Whole-exome sequencing of BRCA-negative breast cancer patients and case–control analyses identify variants associated with breast cancer susceptibility

Lee, Ning Yuan; Hum, Melissa; Amali, Aseervatham Anusha; Lim, Wei Kiat; Wong, Matthew; Myint, Matthew Khine; Tay, Ru Jin; Ong, Pei-Yi; Samol, Jens; Lim, Chia Wei; Ang, Peter; Tan, Min-Han; Lee, Soo-Chin; Lee, Ann S. G.

doi:10.1186/s40246-022-00435-7

Human Genomics

Table 2 Predicted pathogenicity and classifications from databases for 49 selected variants in 37 genes

From: Whole-exome sequencing of BRCA-negative breast cancer patients and case–control analyses identify variants associated with breast cancer susceptibility

Gene	HGVS	RefSNP	Consequence	Protein Change	CADD Score	ClinVar	ACMG Classification (InterVar)
KMT2C	NM_170606.3:c.C2689T	rs772146328	Stopgain	p.R897X	39.0	–	Pathogenic
KMT2C	NM_170606.3:c.C2710T	rs200662726	Stopgain	p.R904X	37.0	–	Pathogenic
RNF43	NM_001305545.1:c.C311T	rs2680701	Nonsyn. SNV	p.P104L	24.0	–	Benign
RNF43	NM_001305545.1:c.G1589C	rs142097313	Nonsyn. SNV	p.R530P	26.5	–	Uncertain significance
RNF43	NM_001305545.1:c.G647A	rs34523089	Nonsyn. SNV	p.R216H	25.4	–	Benign
GPRIN2	NM_014696.4:c.C983G	rs4445576	Nonsyn. SNV	p.S328C	23.1	–	Benign
MUC4	NM_018406.7:c.G8461A	rs868560707	Nonsyn. SNV	p.D2821N	22.1	–	Uncertain significance
H3F3A	NM_002107.6:c.C344G	rs749423281	Nonsyn. SNV	p.A115G	28.8	–	Uncertain significance
AKAP9	NM_005751.4:c.T3430C	rs141039834	Nonsyn. SNV	p.C1144R	20.5	Conflicting interpretations of pathogenicity	Uncertain significance
TPTE2	NM_199254.2:c.483delT	–	Frameshift del	p.F161Lfs*15	22.0	–	Uncertain significance
HLA-B	NM_005514.8:c.A161G	rs9266183	Nonsyn. SNV	p.D54G	23.6	–	Uncertain significance
NRG1	NM_013962.2:c.G172A	rs113317778	Nonsyn. SNV	p.G58R	23.6	–	Benign
ELN	NM_001278913.2:c.G1498C	rs17855988	Nonsyn. SNV	p.G500R	23.2	Benign	Benign
ERBB3	NM_001982.3:c.A3355T	rs773123	Nonsyn. SNV	p.S1119C	23.8	–	Benign
HLA-A	NM_001242758.1:c.268delA	rs756231831	Frameshift del	p.N90Mfs*2	12.03	–	Uncertain significance
HLA-A	NM_001242758.1:c.C791T	rs41548917	Nonsyn. SNV	p.T264I	25.6	–	Uncertain significance
HLA-A	NM_001242758.1:c.G1055T	rs369261720	Nonsyn. SNV	p.S352I	23.6	–	Uncertain significance
HLA-A	NM_001242758.1:c.G565A	rs41562120	Nonsyn. SNV	p.V189M	22.1	–	Uncertain significance
HLA-A	NM_001242758.1:c.G684A	rs372503438	Stopgain	p.W228X	37.0	–	Uncertain significance
HLA-A	NM_001242758.1:c.T547C	rs758168864	Nonsyn. SNV	p.Y183H	24.4	–	Uncertain significance
ROS1	NM_002944.2:c.C3326T	rs2229079	Nonsyn. SNV	p.S1109L	21.1	–	Benign
