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Table 2 Clinical Utility. Top panel. Gene-specific clinical utilities for the top ten ClinVar genes ranked by number of submitted variants. Bottom panel. Coding, non-coding and combined clinical utility for all ClinVar variants. Pathogenic thresholds for each tool were determined as in Fig. 3

From: The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool

Gene VVP CADD SIFT
BRCA2 0.971 0.893 0.004
BRCA1 0.971 0.876 0.003
SCN1A 0.966 0.914 0.277
MLH1 0.943 0.950 0.057
MSH2 0.984 0.973 0.050
LDLR 0.989 0.890 0.033
DMD 0.959 0.932 0.030
ATM 0.957 0.953 0.021
FBN1 0.974 0.935 0.233
CFTR 0.945 0.930 0.073
Utility (All ClinVar Variants)
Coding 0.970 0.900 0.792
Non-coding 0.917 0.715 0.000
Both 0.947 0.818 0.134