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Table 2 Joint distribution of BRCA1/BRCA2 variants (unclassified variants) according to classification using allele frequency, Polyphen, and sequence conservation

From: Evaluation of unclassified variants in the breast cancer susceptibility genes BRCA1 and BRCA2using five methods: results from a population-based study of young breast cancer patients

Gene Classification method Level Conservation Frequency
    Low Moderate High HFUV LFUV
BRCA1 Frequency Low risk (HFUV) 3 1 1   
   High risk (LFUV) 11 13 15   
   P valuea    0.26   
  Polyphen Benign missense 12 10 6 4 24
   Possible damaging 2 3 4 1 8
   Probably damaging 0 1 6 0 7
   P valuea    0.002   0.39
BRCA2 Frequency Low risk (HFUV) 10 6 2   
   High risk (LFUV) 23 23 31   
   P valuea    0.018   
  Polyphen Benign missense 26 11 7 11 33
   Possible damaging 5 10 10 5 20
   Probably damaging 2 8 16 2 24
   P valuea    <0.001   0.089
  1. LFUV, low-frequency unclassified variant; HFUV, high-frequency unclassified variant. aBased on the exact Mantel–Haenszel chi-square test.