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Table 1 Data source for the variants and pathogenicity interpretation

From: CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations

Data name Data source Number of pathogenic variants Number of neutral variants
Training dataset ClinVar (≥ 1 stars) 10,370 14,954
VKGL (≥ 1 lab support) 581 11,129
van der Velde et al. [29] 30,187 274,112
Total * 40,681 293,920
Benchmark dataset ClinVar (≥ 2 stars) 5421 20
VKGL (≥ 2 lab support) 187 11
ExAC 0 5392
Total 5421 5421
Benign Benchmark dataset 1 Niroula et al. [24] 0 60,699
Benign Benchmark dataset 2 GoNL 0 14,426,914
  1. *The total numbers of variants are smaller or equal to the sum of variants from all data sources due to the removal of duplicated variants