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Table 3 Results of final testing using simulated variants

From: Classification of genetic variants in genes associated with Lynch syndrome using a clinical history weighting algorithm

MLH1 Variant type
Pathogenic Benign
 HWA Call Pathogenic 25162 17
Benign 61 50150
No Call 277 333
 Total Trials 25500 50500
 PPV 0.9989
 NPV 0.9992
MSH2 Variant Type
Pathogenic Benign
 HWA Call Pathogenic 24904 29
Benign 69 50306
No Call 527 165
 Total Trials 25500 50500
 PPV 0.9971
 NPV 0.9995
MSH6 Variant Type
Pathogenic Benign
 HWA Call Pathogenic 25038 6
Benign 23 50322
No Call 439 172
 Total Trials 25500 50500
 PPV 0.9992
 NPV 0.9999
  1. Conditional probabilities tables were constructed based on the entire dataset of 79,214 probands
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