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

Table 2

Variants with informative LRs in favor of pathogenicity, estimated by the baseline analysis.

Gene	Variant_ID (GRCh37/hg19)	HGVS nucleotide	HGVS protein	Variant carriers		LR
				Cases	Controls
				N (frequency)	N (frequency)
BRCA1	chr17_41234451_A_G	c.4327C > T	p.(Arg1443)			526.71
	chr17_41215947_T_G	c.5096G > T	p.(Arg1699Leu)			307.47
BRCA2	chr13_32937506_C_G	c.8167G > C	p.(Asp2723His)			8193.33
	chr13_32953453_A_G	c.8755-1G > A	p.?		—	41.18
	chr13_32954180_C_T	c.9154C > T	p.(Arg3052Trp)			86.82
	chr13_32968940_A_T	c.9371A > T	p.(Asn3124Ile)		—	3530.99

Variant nomenclature according to BRCA1 (NM_007294.4, NP_009225.1), BRCA2 (NM_000059.3, NP_000050.2). LR: likelihood ratio.