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Table 4 Number of carriers with likely deleterious missense variants predicted by in silico tools

From: Evaluating the breast cancer predisposition role of rare variants in genes associated with low-penetrance breast cancer risk SNPs

Rare missense variants (MAF ≤ 0.001) Number of carriers Number of total subjects p Valuea OR 95% CI
Cases Control participants Cases Control participants
All 406 353 1043 944 0.512 1.07 0.89–1.28
Condel deleterious 174 136 1043 944 0.182 1.19 0.93–1.53
PolyPhen-2 Probably/possibly deleterious 198 164 1043 944 0.384 1.11 0.88–1.41
CADD score ≥ 15 225 173 1043 944 0.08 1.23 0.98–1.54
SIFT deleterious 171 131 1043 944 0.134 1.22 0.94–1.57
REVEL score ≥ 0.5 88 63 1043 944 0.163 1.29 0.91–1.83
Predicted deleterious by all 58 39 1043 944 0.170 1.37 0.89–2.13
  1. Abbreviations: CADD Combined Annotation Dependent Depletion, MAF Minor allele frequency, PolyPhen-2 Polymorphism Phenotyping version 2, REVEL Rare exome variant ensemble learner
  2. aPearson’s chi-square test with the Yates correction