A Likelihood Ratio Approach for Utilizing Case-Control Data in the Clinical Classification of Rare Sequence Variants: Application to BRCA1 and BRCA2

Table 1

Statistically significant associated variants with breast cancer risk estimated by logistic regression (based on the ACMG/AMP PS4 criterion).

Gene	Variant_ID (GRCh37/hg19)	HGVS nucleotide	HGVS protein	Variant carriers		OR (95% CI)	value
				Cases	Controls
				(frequency)	(frequency)
BRCA2	chr13_32937506_C_G	c.8167G > C	p. (Asp2723His)			12.30 (1.66-91.23)	0.014
	chr13_32954180_C_T	c.9154C > T	p. (Arg3052Trp)			8.32 (1.04-66.48)	0.045

Variant nomenclature according to BRCA2 (NM_000059.3, NP_000050.2). OR: odds ratio; CI: confidence interval.