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Basic variant consequence annotation

  • VEP v113 - Variant Effect Predictor (GENCODE v47 as gene reference database (v19 for grch37))

Insilico predictions of effect of coding variants

  • dBNSFP - database of non-synonymous functional predictions (v5.0, January 2025)

Variant frequency databases

  • gnomAD - germline variant frequencies exome-wide (r2.1.1 (non-cancer subject allele frequencies), r4.1)
  • dbSNP - database of short genetic variants (build 156)
  • Cancer Hotspots - a resource for statistically significant mutations in cancer (v2, 2017)

Variant databases of clinical utility

  • ClinVar - database of clinically related variants (March 2025)
  • CIViC - clinical interpretations of variants in cancer (March 13th 2025)

Protein domains/functional features

Cancer gene knowledge bases

Phenotype ontologies