HLA-DRB1	NM_002124.3:c.118_122del	rs756741350	Frameshift del	p.P40Efs*21	24.7	–	Uncertain significance
HLA-DRB1	NM_002124.3:c.126_127insTTAAGTTT	rs769556955	Frameshift ins	p.E43Lfs*40	24.6	–	Uncertain significance
HLA-DRB1	NM_002124.3:c.C301T	rs17885222	Nonsyn. SNV	p.R101W	25.5	–	Likely benign
NTRK1	NM_001012331.1:c.C1792T	rs6336	Nonsyn. SNV	p.H598Y	27.8	–	Benign
NTRK1	NM_001012331.1:c.G1820T	rs6339	Nonsyn. SNV	p.G607V	22.0	–	Benign
CHIC2	NM_012110.4:c.G36T	rs368360781	Nonsyn. SNV	p.E12D	22.2	–	Uncertain significance
CNTRL	NM_001330762.2:c.G1009A	rs17292952	Nonsyn. SNV	p.A337T	21.9	–	Uncertain significance
ISX	NM_001303508.2:c.G248A	rs8140287	Nonsyn. SNV	p.R83Q	34.0	–	Uncertain significance
MYO5A	NM_000259.3:c.A3960T	rs61731219	Nonsyn. SNV	p.R1320S	21.7	Benign	Benign
TET2	NM_001127208.2:c.C1088T	rs17253672	Nonsyn. SNV	p.P363L	23.3	–	Uncertain significance
BRD7	NM_001173984.3:c.A44C	–	Nonsyn. SNV	p.Y15S	22.8	–	Uncertain significance
CBFA2T3	NM_005187.6:c.G308C	rs61734177	Nonsyn. SNV	p.R103P	22.5	–	Benign
DCC	NM_005215.4:c.A3578G	rs375401214	Nonsyn. SNV	p.Q1193R	23.1	–	Uncertain significance
PTPRB	NM_001206971.3:c.C3412T	rs61754227	Nonsyn. SNV	p.R1138W	25.1	–	Uncertain significance
RNF213	NM_001256071.3:c.C12847A	rs62077764	Nonsyn. SNV	p.L4283I	23.1	–	Benign
RNF213	NM_001256071.3:c.C13945G	rs61745599	Nonsyn. SNV	p.L4649V	24.4	–	Benign
CLIP1	NM_001247997.1:c.C80T	rs34292795	Nonsyn. SNV	p.T27M	23.3	–	Likely benign
CUX1	NM_001202543.2:c.C3317T	rs782176246	Nonsyn. SNV	p.P1106L	24.8	–	Uncertain significance
FBLN2	NM_001998.3:c.G2569T	rs556004379	Nonsyn. SNV	p.V857L	29.0	–	Uncertain significance
GNAS	NM_016592.4:c.A266G	rs563844600	Nonsyn. SNV	p.E89G	23.8	–	Uncertain significance
MAF	NM_001031804.3:c.G655T	rs1030258012	Nonsyn. SNV	p.G219C	22.2	–	Uncertain significance
MGA	NM_001080541.2:c.C1883A	rs61736074	Nonsyn. SNV	p.P628Q	25.8	–	Uncertain significance
MLLT1	NM_005934.4:c.G889A	rs11880101	Nonsyn. SNV	p.A297T	24.8	–	Uncertain significance
NBEA	NM_015678.4:c.C2317A	–	Nonsyn. SNV	p.L773M	27.3	–	Uncertain significance
NUP214	NM_001318324.2:c.A2263G	rs61756081	Nonsyn. SNV	p.I755V	23.6	Benign	Uncertain significance
PDGFRB	NM_001355016.2:c.G1261A	rs41287110	Nonsyn. SNV	p.E421K	21.2	Benign	Benign
RABEP1	NM_001291581.2:c.G1755C	rs61735455	Nonsyn. SNV	p.M585I	22.6	–	Uncertain significance
ZNF479	NM_001370129.1:c.T1421C	rs200382632	Nonsyn. SNV	p.F474S	23.3	–	Likely benign

A dash (“–”) indicates that a variant does not have a RefSNP accession number

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