A benchmark database for variations


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Benign variant

DATASET 1

VariSNP

VariSNP contains datasets selected from dbSNP which were filtered for disease-related variants found in ClinVar, Swiss-Prot and PhenCode. The datasets are categorized according to the functional classes used in dbSNP.

    VariSNP

Reference: Schaafsma G, Vihinen M, 2015. VariSNP: A benchmark database for neutral variations from dbSNP. Hum Mutat. 2015 Feb; 36(2):161-166. doi: 10.1002/humu.22727.  PUBMED  

DATASET 2

Dataset for common variations in various populations in ExAC

63,197 amino acid substitutions having allele frequencies ≥1% and <25% in any of the populations in the ExAC database.

    ExAC
  1. ExAC AAS data
  2. ClinVar test data

Reference: Niroula A, Vihinen M (2019) How good are pathogenicity predictors in detecting benign variants?. PLOS Computational Biology 15(2): e1006481. https://doi.org/10.1371/journal.pcbi.1006481.  PUBMED  


Last updated: 2022-04-09 by Niloofar Shirvanizadeh.