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

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

Rare missense variants (MAF ≤ 0.001)	Number of carriers		Number of total subjects		p Value^a	OR	95% CI
Rare missense variants (MAF ≤ 0.001)	Cases	Control participants	Cases	Control participants	p Value^a	OR	95% CI
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

Abbreviations: CADD Combined Annotation Dependent Depletion, MAF Minor allele frequency, PolyPhen-2 Polymorphism Phenotyping version 2, REVEL Rare exome variant ensemble learner
^aPearson’s chi-square test with the Yates correction

ISSN: 1465-542X