Table 1

Summary of missense variants tested for association with breast cancer risk in Breast Cancer Association Consortium

rs number	Position*	Substitution	Protein alteration	CADD20	PolyPhen	SIFT	MAF	OR (95% CI)	p Value
rs4988345	59924572	c.517C>T	p.Arg173Ser	20.8	Probably damaging	Deleterious	0.0043	1.05 (0.91 to 1.21)	0.49
rs4988346	59924512	c.577G>A	p.Val193Ile	0.342	Benign	Tolerated	0.0044	1.11 (0.97 to 1.28)	0.13
rs4988347	59924505	c.584T>C	p.Leu195Pro	0.578	Benign	Tolerated	0.0022	1.13 (0.93 to 1.37)	0.23
rs28997569	59885956	c.790C>T	p.Arg264Trp	16.72	Probably damaging	Deleterious	0.0011	1.01 (0.76 to 1.34)	0.96
rs28997570	59885856	c.890A>G	p.Lys297Arg	8.669	Benign	Tolerated	0.0016	1.06 (0.84 to 1.34)	0.60
rs4988350	59861668	c.1591T>G	p.Phe531Val	23.8	Probably damaging	Tolerated	0
rs4988349	59861640	c.1619A>T	p.Gln540Leu	16.61	Possibly damaging	Tolerated	0
rs137852986	59793412	c.2392C>T	p.Arg798Ter	39	–	–	0.00021	1.09 (0.58 to 2.03)	0.79
rs28904918	59770797	c.2569A>G	p.Ile857Val	18.50	Probably damaging	Tolerated	6×10⁻⁵	0.87 (0.21 to 3.66)	0.85
rs4986764	59763347	c.2755T>C	p.Ser919Pro	4.321	Benign	Deleterious	0.42	1.00 (0.98 to 1.01)	0.66
rs4988356	59763298	c.2804T>G	p.Val935Gly	1.149	Benign	Deleterious	2×10⁻⁵	0.44 (0.039 to 5.00)	0.51

*hg19 (build 37) position.
CADD, Combined Annotation-Dependent Depletion scores; MAF, minor allele frequency.