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Table 3 Performance overview of all tested tools

From: GAVIN: Gene-Aware Variant INterpretation for medical sequencing

Tool Median sensitivity (%) Median specificity (%)
CADD (thr. 15) 93.6 57.1
CADD (thr. 20) 90.4 68.8
CADD (thr. 25) 71.5 85.3
Condel 70.3 39.5
DANN 63.8 66.7
FATHMM 69.5 61.9
FunSeq 61.7 50.2
GAVIN 91.4 76.9
GWAVA 47.6 26.2
MSC_ClinVar95CI 84.7 64.4
MSC_HGMD99CI 97.1 25.7
PolyPhen2 68.0 46.8
PONP2 47.5 26.9
PredictSNP2 66.8 70.6
PROVEAN 65.9 62.1
SIFT 67.9 57.9