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. Author manuscript; available in PMC: 2025 Jun 24.
Published in final edited form as: Genet Med. 2024 Sep 3;26(12):101249. doi: 10.1016/j.gim.2024.101249

Table 1. Candidate coding/noncoding variant pairs.

Gene;
HGNC ID		 Phenotype Coding Variant HGVS;
chr:pos:ref:alt		 Noncoding Region Variant
Normalized
Specific
Disease		 Abstracted
Selected
HPO Terms		 Details HGVS;
chr:pos:ref:alt		 gnomAD
FAF		 GEL
AF		 SpliceAI PhyloP CADD
GAA;
HGNC:4065		 Limb girdle muscular dystrophy Abnormality of the calf musculature; muscular dystrophy; respiratory insufficiency;
Abnormality of the eye; progressive muscle weakness		 NC_000017.11:g.80118288G>A;
ENST00000302262.8:c.
2577G>A;
p.(Trp859Ter);
chr17:80118288:G:A
Nonsense		 NC_000017.11:g.80101399C>G;
NG_029761.1:g.69768C>G;
chr17:80101399:C:G
Core Promoter		 2.75 × 10−3 3.17 × 10−3 NA −0.19 5.88
NPHP3;
HGNC:7907		 Proteinuric renal disease Abnormal renal corpuscle morphology; abnormal liver morphology; abnormal urine metabolite level NC_000003.12:g.132691199G>A;
ENST00000337331.10:
c.2563C>T;
p.(Gln855Ter);
chr3:132691199:G:A
Nonsense		 NC_000003.12:g.132684549C>T;
ENST00000337331.10:c.3570
+5G>A;chr3:132684549:C:T
Intronic		 5.14 × 10−6 8.95 × 10−5 0.04 6.15 21.0
ALMS1;
HGNC:428		 Cone dysfunction syndrome Abnormal visual electrophysiology; Abnormal eye physiology; Abnormal retinal morphology;
Abnormality of vision		 NC_000002.12:g.73572649del;
ENST00000613296.6:c.
10772del;
p.(Thr3591LysfsTer6);
chr2:73572648:AC:A Frameshift		 NC_000002.12:g.73573562G>A;
ENST00000613296.6:c.11547 +138G>A;
chr2:73573562:G:A
Intronic		 1.72 × 10−3 1.73 × 10−3 0.01 3.84 20.2
LAMA2;
HGNC:6482		 Congenital myopathy Abnormal skeletal muscle morphology; muscle weakness; abnormal muscle physiology; abnormal joint physiology NC_000006.12:g.129316089C>T;
ENST00000421865.3:c.3976C>T;
p.(Arg1326Ter);
chr6:129316089:C:T
Nonsense		 NC_000006.12:g.129475370dup;
ENST00000421865.3:c.7440
-20dup; chr6:129475360:G:GT
Intronic		 4.71 × 10−4 5.88 × 10−4 0.10 NA 8.48
IGHMBP2;
HGNC:5542		 Charcot-Marie-
Tooth disease		 Peripheral axonal degeneration NC_000011.10:g.68936909del;
ENST00000255078.8:
c.2429del;
p.(Pro810LeufsTer21);
chr11:68936904:GC:G Frameshift		 NC_000011.10:g.68929807G>A;
ENST00000255078.8:c.1235
+450G>A;
chr11:68929807:G:A
Intronic		 9.51 × 10−5 1.66 × 10−4 0.12 −1.91 0.21
PKHD1;
HGNC:9016		 Cystic kidney disease Abnormality of urine homeostasis; abnormality of urethra; abnormality of the kidney; abnormal renal morphology NC_000006.12:g.52028249G>A;
ENST00000371117.8:
c.3467C>T;
p.(Ser1156Leu);
chr6:52028249:G:A Missense		 NC_000006.12:g.
51882440T>C;
ENST00000371117.8:c.7350
+653A>G; chr6:51882440:T:
C Intronic		 0.00 7.68 × 10−5 0.95 −0.30 8.22
PAH;
HGNC:8582		 Undiagnosed metabolic disorders Abnormality of metabolism/ homeostasis; tremor;
abnormality of bone mineral density		 NC_000012.12:g.102844359G>C;
ENST00000553106.6:c.1042C>G;
p.(Leu348Val);
chr12:102844359:G:C Missense		 NC_000012.12:g.102843790C>T;
ENST00000553106.6:
c.1066-11G>A;
chr12:102843790:C:T Intronic		 3.74 × 10−4 3.84 × 10−4 0.98 0.88 23.5

Shown are variant details, selected annotations, and phenotypic data relating to the proband. All chromosome coordinates related to GRCh38. AF, allele frequency; FAF, gnomAD v3.0 filtering AF; HPO, Human Phenotype Ontology.