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Table 1 Mean Grantham matrix score 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 Number of variants Grantham matrix score
     Mean Standard deviation Minimum Maximum
BRCA1 Allele frequency Low risk (HFUV) 5 38.2 20.7 10 56
   High risk (LFUV) 39 69.7 45.0 10 194
   P value (t test)   0.13    
  Polyphen Benign missense 28 55.0 42.3 10 180
   Possible damaging 9 65.3 29.4 10 101
   Probably damaging 7 111.9 40.5 71 194
   P for trenda   0.002    
  Sequence conservation Low 14 53.6 44.7 10 180
   Moderate 14 70.9 43.5 10 154
   High 16 73.0 44.2 10 194
   P for trenda   0.24    
BRCA2 Allele frequency Low risk (HFUV) 18 67.7 39.7 5 149
   High risk (LFUV) 77 87.0 52.9 10 205
   P value (t test)   0.15    
  Polyphen Benign missense 44 58.1 41.3 5 194
   Possible-damaging 25 91.4 41.7 21 180
   Probably-damaging 26 118.3 52.3 27 205
   P for trenda   <0.001    
  Sequence conservation Low 33 71.5 49.4 10 194
   Moderate 29 92.1 55.6 5 205
   High 33 87.5 47.8 21 194
   P for trenda   0.20    
  1. LFUV, low-frequency unclassified variant; HFUV, high-frequency unclassified variant. aBased on the F test in a linear regression model.