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Table 1 VCI displayed information type and source

From: ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines

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]