145n27;dgv1915n54;dgv211e199;dgv368e212;esv2421634;esv2663268;esv2760216;esv2760311;esv3626445;esv3892006;nsv517440

11:55572904-55836936;chr11:55590350-55664455;11:55591985-55842207;11:55592738-55703518;11:55593807-55706749;11:55593886-55736880;11:55595852-55685520;11:55596800-55676539;chr11:55596800-55676539;11:55596917-55697316;11:55597770-55664316;11:55597959-55664091;11:55600414-55685447;11:55600414-55685447;11:55600414-55685533;chr11:55600896-55659493;11:55600897-55659493;11:55600897-55659493

0.4107

CMRI:2_pbsv.INV.1044;HPRC:pbsv.INV.4207;IMH

11:1621661-71538522;11:49193342-89651496;11:49211577-89635120;11:49243027-89597882;11:49358811-89347590;11:49403038-89297530;11:49586833-89037283;11:49629782-88995227;11:49736709-88892563;chr11:55597265-55667018;11:55597333-55667017

0.4958

87.48

-1.12753

-3.29256

219429

5.60E-06

1.41E-06

full=NA

0/1

11_55597948_55678392_INV_1

55597948

55678392

80444

INV

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaBND:29968:0:1:0:0:0:0

A]chr11:55678392]

704

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:80444:19,8::704:INV:INV00035040:NA:NA:chr11_55597948-chr11_55678392

0/1:NA:80444:0,0::563:INV:MantaBND_29968_0_1_0_0_0_0:NA:NA:chr11_55597948-chr11_55678392

0/1:NA:80440:0,0::173:INV:6621_1:NA:NA:chr11_55597952-chr11_55678392

split

q11

OR4C6

NM_001004704

55662200

55666096

3896

930

100

txStart-txEnd

5'UTR-3'UTR

55662200

55666096

DDD:35907;dgv144n27;dgv369e212;dgv373e212;dgv382e212;nsv517440

11:55572904-55836936;11:55592738-55693312;11:55593807-55706749;11:55595852-55686087;11:55618742-55674829;11:55635326-55693312

0.4343

DDD:35907;DDD:35912;HI40:ISCA-46458;dbVar;dgv145n27;dgv1915n54;dgv211e199;dgv368e212;dgv377e212;dgv378e212;dgv381e212;dgv383e212;esv2421634;esv2760216;esv2760311;esv3892006;nsv514622;nsv517440

11:55572904-55836936;11:55591985-55842207;11:55592738-55703518;11:55593807-55706749;11:55593886-55736880;11:55595852-55685520;11:55596800-55676539;chr11:55596800-55676539;11:55596917-55697316;11:55600414-55685447;11:55600414-55685447;11:55600414-55685533;11:55606557-55682976;11:55626140-55685520;11:55635326-55667703;11:55635326-55674829;11:55635641-55683696;11:55646170-55674829;chr11:55654858-55836170

0.4529

CMRI:2_pbsv.INV.1044;HPRC:pbsv.INV.4207;IMH

0.4958

90.42

-2.62354

-2.53125

-2.47163

-1.99765

-3.80719

219432

5.13E-03

1.08E-05

full=NA

0/1

11_55597948_55678392_INV_1

55597948

55678392

80444

INV

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaBND:29968:0:1:0:0:0:0

A]chr11:55678392]

704

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:80444:19,8::704:INV:INV00035040:NA:NA:chr11_55597948-chr11_55678392

0/1:NA:80444:0,0::563:INV:MantaBND_29968_0_1_0_0_0_0:NA:NA:chr11_55597948-chr11_55678392

0/1:NA:80440:0,0::173:INV:6621_1:NA:NA:chr11_55597952-chr11_55678392

split

q11

OR4P4

NM_001405919

55635112

55640309

5197

939

txStart-txEnd

5'UTR-3'UTR

55635112

55640309

DDD:35907;dbVar;dgv144n27;dgv369e212;dgv373e212;nsv517440

11:55572904-55836936;11:55592738-55693312;11:55593807-55706749;11:55595852-55686087;chr11:55597674-55664124;chr11:55600896-55659493;11:55618742-55674829

0.4343

1000g;DDD:35907;DDD:35910;DDD:35912;HI40:ISCA-46458;dbVar;dgv145n27;dgv1915n54;dgv211e199;dgv368e212;dgv377e212;esv2421634;esv2663268;esv2760216;esv2760311;esv3626445;esv3892006;nsv517440

0.4529

CMRI:2_pbsv.INV.1044;HPRC:pbsv.INV.4207;IMH

0.4958

87.96

-0.20623

-1.30402

81300

1.76E-02

5.74E-02

full=NA

0/1

11_55597948_55678392_INV_1

55597948

55678392

80444

INV

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaBND:29968:0:1:0:0:0:0

A]chr11:55678392]

704

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:80444:19,8::704:INV:INV00035040:NA:NA:chr11_55597948-chr11_55678392

0/1:NA:80444:0,0::563:INV:MantaBND_29968_0_1_0_0_0_0:NA:NA:chr11_55597948-chr11_55678392

0/1:NA:80440:0,0::173:INV:6621_1:NA:NA:chr11_55597952-chr11_55678392

split

q11

OR4S2

NM_001004059

55648326

55652854

4528

936

txStart-txEnd

5'UTR-3'UTR

55648326

55652854

DDD:35907;dbVar;dgv144n27;dgv369e212;dgv373e212;dgv382e212;nsv517440

11:55572904-55836936;11:55592738-55693312;11:55593807-55706749;11:55595852-55686087;chr11:55597674-55664124;chr11:55600896-55659493;11:55618742-55674829;11:55635326-55693312

0.4343

1000g;DDD:35907;DDD:35910;DDD:35912;HI40:ISCA-46458;dbVar;dgv145n27;dgv1915n54;dgv211e199;dgv368e212;dgv377e212;dgv378e212;dgv381e212;dgv383e212;esv2421634;esv2663268;esv2760216;esv2760311;esv3626445;esv3892006;nsv514622;nsv517440

0.4529

CMRI:2_pbsv.INV.1044;HPRC:pbsv.INV.4207;IMH

0.4958

79.58

1.165

-0.93491

219431

4.74E-10

1.04E-03

full=NA

0/1

20_17303439_17303526_DEL_1

17303439

17303526

-84

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:97657:0:1:0:0:0

AATATATATTATATTAAATATAATATATATTATATATAATATATATTATATTTAATATAATATATATTATATATAATATAATATA

415

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:83:0,0:+:415:DEL:DEL00058353:NA:NA:chr20_17303439-chr20_17303522

0/1:NA:84:0,0:+:385:DEL:MantaDEL_97657_0_1_0_0_0:AATATATATTATATTAAATATAATATATATTATATATAATATATATTATATTTAATATAATATATATTATATATAATATAATATA:AT:chr20_17303442-chr20_17303526

0/1:NA:65:0,0:+:68:DEL:10795:NA:NA:chr20_17303451-chr20_17303516

split

p12.1

PCSK2

NM_001201528

17226106

17484578

intron3-intron3

CDS

43094

17303438

17303526

dbVar

chr20:17301743-17309639

0.01

10.35

0.305053

-0.37288

-0.14209

1.676153

3.923633

5126

9.99E-01

9.94E-01

full=3

0/1

17_8259210_8261028_INV_1

8259210

8261028

1818

INV

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaBND:48483:0:1:0:0:0:1

T]chr17:8261028]

960

PASS

SUPP=3;SUPP_VEC=111;SVLEN=1818;SVTYPE=INV;SVMETHOD=SURVIVOR1.0.7;CHR2=17;END=8261028;CIPOS=0,6;CIEND=0,0;STRANDS=;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;CCDG_Mismatches=234321;CCDG_Mismatches_Count=1;CCDG_Mismatch_SVTYPEs=DEL;Best_CCDG_Mismatch_ID=234321;Best_CCDG_Mismatch_OFP=0.990654;Best_CCDG_Mismatch_SVTYPE=DEL;Best_CCDG_Mismatch_AF=0.0001368;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=INV_17:8260934-8261004;Best_TOPMed_OFP=0.0395822;Best_TOPMed_AF=0.00015;Best_TOPMed_Het=42;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.0042735;TOPMed_Mismatches=DEL_17:8259218-8261018;TOPMed_Mismatches_Count=1;TOPMed_Mismatch_SVTYPEs=DEL;Best_TOPMed_Mismatch_ID=DEL_17:8259218-8261018;Best_TOPMed_Mismatch_OFP=0.990654;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=0.000124;Best_TOPMed_Mismatch_Het=32;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_59918;Best_ThousG_OFP=3.30527e-05;Best_ThousG_AF=0.000468;Best_ThousG_Het=3;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0;ThousG_Mismatches=HGSV_60141;ThousG_Mismatches_Count=1;ThousG_Mismatch_SVTYPEs=DEL;Best_ThousG_Mismatch_ID=HGSV_60141;Best_ThousG_Mismatch_OFP=0.991204;Best_ThousG_Mismatch_SVTYPE=DEL;Best_ThousG_Mismatch_AF=0.000937;Best_ThousG_Mismatch_Het=6;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_INV_chr17_02b6b8d7;Best_gnomAD_OFP=0.000256028;Best_gnomAD_AF=1.6e-05;Best_gnomAD_Het=2;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=3e-05;gnomAD_Mismatches=gnomAD-SV_v3_DEL_chr17_fc0648d6,gnomAD-SV_v3_DEL_chr17_f9c01235;gnomAD_Mismatches_Count=2;gnomAD_Mismatch_SVTYPEs=DEL;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr17_fc0648d6;Best_gnomAD_Mismatch_OFP=0.965366;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=0.000119;Best_gnomAD_Mismatch_Het=15;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:1818:21,6::960:INV:INV00049625:NA:NA:chr17_8259210-chr17_8261028

0/1:NA:1818:0,0::367:INV:MantaBND_48483_0_1_0_0_0_1:NA:NA:chr17_8259210-chr17_8261028

0/1:NA:1812:0,0::242:INV:9205_1:NA:NA:chr17_8259216-chr17_8261028

split

p13.1

PFAS

XM_047436297

8247607

8266746

1819

intron11-intron11

CDS

1010

8259209

8261028

dbVar

chr17:8202867-8297966

0.01

47.86

-0.15132

0.255333

0.133119

-0.80046

0.774299

5198

9.85E-18

2.79E-08

0.9544

Cleft lip;Cleft palate;Hypertelorism;Micrognathia;Microphthalmia;alveolar process atrophy;microphthalmia;ocular hypertelorism;upturned snout

full=NA

0/1

19_4005348_4159440_DEL_1

4005348

4159440

-154090

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:79083:0:1:0:0:0

1740

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:154087:26,11:+:1740:DEL:DEL00054230:NA:NA:chr19_4005348-chr19_4159435

0/1:NA:154090:0,0:+:999:DEL:MantaDEL_79083_0_1_0_0_0:NA:NA:chr19_4005350-chr19_4159440

0/1:NA:154090:0,0:+:650:DEL:10046:NA:NA:chr19_4005350-chr19_4159440

split

p13.3

PIAS4

XM_011528060

4009947

4039386

29439

1590

100

txStart-txEnd

5'UTR-3'UTR

4009947

4039386

IMH

19:1692676-41507766

0.0103

36.28

0.52138

0.896295

0.995383

-0.62518

3.255531

51588

1.00E+00

9.94E-01

full=5

0/1

19_4005230_4159441_DUP_1

4005230

4159441

154171

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:79083:0:1:1:0:0

999

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:154170:21,8:-:600:DUP:DUP00054229:NA:NA:chr19_4005253-chr19_4159423

0/1:NA:154171:0,0:-:999:DUP:MantaDUP_TANDEM_79083_0_1_1_0_0:NA:NA:chr19_4005252-chr19_4159423

0/1:NA:154211:0,0:-:106:DUP:10045:NA:NA:chr19_4005230-chr19_4159441

split

p13.3

PIAS4

XM_011528060

4009947

4039386

29439

1590

100

txStart-txEnd

5'UTR-3'UTR

4009947

4039386

IMH

19:1692676-41507766

0.0103

36.28

0.52138

0.896295

0.995383

-0.62518

3.255531

51588

1.00E+00

9.94E-01

full=3

0/1

2_46140344_46140465_DEL_1

46140344

46140465

-120

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:174550:0:1:0:0:0

AATAAAAGATACAGGAAAAATCCAAGTGCACATGAGGATTTAGTACTAGTATTTGATAAAGGTGGTATTTCAATCAGTGAGGAAAAGATGACCTATTCAACGTAAGGGACTGGGACAACTT

720

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-120;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=2;END=46140464;CIPOS=0,1;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=573589;Best_CCDG_Mismatch_OFP=5.95697e-06;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=0.024;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_2:46099129-46208220;Best_TOPMed_OFP=0.00110915;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=1.19801e-05;Best_TOPMed_Mismatch_ID=INV_2:39986389-47339194;Best_TOPMed_Mismatch_OFP=1.64563e-05;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=2.2e-05;Best_TOPMed_Mismatch_Het=4;Best_TOPMed_Mismatch_HomAlt=1;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_77475;Best_ThousG_Mismatch_OFP=9.02168e-07;Best_ThousG_Mismatch_SVTYPE=INS;Best_ThousG_Mismatch_AF=0.000468;Best_ThousG_Mismatch_Het=3;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr2_7a56e34d;Best_gnomAD_OFP=5.94011e-06;Best_gnomAD_AF=0.00015;Best_gnomAD_Het=18;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000719;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_INV_chr2_a005ba16;Best_gnomAD_Mismatch_OFP=7.13011e-06;Best_gnomAD_Mismatch_SVTYPE=INV;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:121:0,0:+:720:DEL:DEL00006104:NA:NA:chr2_46140344-chr2_46140465

0/1:NA:120:0,0:+:692:DEL:MantaDEL_174550_0_1_0_0_0:AATAAAAGATACAGGAAAAATCCAAGTGCACATGAGGATTTAGTACTAGTATTTGATAAAGGTGGTATTTCAATCAGTGAGGAAAAGATGACCTATTCAACGTAAGGGACTGGGACAACTT:A:chr2_46140344-chr2_46140464

