ClinVar Miner

Submissions for variant NM_007299.4(BRCA1):c.1018C>G (p.Arg340Gly) (rs41293455)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000048522 SCV000076535 likely benign Hereditary breast and ovarian cancer syndrome 2017-12-27 criteria provided, single submitter clinical testing
Ambry Genetics RCV000129043 SCV000172955 likely benign Hereditary cancer-predisposing syndrome 2017-12-20 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Other data supporting benign classification,In silico models in agreement (benign)
Michigan Medical Genetics Laboratories,University of Michigan RCV000019245 SCV000195928 uncertain significance Breast-ovarian cancer, familial 1 2014-11-03 criteria provided, single submitter clinical testing
Counsyl RCV000019245 SCV000488475 benign Breast-ovarian cancer, familial 1 2016-04-20 criteria provided, single submitter clinical testing
GeneDx RCV000427206 SCV000512308 likely benign not specified 2017-10-09 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Color RCV000129043 SCV000683171 likely benign Hereditary cancer-predisposing syndrome 2015-01-20 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588512 SCV000699131 uncertain significance not provided 2016-03-23 criteria provided, single submitter clinical testing Variant summary: The BRCA1 c.4327C>G variant affects a non-conserved nucleotide, resulting in amino acid change from Arg to Gly. 3/4 in-silico tools predict this variant to be benign (SNPs&GO not captured due to low reliability index); and multiple functional studies classify the variant as neutral and have shown R1443G to have comparable to wild type function (Carvalho_2007 and Bouwman_2013). This variant was found in 3/121440 control chromosomes at a frequency of 0.0000247, which does not exceed maximal expected frequency of a pathogenic BRCA1 allele (0.0010005). In addition, one clinical laboratory classified this variant as likely benign without evidence to independently evaluate. The variant has been cited in breast and ovarian cancer without evidence of causality (i.e. co-segregation data). The variant has not been reported to co-occur with other pathogenic variants in inherited cancer genes. Because of the absence of clinical information and the lack of functional studies, the variant was classified as a variant of uncertain significance (VUS)-possibly benign until additional information becomes available.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000588512 SCV000885070 likely benign not provided 2017-10-15 criteria provided, single submitter clinical testing The BRCA1 c.4327C>G; p.Arg1443Gly variant is published in the medical literature with a low probability of pathogenicity (Carvalho 2007, Iversen 2011, Lindor 2012). The variant is listed as benign or likely benign by several clinical laboratories in the ClinVar database (Variation ID: 17676). The variant is listed in the dbSNP variant database (rs41293455) with a low allele frequency in the Genome Aggregation Database (9/277118 alleles). The arginine at this position is weakly conserved across species and computational algorithms (AlignGVGD, PolyPhen2, SIFT) predict this variant is tolerated. Additionally, this variant is reported to behave as wild type in at least one functional assay (Bouwman 2013). Considering available information, this variant is classified as likely benign. References: Bouwman P et al. A high-throughput functional complementation assay for classification of BRCA1 missense variants. Cancer Discov. 2013 Oct;3(10):1142-55. Carvalho MA et al. Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis.Cancer Res. 2007 Feb 15;67(4):1494-501. Iversen ES Jr et al. A computational method to classify variants of uncertain significance using functional assay data with application to BRCA1. Cancer Epidemiol Biomarkers Prev. 2011 Jun;20(6):1078-88. Lindor NM et al. A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS). Hum Mutat. 2012 Jan;33(1):8-21.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000588512 SCV000892186 likely benign not provided 2018-09-30 criteria provided, single submitter clinical testing
OMIM RCV000019245 SCV000039533 pathogenic Breast-ovarian cancer, familial 1 1994-12-01 no assertion criteria provided literature only
Breast Cancer Information Core (BIC) (BRCA1) RCV000019245 SCV000145056 uncertain significance Breast-ovarian cancer, familial 1 2002-05-29 no assertion criteria provided clinical testing
CSER_CC_NCGL; University of Washington Medical Center RCV000048522 SCV000503551 uncertain significance Hereditary breast and ovarian cancer syndrome 2016-08-01 no assertion criteria provided research Found in a 37 year old female patient having exome sequencing for an unrelated indication. No known history of breast cancer. Family history of a mother with breast ancer diagnosed at 50, a maternal grandmother who died of breast cancer at age 58 and a paternal grandmother diagnosed with breast and ovarian cancer.

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