Table 1.
Summary of integrated data sources in VarCards2
| Category | Data source |
|---|---|
| Part one: variation-level implication | |
| Allele frequency | gnomAD, ExAC, 1000 Genomes, ESP, Kaviar, HRC, Mitomap |
| In silico function and pathogenicity prediction | ReVe, CADD, DANN, Eigen, Fathmm-MKL, FATHMM, FitCons, GenoCanyon, REVEL, SIFT, PolyPhen2-HDIV, PolyPhen2-HVAR, LRT, MutationTaster, MutationAssessor, PROVEAN, VEST4, MetaSVM, MetaLR, M-CAP, GERP++, phyloP100way-vertebrate, phastCons100way-vertebrate, SiPhy, Eigen-PC, Fathmm-XF, SIFT4G, LINSIGHT, MutPred2, MVP, MPC, PrimateAI, DEOGEN2, BayesDel-addAF, BayesDel-noAF, ClinPred, LIST-S2, ALoFT, bStatistic, phyloP470way-mammal, phyloP17way-primate, phastCons470way-mammal, phastCons17way-primate, gMVP, VARITY-R, VARITY-ER, VARITY-R-LOO, VARITY-ER-LOO, AlphaMissense, FitCons2, Funseq2, ReMM, CScape, Orion, FIRE, PAFA, CDTS, DVAR, ncER, regBase-REG, regBase-CAN, regBase-PAT, Divan-TSS, Divan-Region, CADD-splice, SCAP, spliceAI, dpsi-max-tissue, dpsi-zscore, dbscSNV-ADA-SCORE, dbscSNV-RF-SCORE, MaxEntScan, GeneSplicer, ESRseq, Spliceogen, Squirl, RegSNPs-intron, MMSplice, KipoiSplice, Synvep, SPiCE-MES, SPiCE-SSF, SPiCE, CADD-SV, AnnotSV, ClassifyCNV, StrVCTVRE, FatHmmW, EFIN-SP, EFIN-HD, PANTHER, PhD-SNP, SNAP, Mitoclass1, SNPDryad, Meta-SNP, CAROL, Condel, COVEC-WMV, MtoolBox, APOGEE, MitoTIP, PON-Classification, CAPICE, FATHMM-indel, PROVEAN-indel |
| Disease-related | ClinVar, InterVar, ICGC, COSMIC, GWAS Catalog |
| Variant information | Gene4Denovo, SPCards |
| Regulatory information | GTEx, VARAdb, GREEN-DB, EPimap EPigenomics |
| Part two: gene-level implication | |
| Basic information | NCBI Gene, Entrez, OMIM, HGNC, Ensembl, GeneCards, UniProtKB |
| Genic intolerance | RVIS, LoFtool, GDI, Episcore, heptanucleotide context intolerance score, pLI score |
| Gene function | Gene Ontology, UniProtKB, InterPro, NCBI BioSystems, InBio Map™ |
| Disease-related | OMIM, ClinVar, GeneReviews, ClinGen, Human Phenotype Ontology, GenCC, DECIPHER, Orpha data, DisGeNET, GTR, Noncode, MGI, Gene4Denovo |
| Gene expression | BrainSpan, GTEx, Allen Brain Atlases, The Human Protein Atlas |
| Target drug | DGIdb, PharmGKB, CTD, Drug Central, Drug Target Commons |
Note: gnomAD, Genome Aggregation Database; ExAC, Exome Aggregation Consortium; 1000 Genomes, The 1000 Genomes Project; ESP, Exome Sequencing Project; Kaviar, Known VARiants; HRC, Haplotype Reference Consortium; Mitomap, A Human Mitochondrial Genome Database; CADD, Combined Annotation Dependent Depletion; DANN, Deep Neural Network-based Annotation; Fathmm-MKL, Functional Analysis Through Hidden Markov Models-Multitask Learning; FATHMM, Functional Analysis Through Hidden Markov Models; FitCons, Fitness Consequences; REVEL, Rare Exome Variant Ensemble Learner; SIFT, Sorting Intolerant From Tolerant; PolyPhen2-HDIV, Polymorphism Phenotyping v2 - HumDiv model; PolyPhen2-HVAR, Polymorphism Phenotyping v2 - HumVar model; LRT, Likelihood Ratio Test; PROVEAN, Protein Variation Effect Analyzer; ClinVar, Clinical Variation Database; ICGC, International Cancer Genome Consortium; COSMIC, Catalogue of Somatic Mutations in Cancer; GWAS Catalog, Genome-Wide Association Studies Catalog; GTEx, Genotype-Tissue Expression project; NCBI, National Center for Biotechnology Information; OMIM, Online Mendelian Inheritance in Man; HGNC, HUGO Gene Nomenclature Committee; UniProtKB, Universal Protein Knowledgebase; RVIS, Residual Variation Intolerance Score; LoFtool, Loss-of-Function tool; GDI, Gene Damage Index; pLI score, probability of Loss-of-Function Intolerance; ClinGen, The Clinical Genome Resource; GenCC; Gene Curation Coalition; DECIPHER, Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources; GTR, Genetic Testing Registry; MGI, Mouse Genome Informatics; DGIdb, The Drug Gene Interaction Database; PharmGKB, The Pharmacogenomics Knowledgebase; CTD; The Comparative Toxicogenomics Database.