0/1:NA:119:0,0:+:311:DEL:1234:NA:NA:chr2_46140345-chr2_46140464

split

p21

PRKCE

XM_005264428

45651278

46187990

122

intron12-intron12

CDS

4627

46140343

46140465

IMH

2:21055811-76514955;2:32873521-53185851

0.1623

5.17

0.65515

-0.35058

-0.00176

0.685911

4.857257

5581

1.00E+00

full=3

0/1

6_161872925_161878005_DEL_1

1.62E+08

-5079

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:130517:0:1:0:0:0

1380

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-5079;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=6;END=161878004;CIPOS=0,3;CIEND=0,1;STRANDS=+;Max_AF=0.004215;Max_Het=183;Max_HomAlt=2;Max_PopMax_AF=0.022463;CCDG_Count=0;Best_CCDG_ID=386885;Best_CCDG_OFP=0.0131656;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=525230;Best_CCDG_Mismatch_OFP=0.0393058;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=6.839e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=1;Best_TOPMed_ID=DEL_6:161872929-161878008;Best_TOPMed_OFP=0.998623;Best_TOPMed_AF=0.00067;Best_TOPMed_Het=183;Best_TOPMed_HomAlt=2;Best_TOPMed_PopMax_AF=0.019193;Best_TOPMed_Mismatch_ID=INV_6:161869430-161880304;Best_TOPMed_Mismatch_OFP=0.467083;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_139376;Best_ThousG_OFP=0.999409;Best_ThousG_AF=0.004215;Best_ThousG_Het=27;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.022463;Best_ThousG_Mismatch_ID=HGSV_139355;Best_ThousG_Mismatch_OFP=0.00980807;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr6_dabe8de7;Best_gnomAD_OFP=0.999409;Best_gnomAD_AF=0.001412;Best_gnomAD_Het=178;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.01802;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_CPX_chr6_d2bb65d8;Best_gnomAD_Mismatch_OFP=0.464096;Best_gnomAD_Mismatch_SVTYPE=CPX;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:5080:18,13:+:1380:DEL:DEL00021210:NA:NA:chr6_161872925-chr6_161878005

0/1:NA:5079:0,0:+:543:DEL:MantaDEL_130517_0_1_0_0_0:NA:NA:chr6_161872925-chr6_161878004

0/1:NA:5076:0,0:+:518:DEL:4201:NA:NA:chr6_161872928-chr6_161878004

split

q26

PRKN

XM_017010908

1.61E+08

1.62E+08

5081

intron6-intron6

CDS

87016

1.62E+08

dbVar

chr6:161780967-162146968;chr6:161853183-162068074;chr6:161857468-161902968

0.01

dbVar

chr6:161747555-162202352;chr6:161872385-161878213

0.01

Parkinson disease;autosomal recessive juvenile Parkinson disease 2;young-onset Parkinson disease

Definitive;Strong;Supportive

22166458[PMID]

5071

602544

Adenocarcinoma of lung, somatic, 211980 (3);Ovarian cancer, somatic, 167000 (3);Parkinson disease, juvenile, type 2, 600116 (3) AR

yes

0.3875

Holoprosencephaly;tau protein deposits

full=1

0/1

10_13652960_13653018_DEL_1

13652960

13653018

-57

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:37558:0:0:0:0:0

ACAGAGGGCAGAGCTGGAATTCCAGCTCCCTCCAGCTGTCAGACTTTGGGCCAGGCAC

720

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:58:0,0:+:720:DEL:DEL00030300:NA:NA:chr10_13652960-chr10_13653018

0/1:NA:57:0,0:+:660:DEL:MantaDEL_37558_0_0_0_0_0:ACAGAGGGCAGAGCTGGAATTCCAGCTCCCTCCAGCTGTCAGACTTTGGGCCAGGCAC:A:chr10_13652960-chr10_13653017

0/1:NA:57:0,0:+:293:DEL:5923:NA:NA:chr10_13652960-chr10_13653017

split

p13

PRPF18

NR_172904

13586964

13655929

intron10-intron10

UTR

1334

13652959

13653018

dbVar

chr10:13543727-13697859;chr10:13580085-13654763

0.01

17.72

0.406129

-0.88084

-0.49222

-0.02436

2.440374

8559

2.68E-04

9.94E-02

full=3

0/1

11_1894044_1915726_DEL_1

1894044

1915726

-21681

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:25948:0:1:0:0:0

830

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

1/1:NA:21679:0,0:+:600:DEL:DEL00033993:NA:NA:chr11_1894047-chr11_1915726

1/1:NA:21681:0,0:+:830:DEL:MantaDEL_25948_0_1_0_0_0:NA:NA:chr11_1894044-chr11_1915725

1/1:NA:21681:0,0:+:827:DEL:6377:NA:NA:chr11_1894044-chr11_1915725

split

p15.5

PRR33

XM_047426236

1887986

1917708

21683

intron1-intron1

5'UTR

1912

1894043

1915726

1000g;HI40:ISCA-46652;dbVar;esv2666901;esv3625119

chr11:1894005-1915726;11:1894006-1915726;11:1894006-1915726;11:1894016-1915772;11:1894020-1915779

0.19

IMH

11:1621661-71538522

0.0179

93.45

1.03E+08

full=1

1/1

22_44860912_44860969_DEL_1

44860912

44860969

-56

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:95612:0:1:0:0:0

TTGGAGAATGTCACTTCTTGGTTTTACAACAATTTTTTTTCTCCCTGTTGCTTGACA

653

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:57:0,0:+:653:DEL:DEL00062432:NA:NA:chr22_44860912-chr22_44860969

1/1:NA:56:0,0:+:486:DEL:MantaDEL_95612_0_1_0_0_0:TTGGAGAATGTCACTTCTTGGTTTTACAACAATTTTTTTTCTCCCTGTTGCTTGACA:T:chr22_44860912-chr22_44860968

0/1:NA:55:0,0:+:272:DEL:11382:NA:NA:chr22_44860913-chr22_44860968

split

q13.31

PRR5-ARHGAP8

NM_181334

44702203

44862784

intron14-intron14

CDS

1077

44860911

44860969

dbVar

chr22:44820754-44869341;chr22:44837184-44861234

0.01

IMH

22:44479419-47655346

0.2479

77.56

-2.62354

0.465669

-1.01906

553158

2.14E-28

0.5199

Cleft lip;Cleft palate;Hypertelorism;Micrognathia;Microphthalmia;cataract

full=3

0/1

8_128092107_128099360_DEL_1

1.28E+08

-7252

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:166772:1:2:0:0:0

1320

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-7252;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=8;END=128099359;CIPOS=0,0;CIEND=0,1;STRANDS=+;Max_AF=0.000156;Max_Het=27;Max_HomAlt=0;Max_PopMax_AF=0.00293606;CCDG_Count=0;Best_CCDG_Mismatch_ID=605159;Best_CCDG_Mismatch_OFP=0.000127629;Best_CCDG_Mismatch_SVTYPE=INV;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=1;Best_TOPMed_ID=DEL_8:128092108-128099360;Best_TOPMed_OFP=0.999862;Best_TOPMed_AF=9.6e-05;Best_TOPMed_Het=27;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.00293606;Best_TOPMed_Mismatch_ID=INV_8:128096507-128103016;Best_TOPMed_Mismatch_OFP=0.172482;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_158111;Best_ThousG_OFP=1;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.000832;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr8_2492fa30;Best_gnomAD_OFP=1;Best_gnomAD_AF=5.6e-05;Best_gnomAD_Het=7;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.001589;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr8_e50742fa;Best_gnomAD_Mismatch_OFP=0.000526648;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:7253:16,12:+:1320:DEL:DEL00027180:NA:NA:chr8_128092107-chr8_128099360

0/1:NA:7252:0,0:+:674:DEL:MantaDEL_166772_1_2_0_0_0:NA:NA:chr8_128092107-chr8_128099359

0/1:NA:7252:0,0:+:548:DEL:5356:NA:NA:chr8_128092107-chr8_128099359

split

q24.21

PVT1

NR_003367

1.28E+08

7254

intron6-intron7

UTR

1.28E+08

dbVar

chr8:128091460-128099839

0.01

5820

full=1

0/1

20_20707383_20707707_DEL_1

20707383

20707707

-323

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:97912:2:2:1:0:0

TCAGGAAAAGGGAAGGAAGAAAAAAAAGGAAAGAAGGAAGGAGAGAAAAGAACAAAATTTCACAATCCAGGAAATGGTAAGCTAAATTATGGGATATGGTCTCAACAAATGTTTGTACTTAAAAATGAGAGGAACAAAACATCAAAAATGCTAATGATAAAATAAAGACAACAGTTACAACTGTAAGTCAATTTGTTCCTACCTAGAGCAACATGAGCAACATATGCACAAAAGGAACTATACGACAATGCTATGTTTTGCTCTGTTTGTATATACAGCATTTGTGAGAGACGGTTCTCTACTCTCTGGTCCAAACCCAGGTCA

420

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-323;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=20;END=20707706;CIPOS=0,1;CIEND=0,1;STRANDS=+;Max_AF=0.001093;Max_Het=93;Max_HomAlt=0;Max_PopMax_AF=0.005067;CCDG_Count=0;Best_CCDG_Mismatch_ID=293405_1;Best_CCDG_Mismatch_OFP=0.00308642;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.000718;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_20:20573614-20734848;Best_TOPMed_OFP=0.00200948;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000108743;Best_TOPMed_Mismatch_ID=DUP_20:20642402-20730900;Best_TOPMed_Mismatch_OFP=0.00366102;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_89805;Best_ThousG_OFP=0.996914;Best_ThousG_AF=0.001093;Best_ThousG_Het=7;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0;ThousG_SV_Cov=0.996914;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr20_ed4ccf3e;Best_gnomAD_OFP=0.996914;Best_gnomAD_AF=0.000742;Best_gnomAD_Het=93;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.005067;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_INV_chr20_01a6ba41;Best_gnomAD_Mismatch_OFP=9.80992e-06;Best_gnomAD_Mismatch_SVTYPE=INV;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:324:0,0:+:420:DEL:DEL00058410:NA:NA:chr20_20707383-chr20_20707707

0/1:NA:323:0,0:+:335:DEL:MantaDEL_97912_2_2_1_0_0:TCAGGAAAAGGGAAGGAAGAAAAAAAAGGAAAGAAGGAAGGAGAGAAAAGAACAAAATTTCACAATCCAGGAAATGGTAAGCTAAATTATGGGATATGGTCTCAACAAATGTTTGTACTTAAAAATGAGAGGAACAAAACATCAAAAATGCTAATGATAAAATAAAGACAACAGTTACAACTGTAAGTCAATTTGTTCCTACCTAGAGCAACATGAGCAACATATGCACAAAAGGAACTATACGACAATGCTATGTTTTGCTCTGTTTGTATATACAGCATTTGTGAGAGACGGTTCTCTACTCTCTGGTCCAAACCCAGGTCA:T:chr20_20707383-chr20_20707706

0/1:NA:322:0,0:+:143:DEL:10805:NA:NA:chr20_20707384-chr20_20707706

split

p11.23

RALGAPA2

NM_020343

20389529

20712644

325

intron1-intron1

CDS

4667

20707382

20707707

dbVar

chr20:20707354-20710228

0.01

22.17

0.73525

1.134025

1.134389

-2.26508

-1.04803

57186

3.03E-17

8.49E-06

full=1

0/1

13_113999035_113999116_DEL_1

1.14E+08

-80

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:14350:0:1:0:0:0

ACAAGTGTGACTGGGGAACGAGGCGACATGTGGGTCCGGGTCAAGCGTGACCGGGGAACGAGGCCACACGTGGGCCCGGGT

550

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-80;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=13;END=113999115;CIPOS=0,23;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=201266_1;Best_CCDG_Mismatch_OFP=0.0123457;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.5229;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_13:113999059-113999115;Best_TOPMed_OFP=0.716049;Best_TOPMed_AF=0.541849;Best_TOPMed_Het=62552;Best_TOPMed_HomAlt=37716;Best_TOPMed_PopMax_AF=0.663503;Best_TOPMed_Mismatch_ID=DUP_13:113973753-114016426;Best_TOPMed_Mismatch_OFP=0.00189807;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0.716049;ThousG_Count=0;Best_ThousG_ID=HGSV_43308;Best_ThousG_OFP=0.716049;Best_ThousG_AF=0.590694;Best_ThousG_Het=1315;Best_ThousG_HomAlt=1215;Best_ThousG_PopMax_AF=0.675538;Best_ThousG_Mismatch_ID=HGSV_43286;Best_ThousG_Mismatch_OFP=0.000320288;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000781;Best_ThousG_Mismatch_Het=5;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr13_0d8739b9;Best_gnomAD_OFP=0.716049;Best_gnomAD_AF=0.439806;Best_gnomAD_Het=38962;Best_gnomAD_HomAlt=8247;Best_gnomAD_PopMax_AF=0.59375;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr13_c178adad;Best_gnomAD_Mismatch_OFP=0.00189798;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:81:0,0:+:300:DEL:DEL00041495:NA:NA:chr13_113999035-chr13_113999116

0/1:NA:80:0,0:+:550:DEL:MantaDEL_14350_0_1_0_0_0:ACAAGTGTGACTGGGGAACGAGGCGACATGTGGGTCCGGGTCAAGCGTGACCGGGGAACGAGGCCACACGTGGGCCCGGGT:A:chr13_113999035-chr13_113999115

0/1:NA:57:0,0:+:251:DEL:7892:NA:NA:chr13_113999058-chr13_113999115

split

q34

RASA3

XM_047430154

1.14E+08

intron19-intron19

CDS

468

1.14E+08

dgv587e212

13:113998170-114004956

0.01

55.88

-2.62354

-2.38034

-2.41351

-0.46153

1.706913

22821

1.91E-10

4.34E-04

full=3

0/1

12_15187735_15190338_DEL_1

15187735

15190338

-2602

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:15943:0:1:0:0:0

1400

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-2602;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=12;END=15190337;CIPOS=0,1;CIEND=0,1;STRANDS=+;Max_AF=0.004527;Max_Het=102;Max_HomAlt=4;Max_PopMax_AF=0.024739;CCDG_Count=0;Best_CCDG_Mismatch_ID=176473_2;Best_CCDG_Mismatch_OFP=0.000384172;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.001368;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=1;Best_TOPMed_ID=DEL_12:15187736-15190337;Best_TOPMed_OFP=1;Best_TOPMed_AF=7e-06;Best_TOPMed_Het=2;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000224316;Best_TOPMed_Mismatch_ID=DUP_12:15170215-15277457;Best_TOPMed_Mismatch_OFP=0.0242718;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_30358;Best_ThousG_OFP=0.999616;Best_ThousG_AF=0.004527;Best_ThousG_Het=29;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.024126;Best_ThousG_Mismatch_ID=HGSV_30359;Best_ThousG_Mismatch_OFP=0.569291;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.003443;Best_ThousG_Mismatch_Het=20;Best_ThousG_Mismatch_HomAlt=1;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr12_0a8412c2;Best_gnomAD_OFP=1;Best_gnomAD_AF=0.000872;Best_gnomAD_Het=102;Best_gnomAD_HomAlt=4;Best_gnomAD_PopMax_AF=0.024739;gnomAD_Mismatches=gnomAD-SV_v3_DUP_chr12_3354a420;gnomAD_Mismatches_Count=1;gnomAD_Mismatch_SVTYPEs=DUP;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr12_3354a420;Best_gnomAD_Mismatch_OFP=0.894194;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.000151;Best_gnomAD_Mismatch_Het=19;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:2603:26,14:+:1400:DEL:DEL00037138:NA:NA:chr12_15187735-chr12_15190338

