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] |