Characterization of BRCA1 and BRCA2 variants in multi-ethnic Asian cohort from a Malaysian case-control study

BMC Cancer

Table 2 BRCA1 variants detected in Malaysian carriers by genotyping

HGVS cDNA	HGVS protein	Reported in BIC^a	AGVGD^b	PolyPhen-2^c	SIFT^d	MAF^e (%)	VF^f in controls (%)	Breast cancer cases	Healthy controls	OR^g	95% CI	p-value
c.571G > A	p.Val191Ile	10	C0	Benign	Damaging	0.30	0.75	5/1218	11/1464	0.53	0.18–1.54	0.242
c.823G > A	p.Gly275Ser	4	C0	Probably damaging	Damaging	0.08	0.14	4/2089	2/1464	1.49	0.27–8.25	0.650
c.1036C > T	p.Pro346Ser	4	C0	Benign	Tolerated	0.13	0.14	5/1219	2/1464	3.30	0.64–17.09	0.155
c.2286A > T	p.Arg762Ser	3	C0	Benign	Damaging	0.13	0.07	6/1218	1/1463	7.44	0.89–62.32	0.064
c.2726A > T	p.Asn909Ile	2	C0	Possibly damaging	Damaging	0.13	0.27	5/2091	4/1462	0.90	0.24–3.37	0.874
c.3625 T > G	p.Leu1209Val	1	C0	Possibly damaging	Damaging	0.04	0.14	1/2058	2/1461	0.18	0.02–2.05	0.168
c.3662A > C	p.Glu1221Ala	3	C0	Probably damaging	Damaging	0.07	0.21	1/1215	3/1454	0.44	0.05–4.19	0.471

^a Breast Cancer Information Core (http://research.nhgri.nih.gov/bic/), an open access online breast cancer mutation database assessed by Oct 2015
^b AGVGD grades: C0, C15, C25, C35, C45, C55, C65 with C65 most likely to interfere with function and C0 least likely. The probability was assessed using the alignment of which from human to sea urchin in BRCA1
^c PolyPhen-2 grades: Benign, Possibly damaging, Probably damaging
^d SIFT grades: Tolerated, Damaging
^e Minor allele frequency, which was detected in the entire cohort
^f Variant frequency, which was detected only in healthy controls
^g Odds ratio, adjusted for ethnicity, age and family history using logistic regression

ISSN: 1471-2407