0/1:NA:2602:0,0:+:891:DEL:MantaDEL_15943_0_1_0_0_0:NA:NA:chr12_15187735-chr12_15190337

0/1:NA:2601:0,0:+:578:DEL:7014:NA:NA:chr12_15187736-chr12_15190337

split

p12.3

RERG

XM_047429797

15107782

15217600

2604

intron1-intron1

5'UTR

27090

15187734

15190338

IMH

12:9566784-31121901;12:9566998-31121904;12:9567304-31122039;12:9568909-31118782

0.2224

34.36

0.626375

0.917174

0.957334

0.950319

0.512215

85004

1.20E-05

1.17E-03

full=3

0/1

12_15188606_15190644_DUP_1

15188606

15190644

2036

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:15943:1:2:0:0:0

1260

PASS

SUPP=3;SUPP_VEC=111;SVLEN=2036;SVTYPE=DUP;SVMETHOD=SURVIVOR1.0.7;CHR2=12;END=15190642;CIPOS=0,1;CIEND=0,2;STRANDS=-;Max_AF=0.003443;Max_Het=20;Max_HomAlt=1;Max_PopMax_AF=0.01855;CCDG_Count=0;Best_CCDG_Mismatch_ID=470186_1;Best_CCDG_Mismatch_OFP=0.000490918;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.001368;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DUP_12:15170215-15277457;Best_TOPMed_OFP=0.0189941;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000107021;Best_TOPMed_Mismatch_ID=DEL_12:15187736-15190337;Best_TOPMed_Mismatch_OFP=0.565758;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_30359;Best_ThousG_OFP=0.966777;Best_ThousG_AF=0.003443;Best_ThousG_Het=20;Best_ThousG_HomAlt=1;Best_ThousG_PopMax_AF=0.01855;Best_ThousG_Mismatch_ID=HGSV_30358;Best_ThousG_Mismatch_OFP=0.565975;Best_ThousG_Mismatch_SVTYPE=DEL;Best_ThousG_Mismatch_AF=0.004527;Best_ThousG_Mismatch_Het=29;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DUP_chr12_12620f4f;Best_gnomAD_OFP=0.849288;Best_gnomAD_AF=8.7e-05;Best_gnomAD_Het=11;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.002608;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr12_0a8412c2;Best_gnomAD_Mismatch_OFP=0.565758;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=0.000872;Best_gnomAD_Mismatch_Het=102;Best_gnomAD_Mismatch_HomAlt=4;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:2035:30,13:-:1260:DUP:DUP00037139:NA:NA:chr12_15188607-chr12_15190642

0/1:NA:2036:0,0:-:711:DUP:MantaDUP_TANDEM_15943_1_2_0_0_0:NA:NA:chr12_15188606-chr12_15190642

0/1:NA:2038:0,0:-:280:DUP:7015:NA:NA:chr12_15188606-chr12_15190644

split

p12.3

RERG

XM_047429797

15107782

15217600

2039

intron1-intron1

5'UTR

26784

15188605

15190644

IMH

12:9566784-31121901;12:9566998-31121904;12:9567304-31122039;12:9568909-31118782

0.2224

34.36

0.626375

0.917174

0.957334

0.950319

0.512215

85004

1.20E-05

1.17E-03

full=3

0/1

17_80301098_80301374_INV_1

80301098

80301374

276

INV

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaBND:55724:0:0:0:0:0:0

T]chr17:80301374]

240

PASS

SUPP=3;SUPP_VEC=111;SVLEN=276;SVTYPE=INV;SVMETHOD=SURVIVOR1.0.7;CHR2=17;END=80301374;CIPOS=0,259;CIEND=-259,0;STRANDS=;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=INV_17:79606853-81315890;Best_TOPMed_OFP=0.000162079;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.25986e-06;Best_TOPMed_Mismatch_ID=DUP_17:80293180-80323606;Best_TOPMed_Mismatch_OFP=0.00910346;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr17_7f9a57b0;Best_gnomAD_Mismatch_OFP=0.00266346;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=1.6e-05;Best_gnomAD_Mismatch_Het=2;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=0

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:276:0,0::240:INV:INV00052505:NA:NA:chr17_80301098-chr17_80301374

0/1:NA:276:0,0::23,23:INV,INV:MantaBND_55724_0_0_0_0_0_0:NA:NA:chr17_80301098-chr17_80301374,chr17_80301357-chr17_80301115

0/1:NA:251:0,0::32:INV:9722:NA:NA:chr17_80301098-chr17_80301349

split

q25.3

RNF213

NM_020954

80260851

80321463

277

intron11-intron11

CDS

2579

80301097

80301374

dbVar

chr17:80246582-80352532

0.01

dbVar

chr17:80274417-80303391

0.01

93.8

-2.52003

-2.53125

-2.34602

-0.37966

2.289337

Moyamoya disease 2

AD;AR

Strong

21048783;22377813;22931863;23850618;23994138;25278557

57674

613768

(Moyamoya disease 2, susceptibility to), 607151 (3) AR,AD

AR,AD

yes

4.91E-55

1.68E-29

0.2179

Holoprosencephaly;MiP motor neuron decreased process quality axon extension involved in axon guidance, abnormal

full=NA

0/1

4_183652348_183652410_DEL_1

1.84E+08

-61

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:156308:0:0:0:0:0

CCCTCTCCCCTGGCTTTTTTTTTTTTTTTTTGAGACAGGGTCTCACTCCATTGCCCAGGCTG

703

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-61;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=4;END=183652409;CIPOS=0,0;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=514836;Best_CCDG_Mismatch_OFP=0.000217671;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=6.839e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_4:183652247-183656966;Best_TOPMed_OFP=0.0131328;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=6.26676e-06;Best_TOPMed_Mismatch_ID=DUP_4:183509740-183794572;Best_TOPMed_Mismatch_OFP=0.000217671;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_119000;Best_ThousG_Mismatch_OFP=0.000257214;Best_ThousG_Mismatch_SVTYPE=INV;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr4_acf5a577;Best_gnomAD_OFP=0.0709382;Best_gnomAD_AF=0.000103;Best_gnomAD_Het=11;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000381;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_INV_chr4_61f32a06;Best_gnomAD_Mismatch_OFP=0.000257027;Best_gnomAD_Mismatch_SVTYPE=INV;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:62:0,0:+:703:DEL:DEL00015760:NA:NA:chr4_183652348-chr4_183652410

0/1:NA:61:0,0:+:370:DEL:MantaDEL_156308_0_0_0_0_0:CCCTCTCCCCTGGCTTTTTTTTTTTTTTTTTGAGACAGGGTCTCACTCCATTGCCCAGGCTG:C:chr4_183652348-chr4_183652409

0/1:NA:61:0,0:+:320:DEL:3022:NA:NA:chr4_183652348-chr4_183652409

split

q35.1

RWDD4

NM_001307922

1.84E+08

intron2-intron2

5'UTR

1024

1.84E+08

gnomAD-SV_v3_DEL_chr4_aa7116c9

chr4:73564711-189048534

0.2162

IMH

4:179407330-186243582

0.2421

39.45

-0.36445

-0.66679

-0.5522

0.428558

0.565034

201965

1.74E-02

4.83E-01

full=1

0/1

9_133718380_133718862_DEL_1

1.34E+08

-481

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:213941:0:1:0:0:0

GTTTATTGTATGTCTCTCCACCAAAATATAGGCACCCAGAGTCAGGGACTTTTATCTTAGTTTCCCTCTTTCTCCAGAAATTAAAGCAGTTTTTAGCCCAAAGTAGCCACTCAGTCGTTCCATGTGTGGACTAAATGCATATACACATAGAACAGGGCTGCAGGGCTGCCCTAACCCCAGAAGCTGCCCGGGAAACAGCCCAGGCCAGGGGAAATGCCGCTGCAGCAGCTGGTTGGGAGGGCAGTGTCATTTGCTGAAGGACGTAGGACTTGTGTGCTCTCATGCCCTTCTGAGGTCATCACTCCACACTGCGCAGACCTTCTCTGTGGATGTTTTGAGGCAAAGCCCTCCAGCTGCCCTGGGTCTGTATTTGACTGCCTGCCAGGACCGTCAGGGTAAGAGCAAGATGGCTTTGAGCTTGGTGGGGTCAGGGGACCGGCCACTTCTCAGGTGTGCCTCTGAGGAGCTTCAGGAGGATGGAC

785

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-481;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=9;END=133718861;CIPOS=0,2;CIEND=0,1;STRANDS=+;Max_AF=0.005308;Max_Het=372;Max_HomAlt=5;Max_PopMax_AF=0.026496;CCDG_Count=0;Best_CCDG_Mismatch_ID=437615_2;Best_CCDG_Mismatch_OFP=0.00207469;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.0007522;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=1;Best_TOPMed_ID=DEL_9:133718383-133718861;Best_TOPMed_OFP=0.995851;Best_TOPMed_AF=0.001356;Best_TOPMed_Het=372;Best_TOPMed_HomAlt=1;Best_TOPMed_PopMax_AF=0.0195774;Best_TOPMed_Mismatch_ID=DUP_9:133630772-133737768;Best_TOPMed_Mismatch_OFP=0.00450476;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_165988;Best_ThousG_OFP=0.995851;Best_ThousG_AF=0.005308;Best_ThousG_Het=24;Best_ThousG_HomAlt=5;Best_ThousG_PopMax_AF=0.026496;ThousG_SV_Cov=0.995851;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr9_09eec3c6;Best_gnomAD_OFP=0.790164;Best_gnomAD_AF=0.002301;Best_gnomAD_Het=282;Best_gnomAD_HomAlt=4;Best_gnomAD_PopMax_AF=0.025407;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr9_771259bb;Best_gnomAD_Mismatch_OFP=0.00388153;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:482:0,0:+:366:DEL:DEL00029807:NA:NA:chr9_133718380-chr9_133718862

0/1:NA:481:0,0:+:785:DEL:MantaDEL_213941_0_1_0_0_0:GTTTATTGTATGTCTCTCCACCAAAATATAGGCACCCAGAGTCAGGGACTTTTATCTTAGTTTCCCTCTTTCTCCAGAAATTAAAGCAGTTTTTAGCCCAAAGTAGCCACTCAGTCGTTCCATGTGTGGACTAAATGCATATACACATAGAACAGGGCTGCAGGGCTGCCCTAACCCCAGAAGCTGCCCGGGAAACAGCCCAGGCCAGGGGAAATGCCGCTGCAGCAGCTGGTTGGGAGGGCAGTGTCATTTGCTGAAGGACGTAGGACTTGTGTGCTCTCATGCCCTTCTGAGGTCATCACTCCACACTGCGCAGACCTTCTCTGTGGATGTTTTGAGGCAAAGCCCTCCAGCTGCCCTGGGTCTGTATTTGACTGCCTGCCAGGACCGTCAGGGTAAGAGCAAGATGGCTTTGAGCTTGGTGGGGTCAGGGGACCGGCCACTTCTCAGGTGTGCCTCTGAGGAGCTTCAGGAGGATGGAC:G:chr9_133718380-chr9_133718861

0/1:NA:479:0,0:+:506:DEL:5829:NA:NA:chr9_133718382-chr9_133718861

split

q34.2

SARDH

XM_047422896

1.34E+08

483

intron7-intron7

CDS

1.34E+08

dbVar

chr9:133707784-133753594

0.01

IMH

9:65437055-134286391

0.2414

61.17

-2.33998

-0.1572

-1.03945

0.591302

0.419139

sarcosinemia

Limited;Supportive

22825317;22825317[PMID];27001897;30612563

1757

604455

[Sarcosinemia], 268900 (3) AR

5.27E-16

8.20E-10

0.3044

Holoprosencephaly;abnormal hippocampus morphology

full=1

0/1

7_84422766_84423628_DEL_1

84422766

84423628

-861

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:111727:0:1:0:0:0

TTATGTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATGAATTGGTATCAGTAAAAAGTAGGAAGTTACAAATTTAGAATGTCAATTGTAATCCCTATAGGGACCAAAGAAATGTATCTCTAAAGTACCAGCATGCAAACTCAGTTTAATTCCCCAGTCTATCCTTTTAACCATGTTATGCTCCTTCTTACTGTAAAAGGAGATTTGAATCATCCACACATTCATTGAGCAAATATGTATTTTCACCATCCAGTGATTAATATTGTAATAGGTTCTGGCATTATAATGCTGAATAAAATATTAAACATAGCTTCCAATAGATAATAGTTTTACCATTGTACAATATTTATTGTAACAATAGAAAAATGTACACAAATCAAAACATTTTCTATCAAATAAGTACAATGTAAAAGAAGACATGTTTGTAGTTCTCATACCATTAGAATACTATGAAAAGATTTGCAATATTAGACTCTAATATGAATTTGTTACTAGGTTAATGTTTGTAAGTTTCAAGTGGTCTCTCCACCTCTTTTACCTCAATTCCTGTCCTTCTTCCACTGCAGTCCCACTGATATCCTTGCCATTTCTTAAAAATACTGGGCATATTTCTGCCTTGAGACCTTTGATTTGCTATTCTTTCAGCAAAAACTCAGTCACTGCACATAACCTGGAGGGTCCTCCCTCACGTATTTCACTTAACCAAAGAGGTCTTCTGTGGTCATCCTGAACAAATGAATTGCATTCCTTCCCAGACACTTCCTATTGTAATTTATTTCCTATCTCTGTAATTATTTTTTTGTCGAAATAGATAGTTATATCATCTATATCTATATTTAAACCTATATCTATCTA

827

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-861;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=7;END=84423627;CIPOS=0,5;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=399968;Best_CCDG_OFP=0.00665745;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=528990;Best_CCDG_Mismatch_OFP=0.00901315;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_7:84422066-84478256;Best_TOPMed_OFP=0.0153403;Best_TOPMed_AF=3.6e-05;Best_TOPMed_Het=10;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000120005;Best_TOPMed_Mismatch_ID=DUP_7:84416081-84427815;Best_TOPMed_Mismatch_OFP=0.0734492;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_145954;Best_ThousG_OFP=0.000426217;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.000832;Best_ThousG_Mismatch_ID=HGSV_140355;Best_ThousG_Mismatch_OFP=5.5682e-06;Best_ThousG_Mismatch_SVTYPE=CPX;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr7_32a2abc1;Best_gnomAD_OFP=0.138541;Best_gnomAD_AF=7.2e-05;Best_gnomAD_Het=9;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000404;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr7_6c78517e;Best_gnomAD_Mismatch_OFP=0.138541;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=3.3e-05;Best_gnomAD_Mismatch_Het=4;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:862:12,10:+:827:DEL:DEL00023602:NA:NA:chr7_84422766-chr7_84423628

