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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