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) |