0/1:NA:861:0,0:+:769:DEL:MantaDEL_111727_0_1_0_0_0:TTATGTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATGAATTGGTATCAGTAAAAAGTAGGAAGTTACAAATTTAGAATGTCAATTGTAATCCCTATAGGGACCAAAGAAATGTATCTCTAAAGTACCAGCATGCAAACTCAGTTTAATTCCCCAGTCTATCCTTTTAACCATGTTATGCTCCTTCTTACTGTAAAAGGAGATTTGAATCATCCACACATTCATTGAGCAAATATGTATTTTCACCATCCAGTGATTAATATTGTAATAGGTTCTGGCATTATAATGCTGAATAAAATATTAAACATAGCTTCCAATAGATAATAGTTTTACCATTGTACAATATTTATTGTAACAATAGAAAAATGTACACAAATCAAAACATTTTCTATCAAATAAGTACAATGTAAAAGAAGACATGTTTGTAGTTCTCATACCATTAGAATACTATGAAAAGATTTGCAATATTAGACTCTAATATGAATTTGTTACTAGGTTAATGTTTGTAAGTTTCAAGTGGTCTCTCCACCTCTTTTACCTCAATTCCTGTCCTTCTTCCACTGCAGTCCCACTGATATCCTTGCCATTTCTTAAAAATACTGGGCATATTTCTGCCTTGAGACCTTTGATTTGCTATTCTTTCAGCAAAAACTCAGTCACTGCACATAACCTGGAGGGTCCTCCCTCACGTATTTCACTTAACCAAAGAGGTCTTCTGTGGTCATCCTGAACAAATGAATTGCATTCCTTCCCAGACACTTCCTATTGTAATTTATTTCCTATCTCTGTAATTATTTTTTTGTCGAAATAGATAGTTATATCATCTATATCTATATTTAAACCTATATCTATCTA:T:chr7_84422766-chr7_84423627

0/1:NA:856:0,0:+:566:DEL:4655:NA:NA:chr7_84422771-chr7_84423627

split

q21.11

SEMA3A

XM_005250110

83955776

84492725

863

intron1-intron1

5'UTR

50865

84422765

84423628

dbVar;gnomAD-SV_v3_DEL_chr7_4d7b9722

chr7:83903053-107770163;chr7:84301051-84453488;chr7:84313235-84708494;chr7:84367300-84480840;chr7:84422065-84478253

0.0172

IMH

7:39507051-100351151;7:45847441-101265654;7:45847453-101265940;7:64004376-105619581;7:67304014-102378889;7:67304239-102379805;7:68170339-98454729;7:77095162-102776972;7:77167460-102703083;7:77537156-100694434;7:80929283-101607772

0.4994

1.46

0.686272

0.083918

0.357968

0.229205

1.44116

Brugada syndrome;Kallmann syndrome;hypogonadotropic hypogonadism 16 with or without anosmia

Strong;Supportive

22416012;22416012[PMID];22927827;24124006;25077900;28075028;28295047;29419413;29432577;30098700;30821013[PMID]

10371

603961

(Hypogonadotropic hypogonadism 16 with or without anosmia), 614897 (3) AD

yes

9.78E-01

9.88E-01

0.599

Cleft lip;Cleft palate;Kallmann syndrome;Micrognathia;Tooth agenesis

Holoprosencephaly;decreased brain size

Holoprosencephaly;axon guidance disrupted, abnormal

full=3

0/1

2_1185338_1185428_DEL_1

1185338

1185428

-89

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:170917:0:0:0:0:0

GTCTGGAGGATGGTAGCCTTCTTCTCACAGTTCCAGTAGTCAGCATCCCAGTAGAGACTCTGTGTGGGAGCTCCAACCGCACATTTCCCC

540

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-89;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=2;END=1185427;CIPOS=0,4;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=493883;Best_CCDG_Mismatch_OFP=0.000296683;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_2:1024951-1193643;Best_TOPMed_OFP=0.00053351;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=1.19835e-05;Best_TOPMed_Mismatch_ID=DUP_2:1172982-1306338;Best_TOPMed_Mismatch_OFP=0.000674875;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_74862;Best_ThousG_Mismatch_OFP=7.91844e-06;Best_ThousG_Mismatch_SVTYPE=INV;Best_ThousG_Mismatch_AF=0.000312;Best_ThousG_Mismatch_Het=2;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr2_6ba1a7d9;Best_gnomAD_OFP=0.000673754;Best_gnomAD_AF=6.3e-05;Best_gnomAD_Het=8;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000102;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr2_978e7d7f;Best_gnomAD_Mismatch_OFP=0.00200071;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=2.4e-05;Best_gnomAD_Mismatch_Het=3;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:90:0,0:+:540:DEL:DEL00005171:NA:NA:chr2_1185338-chr2_1185428

0/1:NA:89:0,0:+:349:DEL:MantaDEL_170917_0_0_0_0_0:GTCTGGAGGATGGTAGCCTTCTTCTCACAGTTCCAGTAGTCAGCATCCCAGTAGAGACTCTGTGTGGGAGCTCCAACCGCACATTTCCCC:G:chr2_1185338-chr2_1185427

0/1:NA:85:0,0:+:212:DEL:1065:NA:NA:chr2_1185342-chr2_1185427

split

p25.3

SNTG2

XM_047444795

950848

1256610

intron8-intron8

CDS

12154

1185337

1185428

dbVar

chr2:1089976-1223555

0.01

72.04

-0.67374

-0.84034

54221

1.31E-14

9.18E-07

full=1

0/1

3_181354497_181354568_DEL_1

1.81E+08

-70

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:169293:0:1:0:0:0

ATGAATGCTAGGTAGCATTCAGTACCTAATGAATGCTAGGTAGCATTCAGTACCTAGCATTCGTTAGGTAC

300

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-70;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=3;END=181354567;CIPOS=0,9;CIEND=0,1;STRANDS=+;Max_AF=8e-06;Max_Het=1;Max_HomAlt=0;Max_PopMax_AF=1.7e-05;CCDG_Count=0;Best_CCDG_Mismatch_ID=328924_1;Best_CCDG_Mismatch_OFP=0.0140845;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.05714;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DUP_3:181345202-181356000;Best_TOPMed_Mismatch_OFP=0.00657407;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_106001;Best_ThousG_Mismatch_OFP=2.01825e-06;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000156;Best_ThousG_Mismatch_Het=1;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr3_0dce689d;Best_gnomAD_OFP=0.859379;Best_gnomAD_AF=8e-06;Best_gnomAD_Het=1;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=1.7e-05;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr3_0a7a5017;Best_gnomAD_Mismatch_OFP=0.605055;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.00175;Best_gnomAD_Mismatch_Het=180;Best_gnomAD_Mismatch_HomAlt=9;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:71:0,0:+:300:DEL:DEL00011750:NA:NA:chr3_181354497-chr3_181354568

0/1:NA:70:0,0:+:81:DEL:MantaDEL_169293_0_1_0_0_0:ATGAATGCTAGGTAGCATTCAGTACCTAATGAATGCTAGGTAGCATTCAGTACCTAGCATTCGTTAGGTAC:A:chr3_181354497-chr3_181354567

0/1:NA:61:0,0:+:104:DEL:2423:NA:NA:chr3_181354506-chr3_181354567

split

q26.33

SOX2-OT

NR_075091

1.81E+08

1.82E+08

intron3-intron3

UTR

178913

1.81E+08

IMH

3:72502419-189537676

0.0342

347689

full=3

0/1

3_8678474_8679351_DEL_1

8678474

8679351

-876

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:157697:0:1:0:0:0

GGACCCCCATTGCAAGGGGGTGAGGCACCCCCCGCGAGGCGGGGACTGAGAGCCAGCCCCTCTTCCCTCCATGGCTCTTAGGACCCCAATCACAGAGGGGGGAACACCCCCCGCGAGGCAGGGACTGAGAGCCAGCCCTTCTTCCCCCCCGGCTTTTGGGACCCCCATCGCAGTGGGGGGAGGCACCCCCCGCGAGGCGGGGATTGAGAGCCAGCCACTCTTCCCCTCCTGGGTCTTAGGACCCCCAACGTGGGGGGGGGAGGCACCACACGCGAGGCGGGGAAAGAGAGCCAGCCCCTCTTCCCTCCCTGCCACTTAGGACCCCATCGCAGGGAGAGGAGGCGGCACTCCCCACGAGGCGGGGACTGAGAACCAATCCCTCTTCCCCCAGCCTGGCTCTTAGGATCCCCATTGCAAGGGAGGGAGGCACCCCCCGCCAGGCGGGGACTGAGAGCCAGCCACTCTTCCCCTCCTGGCTCTTGGGACGCCCATCGCAGGGCGGAGAGTCACCCCCCGCGAGGTGGGGACTGAGAGCCAGCCCCTCTTCCCCCCCTGGCTCTTAGGACACCAAACGCAGGGGAGGAAGCACCCCCCGCGAGGCGGGGACTGAGAGCAAGCACCTCTTTCCCCCCTGGCTCTTAGGACCCAAATTGCGGGGGGGAGGCACCCCCGCGAGGCGGGGACTGAGAGGCAGCCGCTGTTCCCCCACACTGGCTCTTGGGACCCCCATCGCAGGGGGGATGGCACCCTCCGTGAGCGGGGACTGAGAGCCAGCCAATTTTCCCCCTGGCTTTTAGGACCCCCATCGGAGGGGGGGAGCCACCCCCCATGAGGCGGGGACTAAGAGCCAGCCCCTCTTCCCGCCCCTTGCTCTTCC

932

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-876;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=3;END=8679350;CIPOS=0,9;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=311418;Best_CCDG_OFP=0.13731;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=505362;Best_CCDG_Mismatch_OFP=0.342044;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=0.0001368;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_3:8677157-8681292;Best_TOPMed_OFP=0.211989;Best_TOPMed_AF=0.001843;Best_TOPMed_Het=420;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.00302195;Best_TOPMed_Mismatch_ID=DUP_3:8644780-8777094;Best_TOPMed_Mismatch_OFP=0.00662807;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_97811;Best_ThousG_OFP=0.468643;Best_ThousG_AF=0.5392;Best_ThousG_Het=2687;Best_ThousG_HomAlt=369;Best_ThousG_PopMax_AF=0.567726;Best_ThousG_Mismatch_ID=HGSV_97810;Best_ThousG_Mismatch_OFP=0.236032;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.002031;Best_ThousG_Mismatch_Het=13;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr3_e61292ca;Best_gnomAD_OFP=0.567845;Best_gnomAD_AF=0.573604;Best_gnomAD_Het=43550;Best_gnomAD_HomAlt=9608;Best_gnomAD_PopMax_AF=0.612903;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr3_75bb515c;Best_gnomAD_Mismatch_OFP=0.5439;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.039067;Best_gnomAD_Mismatch_Het=4872;Best_gnomAD_Mismatch_HomAlt=27;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

1/1:NA:877:0,0:+:209:DEL:DEL00009230:NA:NA:chr3_8678474-chr3_8679351

1/1:NA:876:0,0:+:932:DEL:MantaDEL_157697_0_1_0_0_0:GGACCCCCATTGCAAGGGGGTGAGGCACCCCCCGCGAGGCGGGGACTGAGAGCCAGCCCCTCTTCCCTCCATGGCTCTTAGGACCCCAATCACAGAGGGGGGAACACCCCCCGCGAGGCAGGGACTGAGAGCCAGCCCTTCTTCCCCCCCGGCTTTTGGGACCCCCATCGCAGTGGGGGGAGGCACCCCCCGCGAGGCGGGGATTGAGAGCCAGCCACTCTTCCCCTCCTGGGTCTTAGGACCCCCAACGTGGGGGGGGGAGGCACCACACGCGAGGCGGGGAAAGAGAGCCAGCCCCTCTTCCCTCCCTGCCACTTAGGACCCCATCGCAGGGAGAGGAGGCGGCACTCCCCACGAGGCGGGGACTGAGAACCAATCCCTCTTCCCCCAGCCTGGCTCTTAGGATCCCCATTGCAAGGGAGGGAGGCACCCCCCGCCAGGCGGGGACTGAGAGCCAGCCACTCTTCCCCTCCTGGCTCTTGGGACGCCCATCGCAGGGCGGAGAGTCACCCCCCGCGAGGTGGGGACTGAGAGCCAGCCCCTCTTCCCCCCCTGGCTCTTAGGACACCAAACGCAGGGGAGGAAGCACCCCCCGCGAGGCGGGGACTGAGAGCAAGCACCTCTTTCCCCCCTGGCTCTTAGGACCCAAATTGCGGGGGGGAGGCACCCCCGCGAGGCGGGGACTGAGAGGCAGCCGCTGTTCCCCCACACTGGCTCTTGGGACCCCCATCGCAGGGGGGATGGCACCCTCCGTGAGCGGGGACTGAGAGCCAGCCAATTTTCCCCCTGGCTTTTAGGACCCCCATCGGAGGGGGGGAGCCACCCCCCATGAGGCGGGGACTAAGAGCCAGCCCCTCTTCCCGCCCCTTGCTCTTCC:G:chr3_8678474-chr3_8679350

0/1:NA:867:0,0:+:731:DEL:1878:NA:NA:chr3_8678483-chr3_8679350

split

p25.3

SSUH2

XM_017006511

8619385

8679868

878

intron1-intron1

5'UTR

353

8678473

8679351

DDD:9536;dbVar

chr3:8611079-8688004;chr3:8629543-8715948;3:8670939-8681891;chr3:8677066-8679629;chr3:8678456-8679420

0.0142

DDD:9538;dbVar;esv2676237

chr3:8615314-8716514;chr3:8677123-8681253;chr3:8677685-8687052;chr3:8677729-8687092;3:8678260-8682556;3:8678416-8682364

0.0476

IMH

3:7779573-24170164

0.1237

72.66

-1.07437

-1.15625

dentin dysplasia type I

Supportive

27680507[PMID]

51066

3.99E-10

2.49E-08

0.6861

Cleft lip;Cleft palate;Hypertelorism;Micrognathia;Microphthalmia;abnormal tooth morphology

