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Table 1 Concordance rate of different combination of algorithms

From: Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines

Variant assertion in ClinVar Variant source Algorithms Variants (n) Concordance (n (%)) False concordance (n (%))
Benign ClinVar* All 18 7346 382 (5.2) 57 (0.8)
Pathogenic ClinVar* All 18 7473 2930 (39.2) 2 (0.03)
Benign ClinVar** All 18 1914 86 (4.5) 12 (0.6)
Pathogenic ClinVar** All 18 1052 492 (46.8) 0 (0)
Benign ClinVar* Polyphen, SIFT, CADD, PROVEAN, MutationTaster 7346 2464 (33.5) 815 (11.1)
Pathogenic ClinVar* Polyphen, SIFT, CADD, PROVEAN, MutationTaster 7473 5904 (79.0) 68 (0.9)
Benign ClinVar* Polyphen, SIFT, CADD 7346 3392 (46.2) 1340 (18.2)
Pathogenic ClinVar* Polyphen, SIFT, CADD 7473 6342 (84.9) 156 (2.1)
  1. ClinVar *: ClinVar variants with one star or above review status
  2. ClinVar **: ClinVar variants with two stars or above review status