Table 1.

Calculations of positive predictive value (PPV), negative predictive value (NPV), sensitivity, specificity, and accuracy for BRCA1 (N = 131 Benign, N = 34 Pathogenic) and BRCA2 (N = 129 Benign, N = 13 Pathogenic).

Gene	PolyPhen-2										SIFT
	HumDiv					HumVar					PPV	NPV (%)	Sensitivity	Specificity	Accuracy
	PPV	NPV	Sensitivity	Specificity	Accuracy	PPV	NPV	Sensitivity	Specificity	Accuracy
BRCA1	32.61% (28.00% to 37.58%)	94.52% (87.14% to 97.77%)	88.24% (72.55% to 96.70%)	52.67% (43.77% to 61.45%)	60.00% (52.10% to 67.54%)	33.85% (26.52% to 42.03%)	88.00% (82.08% to 92.15%)	64.71% (46.49% to 80.25%)	67.18% (58.43% to 75.12%)	66.67% (58.92% to 73.80%)	32.38% (29.03% to 35.92%)	100	100% (89.72% to 100.00%)	45.80% (37.07% to 54.73%)	56.97% (49.04% to 64.64%)
BRCA2	19.12% (16.21% to 22.41)	100%	100% (75.29% to 100.00%)	57.36% (48.36% to 66.03%)	61.27% (52.74% to 69.32%)	27.91% (21.52% to 35.33%)	98.99% (93.70% to 99.85%)	92.31% (63.97% to 99.81%)	75.97% (67.66% to 83.05%)	77.46% (69.70% to 84.05%)	17.11% (14.74% to 19.76%)	100	100% (75.29% to 100.00%)	51.16% (42.21% to 60.06%)	55.63% (47.07% to 63.96%)