Micrognathia;ceratobranchial 5 tooth absent, abnormal

full=3

0/1

16_2467675_2468572_DUP_1

2467675

2468572

895

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:56354:0:1:2:0:0

1380

PASS

SUPP=3;SUPP_VEC=111;SVLEN=895;SVTYPE=DUP;SVMETHOD=SURVIVOR1.0.7;CHR2=16;END=2468570;CIPOS=0,1;CIEND=0,2;STRANDS=-;Max_AF=0.0003419;Max_Het=5;Max_HomAlt=7;Max_PopMax_AF=0.003858;CCDG_Count=1;Best_CCDG_ID=481787;Best_CCDG_OFP=1;Best_CCDG_AF=0.0003419;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=221169;Best_CCDG_Mismatch_OFP=0.198934;Best_CCDG_Mismatch_SVTYPE=DEL;Best_CCDG_Mismatch_AF=0.0001368;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_Mismatch_ID=DEL_16:2465690-2470192;Best_TOPMed_Mismatch_OFP=0.198934;Best_TOPMed_Mismatch_SVTYPE=DEL;Best_TOPMed_Mismatch_AF=4.6e-05;Best_TOPMed_Mismatch_Het=13;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=0;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_54243;Best_ThousG_Mismatch_OFP=0.000139509;Best_ThousG_Mismatch_SVTYPE=CPX;Best_ThousG_Mismatch_AF=0.000781;Best_ThousG_Mismatch_Het=5;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DUP_chr16_bfcd0fc2;Best_gnomAD_OFP=1;Best_gnomAD_AF=0.000151;Best_gnomAD_Het=5;Best_gnomAD_HomAlt=7;Best_gnomAD_PopMax_AF=0.003858;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DEL_chr16_a2b17a52;Best_gnomAD_Mismatch_OFP=0.565953;Best_gnomAD_Mismatch_SVTYPE=DEL;Best_gnomAD_Mismatch_AF=0.000112;Best_gnomAD_Mismatch_Het=12;Best_gnomAD_Mismatch_HomAlt=1;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:896:29,11:-:1380:DUP:DUP00045666:NA:NA:chr16_2467676-chr16_2468572

0/1:NA:895:0,0:-:681:DUP:MantaDUP_TANDEM_56354_0_1_2_0_0:NA:NA:chr16_2467675-chr16_2468570

0/1:NA:895:0,0:-:237:DUP:8673:NA:NA:chr16_2467675-chr16_2468570

split

p13.3

TEDC2-AS1

NR_135198

2464949

2468213

539

txStart-exon1

UTR

539

2467674

2468213

dbVar

chr16:2465689-2470192

0.01

729652

full=3

0/1

16_2467665_2468169_DEL_1

2467665

2468169

-503

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:56354:0:1:0:1:0

ACCCAGAGGTAGCAGCTGACTCCTCGGGCTCCCGGCTGGCGTCACCGCCTCTGGAGCCAATGGGCTCTGACGTGGCGAGCCTGGAACGCCACTGGGACTGCGCGGGCGTCCACACCACCCACCGAGCGCGGCCACCGCGTTGGCGGCATGAGCGCGCTCGAGCCTCCCCCAGCGGCGCCCGCCTCGCCCCCCGGGCCGGGTCTGGCGCACCCGGAACCCCCCGGGGCCCTGCGCGCCCTGCTCTTGGCCACCGGCGGCGCTGGGGGCTCGTGGCCTCGCTGCATTCTGCCGTTCGGTGCCGTGGCCGTGCTGGCTGGTGCGGCTGCCACGGCCATCACCTTCTCGCTGCGGGGACCCCGCCTGGACCTGGCCCAGGGCTCGTCGCTGGCCGCGCTCAGTGCGGGCCTGGGGCTTCTGACCGCCGCCTTCCTGTGCTGGCGCGCTCGGCGGAGGCGAAGGGCCGGGCGCAGGGAGCCGGGGGCGCCCTGAGCCGCGGGCGAGGCC

458

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-503;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=16;END=2468168;CIPOS=0,3;CIEND=0,1;STRANDS=+;Max_AF=0.000112;Max_Het=12;Max_HomAlt=1;Max_PopMax_AF=0.00273;CCDG_Count=0;Best_CCDG_ID=221169;Best_CCDG_OFP=0.111901;Best_CCDG_AF=0.0001368;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=481787;Best_CCDG_Mismatch_OFP=0.5404;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=0.0003419;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_16:2465690-2470192;Best_TOPMed_OFP=0.111901;Best_TOPMed_AF=4.6e-05;Best_TOPMed_Het=13;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000119907;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_54243;Best_ThousG_Mismatch_OFP=0.015873;Best_ThousG_Mismatch_SVTYPE=CPX;Best_ThousG_Mismatch_AF=0.000781;Best_ThousG_Mismatch_Het=5;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr16_a2b17a52;Best_gnomAD_OFP=0.955888;Best_gnomAD_AF=0.000112;Best_gnomAD_Het=12;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.00273;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr16_bfcd0fc2;Best_gnomAD_Mismatch_OFP=0.5404;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.000151;Best_gnomAD_Mismatch_Het=5;Best_gnomAD_Mismatch_HomAlt=7;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:504:23,4:+:420:DEL:DEL00045665:NA:NA:chr16_2467665-chr16_2468169

0/1:NA:503:0,0:+:238:DEL:MantaDEL_56354_0_1_0_1_0:ACCCAGAGGTAGCAGCTGACTCCTCGGGCTCCCGGCTGGCGTCACCGCCTCTGGAGCCAATGGGCTCTGACGTGGCGAGCCTGGAACGCCACTGGGACTGCGCGGGCGTCCACACCACCCACCGAGCGCGGCCACCGCGTTGGCGGCATGAGCGCGCTCGAGCCTCCCCCAGCGGCGCCCGCCTCGCCCCCCGGGCCGGGTCTGGCGCACCCGGAACCCCCCGGGGCCCTGCGCGCCCTGCTCTTGGCCACCGGCGGCGCTGGGGGCTCGTGGCCTCGCTGCATTCTGCCGTTCGGTGCCGTGGCCGTGCTGGCTGGTGCGGCTGCCACGGCCATCACCTTCTCGCTGCGGGGACCCCGCCTGGACCTGGCCCAGGGCTCGTCGCTGGCCGCGCTCAGTGCGGGCCTGGGGCTTCTGACCGCCGCCTTCCTGTGCTGGCGCGCTCGGCGGAGGCGAAGGGCCGGGCGCAGGGAGCCGGGGGCGCCCTGAGCCGCGGGCGAGGCC:A:chr16_2467665-chr16_2468168

0/1:NA:500:0,0:+:458:DEL:8672:NA:NA:chr16_2467668-chr16_2468168

split

p13.3

TEDC2-AS1

NR_135198

2464949

2468213

505

exon1-exon1

UTR

2467664

2468169

dbVar

chr16:2465689-2470192

0.01

729652

full=1

0/1

5_110536114_110536179_DEL_1

1.11E+08

-64

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:138498:0:1:0:0:0

TCTTTTTCTGTCTTTTCCTTTCCAACGTGGGACCCTTGGTAGGCAGTGCCTAAACACAGAGGCAA

600

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-64;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=5;END=110536178;CIPOS=0,2;CIEND=0,1;STRANDS=+;Max_AF=0.002343;Max_Het=47;Max_HomAlt=1;Max_PopMax_AF=0.012521;CCDG_Count=0;Best_CCDG_ID=362171;Best_CCDG_OFP=0.000803938;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=362176_1;Best_CCDG_Mismatch_OFP=0.0153846;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.0003419;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_5:110533678-110539832;Best_TOPMed_OFP=0.0105588;Best_TOPMed_AF=1.1e-05;Best_TOPMed_Het=3;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=3.5929e-05;Best_TOPMed_Mismatch_ID=DUP_5:110530357-110547459;Best_TOPMed_Mismatch_OFP=0.00380028;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_125856;Best_ThousG_OFP=0.969231;Best_ThousG_AF=0.002343;Best_ThousG_Het=15;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.012521;Best_ThousG_Mismatch_ID=HGSV_125854;Best_ThousG_Mismatch_OFP=0.00379961;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000312;Best_ThousG_Mismatch_Het=2;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr5_0be7075e;Best_gnomAD_OFP=0.955882;Best_gnomAD_AF=0.000389;Best_gnomAD_Het=47;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.01;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr5_9c1766b7;Best_gnomAD_Mismatch_OFP=0.00379961;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:65:0,0:+:600:DEL:DEL00017207:NA:NA:chr5_110536114-chr5_110536179

0/1:NA:64:0,0:+:400:DEL:MantaDEL_138498_0_1_0_0_0:TCTTTTTCTGTCTTTTCCTTTCCAACGTGGGACCCTTGGTAGGCAGTGCCTAAACACAGAGGCAA:T:chr5_110536114-chr5_110536178

0/1:NA:62:0,0:+:251:DEL:3385:NA:NA:chr5_110536116-chr5_110536178

split

q22.1

TMEM232

XR_001742182

1.1E+08

1.11E+08

intron14-intron14

UTR

32267

1.11E+08

dbVar

chr5:110269511-110611886;chr5:110415987-110736461

0.01

IMH

5:85192778-162907706;5:96855635-159536527;5:99219064-135784342;5:99223293-135778815

0.5229

77.61

642987

7.93E-12

full=1

0/1

14_90700685_90700781_DEL_1

90700685

90700781

-95

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:77015:0:1:0:0:0

TATGTATCTGCTTTTCCAGAGTTGTAAGTGTTGACAAAGACAATGTCATTCTGGATATTGTCAACACTTACAACTCCGGAAAAGCAGATACATACC

240

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-95;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=14;END=90700780;CIPOS=0,8;CIEND=0,1;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_Mismatch_ID=208341_1;Best_CCDG_Mismatch_OFP=0.0104167;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.08852;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_14:90676902-90708200;Best_TOPMed_OFP=0.00306709;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=1.19772e-05;Best_TOPMed_Mismatch_ID=INV_14:90104469-93174563;Best_TOPMed_Mismatch_OFP=3.12694e-05;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_47084;Best_ThousG_Mismatch_OFP=3.6584e-06;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000312;Best_ThousG_Mismatch_Het=2;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=0;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr14_a1dd9329;Best_gnomAD_OFP=4.75114e-06;Best_gnomAD_AF=0.000141;Best_gnomAD_Het=16;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.000682;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_CPX_chr14_821da3bd;Best_gnomAD_Mismatch_OFP=1.57307e-06;Best_gnomAD_Mismatch_SVTYPE=CPX;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:96:0,0:+:240:DEL:DEL00042995:NA:NA:chr14_90700685-chr14_90700781

0/1:NA:95:0,0:+:133:DEL:MantaDEL_77015_0_1_0_0_0:TATGTATCTGCTTTTCCAGAGTTGTAAGTGTTGACAAAGACAATGTCATTCTGGATATTGTCAACACTTACAACTCCGGAAAAGCAGATACATACC:T:chr14_90700685-chr14_90700780

0/1:NA:87:0,0:+:128:DEL:8205:NA:NA:chr14_90700693-chr14_90700780

split

q32.11

TTC7B

NM_001010854

90524563

90816430

intron5-intron5

CDS

5106

90700684

90700781

gnomAD-SV_v3_DEL_chr14_aa7bf92b

chr14:56471274-99420950

0.633

IMH

14:23629193-97505158

0.4022

30.86

1.071135

-0.91594

-0.36248

-0.28547

2.065498

145567

1.00E+00

full=1

0/1

16_78728053_78738602_DEL_1

78728053

78738602

-10548

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:62766:0:1:0:0:0

1800

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-10548;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=16;END=78738601;CIPOS=0,3;CIEND=0,1;STRANDS=+;Max_AF=0.001873;Max_Het=123;Max_HomAlt=0;Max_PopMax_AF=0.008547;CCDG_Count=0;Best_CCDG_ID=230135;Best_CCDG_OFP=0.314722;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;Best_CCDG_Mismatch_ID=484122;Best_CCDG_Mismatch_OFP=0.0155123;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=1;Best_TOPMed_ID=DEL_16:78728057-78738605;Best_TOPMed_OFP=0.999337;Best_TOPMed_AF=0.000436;Best_TOPMed_Het=123;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.00611532;Best_TOPMed_Mismatch_ID=DUP_16:78644060-78859840;Best_TOPMed_Mismatch_OFP=0.0488873;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_58285;Best_ThousG_OFP=0.999716;Best_ThousG_AF=0.001873;Best_ThousG_Het=12;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.008547;Best_ThousG_Mismatch_ID=HGSV_58282;Best_ThousG_Mismatch_OFP=0.00994917;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.000312;Best_ThousG_Mismatch_Het=2;Best_ThousG_Mismatch_HomAlt=0;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr16_c42f3f93;Best_gnomAD_OFP=0.999716;Best_gnomAD_AF=0.000389;Best_gnomAD_Het=49;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.007893;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr16_b692be56;Best_gnomAD_Mismatch_OFP=0.29302;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:10549:13,16:+:1800:DEL:DEL00048734:NA:NA:chr16_78728053-chr16_78738602

0/1:NA:10548:0,0:+:636:DEL:MantaDEL_62766_0_1_0_0_0:NA:NA:chr16_78728053-chr16_78738601

0/1:NA:10545:0,0:+:665:DEL:9063:NA:NA:chr16_78728056-chr16_78738601

split

q23.1

WWOX

NM_001291997

78099653

79212667

10550

intron7-intron7

CDS

295300

78728052

78738602

dbVar

chr16:77756392-78780785

0.01

dbVar

chr16:78522932-78900915;chr16:78680867-78881706;chr16:78727479-78738769;chr16:78728023-78738636

0.01

IMH

16:29226964-88193867

0.4997

0.38

-3.32067

-3.50356

46,XY partial gonadal dysgenesis;autosomal recessive spinocerebellar ataxia 12;developmental and epileptic encephalopathy;developmental and epileptic encephalopathy, 28;undetermined early-onset epileptic encephalopathy

AD;AR

Definitive;Moderate;Strong;Supportive

22071891[PMID];24369382;24369382[PMID];24456803;25411445;25411445[PMID]

51741

605131

Developmental and epileptic encephalopathy 28, 616211 (3) AR;Esophageal squamous cell carcinoma, somatic, 133239 (3);Spinocerebellar ataxia, AR 12, 614322 (3) AR

yes

1.24E-15

1.94E-08

0.4271

Cleft lip;Cleft palate;Developmental and epileptic encephalopathy 28;Long philtrum

