Table 1 VCI displayed information type and source
Information type | Displayed data | Data source |
|---|---|---|
Basic Information | • Variant ID • HGVS terms | ClinGen Allele Registry [17] |
• ClinVar Variation ID • ClinVar Overall interpretation • ClinVar Submitted interpretations • ClinVar Primary transcript • RefSeq transcripts • dbSNP variant ID • Entrez Gene ID | NCBI E-utilities [18] | |
• RefSeq transcripts • Ensembl transcripts • Molecular consequences | Ensembl VEP [19] | |
• Monarch Disease Ontology (Mondo) human disease term(s) | Ontology Lookup Service [20] | |
• Phenotypic abnormality term(s) | Human Phenotype Ontology (HPO) [21] | |
Population | • Allele frequencies ◦ gnomAD ◦ ExAC ◦ Exome Sequencing Project | MyVariant.info [22] |
• Allele frequencies ◦ PAGE Study | GGV Browser [23] | |
• Allele frequencies ◦ 1000 Genomes | Ensembl VEP [19] | |
Variant Type | • In silico predictor scores ◦ REVEL ◦ SIFT • PolyPhen2 • LRT • MutationTaster • MutationAssessor ◦ FATHMM ◦ PROVEAN ◦ MetaSVM ◦ MetaLR ◦ CADD ◦ FATHMM-MKL ◦ fitCons • Conservation analysis scores ◦ phyloP100way ◦ phyloP30way ◦ phastCons100way ◦ phastCons30way ◦ GERP++ ◦ SiPhy | MyVariant.info [22] |
Experimental | • Experimental functional data | ClinGen Functional Data Repository (FDRepo) |
Gene-Centric | • Gene symbol | HGNC [24] |
• ExAC constraint scores • UniProt protein ID • GeneCards gene | MyGene.info [25] |