Holoprosencephaly;increased brain weight

Microphthalmia;eye decreased size, abnormal

full=1

0/1

16_69820426_69824902_DEL_1

69820426

69824902

-4474

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:61841:0:1:0:0:0

1773

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-4474;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=16;END=69824902;CIPOS=-2,0;CIEND=-2,0;STRANDS=+;Max_AF=0.001768;Max_Het=205;Max_HomAlt=1;Max_PopMax_AF=0.004054;CCDG_Count=0;Best_CCDG_Mismatch_ID=483870;Best_CCDG_Mismatch_OFP=0.452395;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=0.005368;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=0;Best_TOPMed_ID=DEL_16:69819704-69827126;Best_TOPMed_OFP=0.602775;Best_TOPMed_AF=4e-06;Best_TOPMed_Het=1;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0;Best_TOPMed_Mismatch_ID=DUP_16:69677028-69924914;Best_TOPMed_Mismatch_OFP=0.0180525;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_Mismatch_ID=HGSV_57643;Best_ThousG_Mismatch_OFP=0.442054;Best_ThousG_Mismatch_SVTYPE=DUP;Best_ThousG_Mismatch_AF=0.004995;Best_ThousG_Mismatch_Het=30;Best_ThousG_Mismatch_HomAlt=1;ThousG_SV_Cov=0;gnomAD_Count=3;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr16_a548fb8d;Best_gnomAD_OFP=0.918212;Best_gnomAD_AF=0.001768;Best_gnomAD_Het=205;Best_gnomAD_HomAlt=1;Best_gnomAD_PopMax_AF=0.004054;gnomAD_Mismatches=gnomAD-SV_v3_DUP_chr16_713063eb;gnomAD_Mismatches_Count=1;gnomAD_Mismatch_SVTYPEs=DUP;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr16_713063eb;Best_gnomAD_Mismatch_OFP=0.87503;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=0.069756;Best_gnomAD_Mismatch_Het=2968;Best_gnomAD_Mismatch_HomAlt=1072;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:4474:15,18:+:1773:DEL:DEL00048414:NA:NA:chr16_69820426-chr16_69824900

0/1:NA:4474:0,0:+:999:DEL:MantaDEL_61841_0_1_0_0_0:NA:NA:chr16_69820428-chr16_69824902

0/1:NA:4474:0,0:+:983:DEL:9002:NA:NA:chr16_69820428-chr16_69824902

split

q22.1

WWP2

NM_001270455

69762331

69910405

4477

intron4-intron4

CDS

15223

69820425

69824902

dbVar

chr16:69677025-69924863;chr16:69762176-69924258;chr16:69815142-69824970

0.01

dbVar

chr16:69820414-69824905

0.01

IMH

16:15020811-70019806;16:29226964-88193867

0.4997

16.36

1.36334

1.814698

11060

1.65E-01

9.78E-01

0.6812

Cleft lip;Cleft palate;Hypertelorism;Micrognathia;Microphthalmia;abnormal jaw morphology;abnormal snout morphology

Cleft palate;palate decreased size, abnormal

full=3

0/1

19_4005348_4159440_DEL_1

4005348

4159440

-154090

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:79083:0:1:0:0:0

1740

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:154087:26,11:+:1740:DEL:DEL00054230:NA:NA:chr19_4005348-chr19_4159435

0/1:NA:154090:0,0:+:999:DEL:MantaDEL_79083_0_1_0_0_0:NA:NA:chr19_4005350-chr19_4159440

0/1:NA:154090:0,0:+:650:DEL:10046:NA:NA:chr19_4005350-chr19_4159440

split

p13.3

ZBTB7A

XM_005259570

4043302

4055521

12219

1905

100

txStart-txEnd

5'UTR-3'UTR

4043302

4055521

Neurodevelopmental_delay

dbVar

chr19:4019786-4065415

0.01

IMH

19:1692676-41507766

0.0103

46.6

0.025969

0.397011

0.402117

complex neurodevelopmental disorder;macrocephaly, neurodevelopmental delay, lymphoid hyperplasia, and persistent fetal hemoglobin

Strong

27252013;28135719;29738522;31645653;34515416

51341

605878

Macrocephaly, neurodevelopmental delay, lymphoid hyperplasia, and persistent fetal hemoglobin, 619769 (3) AD

yes

9.59E-01

0.3097

Dental crowding;Macrocephaly, neurodevelopmental delay, lymphoid hyperplasia, and persistent fetal hemoglobin;Micrognathia

full=5

0/1

19_4005230_4159441_DUP_1

4005230

4159441

154171

DUP

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDUP:TANDEM:79083:0:1:1:0:0

999

PASS

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:154170:21,8:-:600:DUP:DUP00054229:NA:NA:chr19_4005253-chr19_4159423

0/1:NA:154171:0,0:-:999:DUP:MantaDUP_TANDEM_79083_0_1_1_0_0:NA:NA:chr19_4005252-chr19_4159423

0/1:NA:154211:0,0:-:106:DUP:10045:NA:NA:chr19_4005230-chr19_4159441

split

p13.3

ZBTB7A

XM_005259570

4043302

4055521

12219

1905

100

txStart-txEnd

5'UTR-3'UTR

4043302

4055521

Neurodevelopmental_delay

dbVar

chr19:4019786-4065415

0.01

IMH

19:1692676-41507766

0.0103

46.6

0.025969

0.397011

0.402117

complex neurodevelopmental disorder;macrocephaly, neurodevelopmental delay, lymphoid hyperplasia, and persistent fetal hemoglobin

Strong

27252013;28135719;29738522;31645653;34515416

51341

605878

Macrocephaly, neurodevelopmental delay, lymphoid hyperplasia, and persistent fetal hemoglobin, 619769 (3) AD

yes

9.59E-01

0.3097

Dental crowding;Macrocephaly, neurodevelopmental delay, lymphoid hyperplasia, and persistent fetal hemoglobin;Micrognathia

full=3

0/1

8_134624854_134624959_DEL_1

1.35E+08

-104

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:223528:0:1:0:0:0

TCATATGCATTCATTTATAATTAACACTGCACTAATATTCTAAAGTACCTATTCTAAATTGCCCAAGAACTAATTAAATCTCAGAATGCCCCAGAGAGTAAAGTG

660

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-104;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=8;END=134624958;CIPOS=0,0;CIEND=0,1;STRANDS=+;Max_AF=0.00641;Max_Het=1273;Max_HomAlt=108;Max_PopMax_AF=0.073634;CCDG_Count=0;Best_CCDG_Mismatch_ID=534379;Best_CCDG_Mismatch_OFP=0.0102971;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=0.0001026;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=1;Best_TOPMed_ID=DEL_8:134624855-134624958;Best_TOPMed_OFP=1;Best_TOPMed_AF=0.005011;Best_TOPMed_Het=1273;Best_TOPMed_HomAlt=10;Best_TOPMed_PopMax_AF=0.00766061;Best_TOPMed_Mismatch_ID=DUP_8:134613175-134625901;Best_TOPMed_Mismatch_OFP=0.00824953;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=1;Best_ThousG_ID=HGSV_158426;Best_ThousG_OFP=1;Best_ThousG_AF=0.002029;Best_ThousG_Het=9;Best_ThousG_HomAlt=2;Best_ThousG_PopMax_AF=0.003943;ThousG_SV_Cov=1;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr8_1374fbf9;Best_gnomAD_OFP=1;Best_gnomAD_AF=0.00641;Best_gnomAD_Het=592;Best_gnomAD_HomAlt=108;Best_gnomAD_PopMax_AF=0.073634;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr8_5d030293;Best_gnomAD_Mismatch_OFP=0.0102971;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:105:0,0:+:660:DEL:DEL00027262:NA:NA:chr8_134624854-chr8_134624959

0/1:NA:104:0,0:+:457:DEL:MantaDEL_223528_0_1_0_0_0:TCATATGCATTCATTTATAATTAACACTGCACTAATATTCTAAAGTACCTATTCTAAATTGCCCAAGAACTAATTAAATCTCAGAATGCCCCAGAGAGTAAAGTG:T:chr8_134624854-chr8_134624958

0/1:NA:104:0,0:+:323:DEL:5373:NA:NA:chr8_134624854-chr8_134624958

split

q24.22

ZFAT

XM_011517204

1.34E+08

1.35E+08

106

intron2-intron2

CDS

12501

1.35E+08

dbVar

chr8:134608227-134779707

0.01

gnomAD-SV_v3_DEL_chr8_d4501b6e

chr8:133866055-134670293

0.1984

57.4

0.119428

-1.40202

-1.01818

-0.95443

1.113052

57623

610931

(Autoimmune thyroid disease, susceptibility to, 3), 608175 (3)

1.28E-08

2.93E-03

0.6411

Cleft lip;Cleft palate;Hypertelorism;Micrognathia;Microphthalmia;abnormal tooth morphology

full=3

0/1

1_35391781_35391915_DEL_1

35391781

35391915

-133

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:191761:0:1:0:0:0

GCCTGTAATCTCAGCACTTTGGGAGGCTGAGGCAGGCGGATCACGAGGTCAGGAGTTTGAGACCATCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAATACAAAAAATTAGCTGGGTGTGGTGCTGCGCA

709

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-133;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=1;END=35391914;CIPOS=0,35;CIEND=0,1;STRANDS=+;Max_AF=0.00504;Max_Het=1296;Max_HomAlt=10;Max_PopMax_AF=0.037304;CCDG_Count=0;Best_CCDG_Mismatch_ID=124771_2;Best_CCDG_Mismatch_OFP=0.00746269;Best_CCDG_Mismatch_SVTYPE=BND;Best_CCDG_Mismatch_AF=0.003761;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=0;TOPMed_Count=1;Best_TOPMed_ID=DEL_1:35391782-35391914;Best_TOPMed_OFP=1;Best_TOPMed_AF=0.00504;Best_TOPMed_Het=1296;Best_TOPMed_HomAlt=10;Best_TOPMed_PopMax_AF=0.037304;Best_TOPMed_Mismatch_ID=INV_1:34936904-38057517;Best_TOPMed_Mismatch_OFP=4.29403e-05;Best_TOPMed_Mismatch_SVTYPE=INV;Best_TOPMed_Mismatch_AF=4e-06;Best_TOPMed_Mismatch_Het=1;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_2476;Best_ThousG_OFP=0.738806;Best_ThousG_AF=0.006712;Best_ThousG_Het=39;Best_ThousG_HomAlt=2;Best_ThousG_PopMax_AF=0.022463;ThousG_SV_Cov=0.738806;gnomAD_Count=1;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr1_2f5ed07a;Best_gnomAD_OFP=0.850746;Best_gnomAD_AF=0.003285;Best_gnomAD_Het=405;Best_gnomAD_HomAlt=4;Best_gnomAD_PopMax_AF=0.017792;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_INV_chr1_02e3c92a;Best_gnomAD_Mismatch_OFP=7.105e-06;Best_gnomAD_Mismatch_SVTYPE=INV;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:134:0,0:+:525:DEL:DEL00001573:NA:NA:chr1_35391781-chr1_35391915

0/1:NA:133:0,0:+:709:DEL:MantaDEL_191761_0_1_0_0_0:GCCTGTAATCTCAGCACTTTGGGAGGCTGAGGCAGGCGGATCACGAGGTCAGGAGTTTGAGACCATCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAATACAAAAAATTAGCTGGGTGTGGTGCTGCGCA:G:chr1_35391781-chr1_35391914

0/1:NA:98:0,0:+:314:DEL:329:NA:NA:chr1_35391816-chr1_35391914

split

p34.3

ZMYM4

XR_007064890

35268708

35397428

135

intron16-intron16

UTR

296

35391780

35391915

gnomAD-SV_v3_DEL_chr1_cf5f2df8

chr1:13203398-167621949

0.1676

IMH

1:7601938-50381771;1:10187873-186857210;1:16798094-234784887;1:31594523-94732184

0.4698

13.84

1.343073

1.513139

1.782499

0.708669

2.831411

9202

1.0000e

full=1

0/1

9_112981593_113019974_DEL_1

1.13E+08

-38381

DEL

ILS_AP001,ILS_AP001_1,ILS_AP001_2

MantaDEL:212049:1:3:0:0:0

809

PASS

SUPP=3;SUPP_VEC=111;SVLEN=-38381;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=9;END=113019974;CIPOS=0,0;CIEND=-2,0;STRANDS=+;Max_AF=0;Max_Het=0;Max_HomAlt=0;Max_PopMax_AF=0;CCDG_Count=0;Best_CCDG_ID=435250;Best_CCDG_OFP=0.597161;Best_CCDG_AF=3.419e-05;Best_CCDG_Het=0;Best_CCDG_HomAlt=0;Best_CCDG_PopMax_AF=0;CCDG_Mismatches=537047;CCDG_Mismatches_Count=1;CCDG_Mismatch_SVTYPEs=DUP;Best_CCDG_Mismatch_ID=537047;Best_CCDG_Mismatch_OFP=0.903893;Best_CCDG_Mismatch_SVTYPE=DUP;Best_CCDG_Mismatch_AF=3.419e-05;Best_CCDG_Mismatch_Het=0;Best_CCDG_Mismatch_HomAlt=0;SV_Cov=1;CCDG_SV_Cov=1;TOPMed_Count=0;Best_TOPMed_ID=DEL_9:112952557-113025211;Best_TOPMed_OFP=0.52827;Best_TOPMed_AF=0.000114;Best_TOPMed_Het=32;Best_TOPMed_HomAlt=0;Best_TOPMed_PopMax_AF=0.000162979;TOPMed_Mismatches=DUP_9:112979208-113021665;TOPMed_Mismatches_Count=1;TOPMed_Mismatch_SVTYPEs=DUP;Best_TOPMed_Mismatch_ID=DUP_9:112979208-113021665;Best_TOPMed_Mismatch_OFP=0.903978;Best_TOPMed_Mismatch_SVTYPE=DUP;Best_TOPMed_Mismatch_AF=7e-06;Best_TOPMed_Mismatch_Het=2;Best_TOPMed_Mismatch_HomAlt=0;TOPMed_SV_Cov=1;ThousG_Count=0;Best_ThousG_ID=HGSV_164762;Best_ThousG_OFP=0.182065;Best_ThousG_AF=0.000156;Best_ThousG_Het=1;Best_ThousG_HomAlt=0;Best_ThousG_PopMax_AF=0.00056;Best_ThousG_Mismatch_ID=HGSV_164763;Best_ThousG_Mismatch_OFP=0.118415;Best_ThousG_Mismatch_SVTYPE=CPX;Best_ThousG_Mismatch_AF=0.039806;Best_ThousG_Mismatch_Het=231;Best_ThousG_Mismatch_HomAlt=12;ThousG_SV_Cov=0.299515;gnomAD_Count=0;Best_gnomAD_ID=gnomAD-SV_v3_DEL_chr9_21e41c3e;Best_gnomAD_OFP=0.597161;Best_gnomAD_AF=9.5e-05;Best_gnomAD_Het=12;Best_gnomAD_HomAlt=0;Best_gnomAD_PopMax_AF=0.001272;Best_gnomAD_Mismatch_ID=gnomAD-SV_v3_DUP_chr9_3bb074cb;Best_gnomAD_Mismatch_OFP=0.429264;Best_gnomAD_Mismatch_SVTYPE=DUP;Best_gnomAD_Mismatch_AF=8e-06;Best_gnomAD_Mismatch_Het=1;Best_gnomAD_Mismatch_HomAlt=0;gnomAD_SV_Cov=1

GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

0/1:NA:38379:19,9:+:809:DEL:DEL00029120:NA:NA:chr9_112981593-chr9_113019972

0/1:NA:38381:0,0:+:557:DEL:MantaDEL_212049_1_3_0_0_0:NA:NA:chr9_112981593-chr9_113019974

0/1:NA:38381:0,0:+:281:DEL:5715:NA:NA:chr9_112981593-chr9_113019974

split

q32

ZNF883

NM_001101338

1.13E+08

24064

1140

txStart-txEnd

5'UTR-3'UTR

1.13E+08

dbVar

chr9:112958718-113090720

0.01

dbVar

chr9:112952556-113025206

0.01

IMH

9:65437055-134286391;9:80897170-125694547;9:89671548-130954998

0.4714

169834

full=1

0/1

Open in a new tab

Disclosures

Human subjects: Informed consent for treatment and open access publication was obtained or waived by all participants in this study. IEC All India Institute of Medical Sciences, Bhubaneswar issued approval T/IM-NF/Anatomy/23/44.

Conflicts of interest: In compliance with the ICMJE uniform disclosure form, all authors declare the following:

Payment/services info: All authors have declared that no financial support was received from any organization for the submitted work.

Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work.

Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work.

Author Contributions

Concept and design: Praisy Joy, Sunil K. Raghav

Acquisition, analysis, or interpretation of data: Praisy Joy, Sudeshna Datta, Sanjukta Sahoo, Tapas Kumar Som, Prabhas R. Tripathy, Manisha R. Gaikwad, Pavithra Ayyanar, Sunil K. Raghav

Drafting of the manuscript: Praisy Joy, Sudeshna Datta, Sanjukta Sahoo

Critical review of the manuscript for important intellectual content: Praisy Joy, Tapas Kumar Som, Prabhas R. Tripathy, Manisha R. Gaikwad, Pavithra Ayyanar, Sunil K. Raghav

Supervision: Sunil K. Raghav

References

1.Prevalence, predictors, and outcomes of major congenital anomalies: a population-based register study. Al-Dewik N, Samara M, Younes S, et al. Sci Rep. 2023;13:2198. doi: 10.1038/s41598-023-27935-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
2.8 December. Geneva: World Health Organization; [ Dec; 2026 ]. 1970. Basic Tabulation List With Alphabetical Index; p. 331. [Google Scholar]
3.Unraveling the challenges: a critical review of congenital malformations in low socioeconomic strata of developing countries. Shetty N, Mantri S, Agarwal S, Potdukhe A, Wanjari MB, Taksande AB, Yelne S. https://www.cureus.com/articles/164063-unraveling-the-challenges-a-critical-review-of-congenital-malformations-in-low-socioeconomic-strata-of-developing-countries. Cureus. 2023;15:0. doi: 10.7759/cureus.41800. [DOI] [PMC free article] [PubMed] [Google Scholar]
4.The prevalence and pattern of congenital anomalies among neonates admitted in a tertiary care hospital in the Andaman and Nicobar Islands: a retrospective study. Sravani T, Palaniappan P, Shaju V. https://www.cureus.com/articles/198531-the-prevalence-and-pattern-of-congenital-anomalies-among-neonates-admitted-in-a-tertiary-care-hospital-in-the-andaman-and-nicobar-islands-a-retrospective-study. Cureus. 2023;15:0. doi: 10.7759/cureus.47853. [DOI] [PMC free article] [PubMed] [Google Scholar]
5.A structural variation reference for medical and population genetics. Collins RL, Brand H, Karczewski KJ, et al. Nature. 2020;581:444–451. doi: 10.1038/s41586-020-2287-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
6.The landscape of somatic copy-number alteration across human cancers. Beroukhim R, Mermel CH, Porter D, et al. Nature. 2010;463:899–905. doi: 10.1038/nature08822. [DOI] [PMC free article] [PubMed] [Google Scholar]
7.fastp: an ultra-fast all-in-one FASTQ preprocessor. Chen S, Zhou Y, Chen Y, Gu J. Bioinformatics. 2018;34:0–90. doi: 10.1093/bioinformatics/bty560. [DOI] [PMC free article] [PubMed] [Google Scholar]
8.Fast and accurate short read alignment with Burrows-Wheeler transform. Li H, Durbin R. Bioinformatics. 2009;25:1754–1760. doi: 10.1093/bioinformatics/btp324. [DOI] [PMC free article] [PubMed] [Google Scholar]
9.From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Van der Auwera GA, Carneiro MO, Hartl C, et al. Curr Protoc Bioinformatics. 2013;43 doi: 10.1002/0471250953.bi1110s43. [DOI] [PMC free article] [PubMed] [Google Scholar]
10.A framework for variation discovery and genotyping using next-generation DNA sequencing data. DePristo MA, Banks E, Poplin R, et al. Nat Genet. 2011;43:491–498. doi: 10.1038/ng.806. [DOI] [PMC free article] [PubMed] [Google Scholar]
11.The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. McKenna A, Hanna M, Banks E, et al. Genome Res. 2010;20:1297–1303. doi: 10.1101/gr.107524.110. [DOI] [PMC free article] [PubMed] [Google Scholar]
12.DELLY: structural variant discovery by integrated paired-end and split-read analysis. Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. Bioinformatics. 2012;28:0–9. doi: 10.1093/bioinformatics/bts378. [DOI] [PMC free article] [PubMed] [Google Scholar]
13.Carlson M. org.Hs.eg.db [Internet. Genome wide annotation for human. Bioconductor. [ Apr; 2025 ]. 2017. https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html
14.Hervé Pagès MC. Manipulation of SQLite-based annotations in Bioconductor. AnnotationDbi [Internet]. Bioconductor. [ Apr; 2025 ]. 2017. https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html
15.Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Chen X, Schulz-Trieglaff O, Shaw R, et al. Bioinformatics. 2016;32:1220–1222. doi: 10.1093/bioinformatics/btv710. [DOI] [PubMed] [Google Scholar]
16.Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Jeffares DC, Jolly C, Hoti M, et al. Nat Commun. 2017;8:14061. doi: 10.1038/ncomms14061. [DOI] [PMC free article] [PubMed] [Google Scholar]
17.Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate. Nicholas TJ, Cormier MJ, Quinlan AR. BMC Bioinformatics. 2022;23:490. doi: 10.1186/s12859-022-05008-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
18.Mapping and characterization of structural variation in 17,795 human genomes. Abel HJ, Larson DE, Regier AA, et al. Nature. 2020;583:83–89. doi: 10.1038/s41586-020-2371-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
19.High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Byrska-Bishop M, Evani US, Zhao X, et al. https://www.cell.com/cell/fulltext/S0092-8674(22)00991-6. Cell. 2022;185:3426–3440. doi: 10.1016/j.cell.2022.08.004. [DOI] [PMC free article] [PubMed] [Google Scholar]
20.Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Taliun D, Harris DN, Kessler MD, et al. Nature. 2021;590:290–299. doi: 10.1038/s41586-021-03205-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
21.AnnotSV: an integrated tool for structural variations annotation. Geoffroy V, Herenger Y, Kress A, Stoetzel C, Piton A, Dollfus H, Muller J. Bioinformatics. 2018;34:3572–3574. doi: 10.1093/bioinformatics/bty304. [DOI] [PubMed] [Google Scholar]
22.The Database of Genomic Variants: a curated collection of structural variation in the human genome. MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW. Nucleic Acids Res. 2014;42:0–92. doi: 10.1093/nar/gkt958. [DOI] [PMC free article] [PubMed] [Google Scholar]
23.The ExAC browser: displaying reference data information from over 60 000 exomes. Karczewski KJ, Weisburd B, Thomas B, et al. Nucleic Acids Res. 2017;45:0–5. doi: 10.1093/nar/gkw971. [DOI] [PMC free article] [PubMed] [Google Scholar]
24.Searching Online Mendelian Inheritance in Man (OMIM): a knowledgebase of human genes and genetic phenotypes. Amberger JS, Hamosh A. Curr Protoc Bioinformatics. 2017;58:1. doi: 10.1002/cpbi.27. [DOI] [PMC free article] [PubMed] [Google Scholar]
25.DbVar and DGVa: public archives for genomic structural variation. Lappalainen I, Lopez J, Skipper L, et al. Nucleic Acids Res. 2013;41:0–41. doi: 10.1093/nar/gks1213. [DOI] [PMC free article] [PubMed] [Google Scholar]
26.Improved exome prioritization of disease genes through cross-species phenotype comparison. Robinson PN, Köhler S, Oellrich A, et al. Genome Res. 2014;24:340–348. doi: 10.1101/gr.160325.113. [DOI] [PMC free article] [PubMed] [Google Scholar]
27.ClinGen Variant Curation Expert Panel experiences and standardized processes for disease and gene-level specification of the ACMG/AMP guidelines for sequence variant interpretation. Rivera-Muñoz EA, Milko LV, Harrison SM, et al. Hum Mutat. 2018;39:1614–1622. doi: 10.1002/humu.23645. [DOI] [PMC free article] [PubMed] [Google Scholar]
28.VarElect: the phenotype-based variation prioritizer of the GeneCards Suite. Stelzer G, Plaschkes I, Oz-Levi D, et al. BMC Genomics. 2016;17 Suppl 2:444. doi: 10.1186/s12864-016-2722-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
29.clusterProfiler: an R package for comparing biological themes among gene clusters. Yu G, Wang LG, Han Y, He QY. OMICS. 2012;16:284–287. doi: 10.1089/omi.2011.0118. [DOI] [PMC free article] [PubMed] [Google Scholar]
30.karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Gel B, Serra E. Bioinformatics. 2017;33:3088–3090. doi: 10.1093/bioinformatics/btx346. [DOI] [PMC free article] [PubMed] [Google Scholar]
31.Visualizing genomic data using Gviz and Bioconductor. Hahne F, Ivanek R. http://link.springer.com/10.1007/978-1-4939-3578-9_16. Methods Mol Biol. 2016;1418:335–351. doi: 10.1007/978-1-4939-3578-9_16. [DOI] [PubMed] [Google Scholar]
32.Deletion of chromosome 21 disturbs human brain morphogenesis. Yao G, Chen XN, Flores-Sarnat L, et al. Genet Med. 2006;8:1–7. doi: 10.1097/01.gim.0000195892.60506.3f. [DOI] [PubMed] [Google Scholar]
33.Holoprosencephaly. Dubourg C, Bendavid C, Pasquier L, Henry C, Odent S, David V. Orphanet J Rare Dis. 2007;2:8. doi: 10.1186/1750-1172-2-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
34.A de novo 1.4-Mb deletion at 21q22.11 in a boy with developmental delay. Fukai R, Hiraki Y, Nishimura G, et al. Am J Med Genet A. 2014;164A:1021–1028. doi: 10.1002/ajmg.a.36377. [DOI] [PubMed] [Google Scholar]
35.Dissection of partial 21q monosomy in different phenotypes: clinical and molecular characterization of five cases and review of the literature. Errichiello E, Novara F, Cremante A, et al. Mol Cytogenet. 2016;9:21. doi: 10.1186/s13039-016-0230-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
36.Sacharow SJ, Levy HL. GeneReviews® [Internet] Seattle: University of Washington; 2025. Homocystinuria caused by cystathionine beta-synthase deficiency. [Google Scholar]
37.Subtelomeric 6.7 Mb trisomy 10p and 5.6 Mb monosomy 21q detected by FISH and array-CGH in three related patients. Szabó GP, Knegt AC, Ujfalusi A, Balogh E, Szabó T, Oláh É. Am J Med Genet A. 2012;158A:869–876. doi: 10.1002/ajmg.a.35236. [DOI] [PubMed] [Google Scholar]
38.Molecular mapping of 21 features associated with partial monosomy 21: involvement of the APP-SOD1 region. Chettouh Z, Croquette MF, Delobel B, et al. https://pmc.ncbi.nlm.nih.gov/articles/PMC1801243/ Am J Hum Genet. 1995;57:62–71. [PMC free article] [PubMed] [Google Scholar]
39.Ocular phenotype associated with DYRK1A variants. Méjécase C, Way CM, Owen N, Moosajee M. Genes (Basel) 2021;12 doi: 10.3390/genes12020234. [DOI] [PMC free article] [PubMed] [Google Scholar]
40.Whole-exome sequencing identified a novel DYRK1A variant in a patient with intellectual developmental disorder, autosomal dominant 7. Obara K, Abe E, Toyoshima I. https://www.cureus.com/articles/130318-whole-exome-sequencing-identified-a-novel-dyrk1a-variant-in-a-patient-with-intellectual-developmental-disorder-autosomal-dominant-7. Cureus. 2023;15:0. doi: 10.7759/cureus.33379. [DOI] [PMC free article] [PubMed] [Google Scholar]
41.Germline mutations in genes within the MAPK pathway cause cardio-facio-cutaneous syndrome. Rodriguez-Viciana P, Tetsu O, Tidyman WE, et al. Science. 2006;311:1287–1290. doi: 10.1126/science.1124642. [DOI] [PubMed] [Google Scholar]
42.Heterozygous variants in ZBTB7A cause a neurodevelopmental disorder associated with symptomatic overgrowth of pharyngeal lymphoid tissue, macrocephaly, and elevated fetal hemoglobin. von der Lippe C, Tveten K, Prescott TE, et al. Am J Med Genet A. 2022;188:272–282. doi: 10.1002/ajmg.a.62492. [DOI] [PubMed] [Google Scholar]
43.PIAS4 is associated with macro/microcephaly in the novel interstitial 19p13.3 microdeletion/microduplication syndrome. Nevado J, Rosenfeld JA, Mena R, et al. Eur J Hum Genet. 2015;23:1615–1626. doi: 10.1038/ejhg.2015.51. [DOI] [PMC free article] [PubMed] [Google Scholar]
44.The past, present, and future for constitutional ring chromosomes: a report of the international consortium for human ring chromosomes. Li P, Dupont B, Hu Q, et al. https://www.cell.com/hgg-advances/fulltext/S2666-2477(22)00055-0. HGG Adv. 2022;13:100139. doi: 10.1016/j.xhgg.2022.100139. [DOI] [PMC free article] [PubMed] [Google Scholar]
45.Prenatal diagnosis and molecular cytogenetic characterization of a pure ring chromosome 21 with a 4.657-Mb 21q22.3 deletion. Chen CP, Wang LK, Chern SR, et al. Taiwan J Obstet Gynecol. 2021;60:157–160. doi: 10.1016/j.tjog.2020.11.024. [DOI] [PubMed] [Google Scholar]
46.Molecular characterization of de novo ring chromosome 21 in a child with seizures, growth retardation, and multiple congenital anomalies. Ambulkar PS, Liehr T, Jain M, Waghmare J, Gangane N, Narang P, Pal AK. https://link.springer.com/article/10.1007/s12041-023-01439-5. J Genet. 2023;102:44. [PubMed] [Google Scholar]
47.Genotype-phenotype correlations in Down syndrome identified by array CGH in 30 cases of partial trisomy and partial monosomy chromosome 21. Lyle R, Béna F, Gagos S, et al. Eur J Hum Genet. 2009;17:454–466. doi: 10.1038/ejhg.2008.214. [DOI] [PMC free article] [PubMed] [Google Scholar]
48.Mimicking hypoxic-ischemic encephalopathy in a newborn with 21q deletion originating from ring chromosome 21. Moon JU, Yum SK. Children (Basel) 2023;10 doi: 10.3390/children10091461. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF1] 1.Prevalence, predictors, and outcomes of major congenital anomalies: a population-based register study. Al-Dewik N, Samara M, Younes S, et al. Sci Rep. 2023;13:2198. doi: 10.1038/s41598-023-27935-3. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF2] 2.8 December. Geneva: World Health Organization; [ Dec; 2026 ]. 1970. Basic Tabulation List With Alphabetical Index; p. 331. [Google Scholar]

[REF3] 3.Unraveling the challenges: a critical review of congenital malformations in low socioeconomic strata of developing countries. Shetty N, Mantri S, Agarwal S, Potdukhe A, Wanjari MB, Taksande AB, Yelne S. https://www.cureus.com/articles/164063-unraveling-the-challenges-a-critical-review-of-congenital-malformations-in-low-socioeconomic-strata-of-developing-countries. Cureus. 2023;15:0. doi: 10.7759/cureus.41800. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF4] 4.The prevalence and pattern of congenital anomalies among neonates admitted in a tertiary care hospital in the Andaman and Nicobar Islands: a retrospective study. Sravani T, Palaniappan P, Shaju V. https://www.cureus.com/articles/198531-the-prevalence-and-pattern-of-congenital-anomalies-among-neonates-admitted-in-a-tertiary-care-hospital-in-the-andaman-and-nicobar-islands-a-retrospective-study. Cureus. 2023;15:0. doi: 10.7759/cureus.47853. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF5] 5.A structural variation reference for medical and population genetics. Collins RL, Brand H, Karczewski KJ, et al. Nature. 2020;581:444–451. doi: 10.1038/s41586-020-2287-8. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF6] 6.The landscape of somatic copy-number alteration across human cancers. Beroukhim R, Mermel CH, Porter D, et al. Nature. 2010;463:899–905. doi: 10.1038/nature08822. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF7] 7.fastp: an ultra-fast all-in-one FASTQ preprocessor. Chen S, Zhou Y, Chen Y, Gu J. Bioinformatics. 2018;34:0–90. doi: 10.1093/bioinformatics/bty560. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF8] 8.Fast and accurate short read alignment with Burrows-Wheeler transform. Li H, Durbin R. Bioinformatics. 2009;25:1754–1760. doi: 10.1093/bioinformatics/btp324. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF9] 9.From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Van der Auwera GA, Carneiro MO, Hartl C, et al. Curr Protoc Bioinformatics. 2013;43 doi: 10.1002/0471250953.bi1110s43. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF10] 10.A framework for variation discovery and genotyping using next-generation DNA sequencing data. DePristo MA, Banks E, Poplin R, et al. Nat Genet. 2011;43:491–498. doi: 10.1038/ng.806. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF11] 11.The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. McKenna A, Hanna M, Banks E, et al. Genome Res. 2010;20:1297–1303. doi: 10.1101/gr.107524.110. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF12] 12.DELLY: structural variant discovery by integrated paired-end and split-read analysis. Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. Bioinformatics. 2012;28:0–9. doi: 10.1093/bioinformatics/bts378. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF13] 13.Carlson M. org.Hs.eg.db [Internet. Genome wide annotation for human. Bioconductor. [ Apr; 2025 ]. 2017. https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html

[REF14] 14.Hervé Pagès MC. Manipulation of SQLite-based annotations in Bioconductor. AnnotationDbi [Internet]. Bioconductor. [ Apr; 2025 ]. 2017. https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html

[REF15] 15.Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Chen X, Schulz-Trieglaff O, Shaw R, et al. Bioinformatics. 2016;32:1220–1222. doi: 10.1093/bioinformatics/btv710. [DOI] [PubMed] [Google Scholar]

[REF16] 16.Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Jeffares DC, Jolly C, Hoti M, et al. Nat Commun. 2017;8:14061. doi: 10.1038/ncomms14061. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF17] 17.Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate. Nicholas TJ, Cormier MJ, Quinlan AR. BMC Bioinformatics. 2022;23:490. doi: 10.1186/s12859-022-05008-y. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF18] 18.Mapping and characterization of structural variation in 17,795 human genomes. Abel HJ, Larson DE, Regier AA, et al. Nature. 2020;583:83–89. doi: 10.1038/s41586-020-2371-0. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF19] 19.High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Byrska-Bishop M, Evani US, Zhao X, et al. https://www.cell.com/cell/fulltext/S0092-8674(22)00991-6. Cell. 2022;185:3426–3440. doi: 10.1016/j.cell.2022.08.004. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF20] 20.Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Taliun D, Harris DN, Kessler MD, et al. Nature. 2021;590:290–299. doi: 10.1038/s41586-021-03205-y. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF21] 21.AnnotSV: an integrated tool for structural variations annotation. Geoffroy V, Herenger Y, Kress A, Stoetzel C, Piton A, Dollfus H, Muller J. Bioinformatics. 2018;34:3572–3574. doi: 10.1093/bioinformatics/bty304. [DOI] [PubMed] [Google Scholar]

[REF22] 22.The Database of Genomic Variants: a curated collection of structural variation in the human genome. MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW. Nucleic Acids Res. 2014;42:0–92. doi: 10.1093/nar/gkt958. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF23] 23.The ExAC browser: displaying reference data information from over 60 000 exomes. Karczewski KJ, Weisburd B, Thomas B, et al. Nucleic Acids Res. 2017;45:0–5. doi: 10.1093/nar/gkw971. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF24] 24.Searching Online Mendelian Inheritance in Man (OMIM): a knowledgebase of human genes and genetic phenotypes. Amberger JS, Hamosh A. Curr Protoc Bioinformatics. 2017;58:1. doi: 10.1002/cpbi.27. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF25] 25.DbVar and DGVa: public archives for genomic structural variation. Lappalainen I, Lopez J, Skipper L, et al. Nucleic Acids Res. 2013;41:0–41. doi: 10.1093/nar/gks1213. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF26] 26.Improved exome prioritization of disease genes through cross-species phenotype comparison. Robinson PN, Köhler S, Oellrich A, et al. Genome Res. 2014;24:340–348. doi: 10.1101/gr.160325.113. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF27] 27.ClinGen Variant Curation Expert Panel experiences and standardized processes for disease and gene-level specification of the ACMG/AMP guidelines for sequence variant interpretation. Rivera-Muñoz EA, Milko LV, Harrison SM, et al. Hum Mutat. 2018;39:1614–1622. doi: 10.1002/humu.23645. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF28] 28.VarElect: the phenotype-based variation prioritizer of the GeneCards Suite. Stelzer G, Plaschkes I, Oz-Levi D, et al. BMC Genomics. 2016;17 Suppl 2:444. doi: 10.1186/s12864-016-2722-2. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF29] 29.clusterProfiler: an R package for comparing biological themes among gene clusters. Yu G, Wang LG, Han Y, He QY. OMICS. 2012;16:284–287. doi: 10.1089/omi.2011.0118. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF30] 30.karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Gel B, Serra E. Bioinformatics. 2017;33:3088–3090. doi: 10.1093/bioinformatics/btx346. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF31] 31.Visualizing genomic data using Gviz and Bioconductor. Hahne F, Ivanek R. http://link.springer.com/10.1007/978-1-4939-3578-9_16. Methods Mol Biol. 2016;1418:335–351. doi: 10.1007/978-1-4939-3578-9_16. [DOI] [PubMed] [Google Scholar]

[REF32] 32.Deletion of chromosome 21 disturbs human brain morphogenesis. Yao G, Chen XN, Flores-Sarnat L, et al. Genet Med. 2006;8:1–7. doi: 10.1097/01.gim.0000195892.60506.3f. [DOI] [PubMed] [Google Scholar]

[REF33] 33.Holoprosencephaly. Dubourg C, Bendavid C, Pasquier L, Henry C, Odent S, David V. Orphanet J Rare Dis. 2007;2:8. doi: 10.1186/1750-1172-2-8. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF34] 34.A de novo 1.4-Mb deletion at 21q22.11 in a boy with developmental delay. Fukai R, Hiraki Y, Nishimura G, et al. Am J Med Genet A. 2014;164A:1021–1028. doi: 10.1002/ajmg.a.36377. [DOI] [PubMed] [Google Scholar]

[REF35] 35.Dissection of partial 21q monosomy in different phenotypes: clinical and molecular characterization of five cases and review of the literature. Errichiello E, Novara F, Cremante A, et al. Mol Cytogenet. 2016;9:21. doi: 10.1186/s13039-016-0230-3. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF36] 36.Sacharow SJ, Levy HL. GeneReviews® [Internet] Seattle: University of Washington; 2025. Homocystinuria caused by cystathionine beta-synthase deficiency. [Google Scholar]

[REF37] 37.Subtelomeric 6.7 Mb trisomy 10p and 5.6 Mb monosomy 21q detected by FISH and array-CGH in three related patients. Szabó GP, Knegt AC, Ujfalusi A, Balogh E, Szabó T, Oláh É. Am J Med Genet A. 2012;158A:869–876. doi: 10.1002/ajmg.a.35236. [DOI] [PubMed] [Google Scholar]

[REF38] 38.Molecular mapping of 21 features associated with partial monosomy 21: involvement of the APP-SOD1 region. Chettouh Z, Croquette MF, Delobel B, et al. https://pmc.ncbi.nlm.nih.gov/articles/PMC1801243/ Am J Hum Genet. 1995;57:62–71. [PMC free article] [PubMed] [Google Scholar]

[REF39] 39.Ocular phenotype associated with DYRK1A variants. Méjécase C, Way CM, Owen N, Moosajee M. Genes (Basel) 2021;12 doi: 10.3390/genes12020234. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF40] 40.Whole-exome sequencing identified a novel DYRK1A variant in a patient with intellectual developmental disorder, autosomal dominant 7. Obara K, Abe E, Toyoshima I. https://www.cureus.com/articles/130318-whole-exome-sequencing-identified-a-novel-dyrk1a-variant-in-a-patient-with-intellectual-developmental-disorder-autosomal-dominant-7. Cureus. 2023;15:0. doi: 10.7759/cureus.33379. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF41] 41.Germline mutations in genes within the MAPK pathway cause cardio-facio-cutaneous syndrome. Rodriguez-Viciana P, Tetsu O, Tidyman WE, et al. Science. 2006;311:1287–1290. doi: 10.1126/science.1124642. [DOI] [PubMed] [Google Scholar]

[REF42] 42.Heterozygous variants in ZBTB7A cause a neurodevelopmental disorder associated with symptomatic overgrowth of pharyngeal lymphoid tissue, macrocephaly, and elevated fetal hemoglobin. von der Lippe C, Tveten K, Prescott TE, et al. Am J Med Genet A. 2022;188:272–282. doi: 10.1002/ajmg.a.62492. [DOI] [PubMed] [Google Scholar]

[REF43] 43.PIAS4 is associated with macro/microcephaly in the novel interstitial 19p13.3 microdeletion/microduplication syndrome. Nevado J, Rosenfeld JA, Mena R, et al. Eur J Hum Genet. 2015;23:1615–1626. doi: 10.1038/ejhg.2015.51. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF44] 44.The past, present, and future for constitutional ring chromosomes: a report of the international consortium for human ring chromosomes. Li P, Dupont B, Hu Q, et al. https://www.cell.com/hgg-advances/fulltext/S2666-2477(22)00055-0. HGG Adv. 2022;13:100139. doi: 10.1016/j.xhgg.2022.100139. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF45] 45.Prenatal diagnosis and molecular cytogenetic characterization of a pure ring chromosome 21 with a 4.657-Mb 21q22.3 deletion. Chen CP, Wang LK, Chern SR, et al. Taiwan J Obstet Gynecol. 2021;60:157–160. doi: 10.1016/j.tjog.2020.11.024. [DOI] [PubMed] [Google Scholar]

[REF46] 46.Molecular characterization of de novo ring chromosome 21 in a child with seizures, growth retardation, and multiple congenital anomalies. Ambulkar PS, Liehr T, Jain M, Waghmare J, Gangane N, Narang P, Pal AK. https://link.springer.com/article/10.1007/s12041-023-01439-5. J Genet. 2023;102:44. [PubMed] [Google Scholar]

[REF47] 47.Genotype-phenotype correlations in Down syndrome identified by array CGH in 30 cases of partial trisomy and partial monosomy chromosome 21. Lyle R, Béna F, Gagos S, et al. Eur J Hum Genet. 2009;17:454–466. doi: 10.1038/ejhg.2008.214. [DOI] [PMC free article] [PubMed] [Google Scholar]

[REF48] 48.Mimicking hypoxic-ischemic encephalopathy in a newborn with 21q deletion originating from ring chromosome 21. Moon JU, Yum SK. Children (Basel) 2023;10 doi: 10.3390/children10091461. [DOI] [PMC free article] [PubMed] [Google Scholar]

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Congenital Anomalies in a Neonate With Partial Monosomy of Chromosome 21 q Arm: A Case Report

Praisy Joy

Sudeshna Datta

Sanjukta Sahoo

Tapas Kumar Som

Prabhas R Tripathy

Manisha R Gaikwad

Pavithra Ayyanar

Sunil K Raghav

Abstract

Introduction

Case presentation

Figure 1. Cytogenetic analysis reveals r(21) and deletion of q arm.

Figure 2. Whole genome analysis uncovered partial monosomy of chromosome 21 and reciprocal deletion and duplication on chromosome 19.

Discussion

Conclusions

Appendices

Figure 3. Distribution of structural variants.

Table 1. Genes annotated in the copy-number variant (CNV) region.

Table 2. Gene-phenotype correlation list from VarElect.

Table 3. Functional annotation of structural variants.

Disclosures

Author Contributions

References

ACTIONS

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PERMALINK

Congenital Anomalies in a Neonate With Partial Monosomy of Chromosome 21 q Arm: A Case Report

Praisy Joy

Sudeshna Datta

Sanjukta Sahoo

Tapas Kumar Som

Prabhas R Tripathy

Manisha R Gaikwad

Pavithra Ayyanar

Sunil K Raghav

Abstract

Introduction

Case presentation

Figure 1. Cytogenetic analysis reveals r(21) and deletion of q arm.

Figure 2. Whole genome analysis uncovered partial monosomy of chromosome 21 and reciprocal deletion and duplication on chromosome 19.

Discussion

Conclusions

Appendices

Figure 3. Distribution of structural variants.

Table 1. Genes annotated in the copy-number variant (CNV) region.

Table 2. Gene-phenotype correlation list from VarElect.

Table 3. Functional annotation of structural variants.

Disclosures

Author Contributions

References

ACTIONS

PERMALINK

RESOURCES

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