ClinVar Miner

Submissions for variant NM_007294.4(BRCA1):c.548-9del (rs273902774)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000159865 SCV000209914 likely benign not specified 2018-01-30 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.
Invitae RCV001080904 SCV000253518 benign Hereditary breast and ovarian cancer syndrome 2020-12-06 criteria provided, single submitter clinical testing
Counsyl RCV000031259 SCV000489382 likely benign Breast-ovarian cancer, familial 1 2016-09-27 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000159865 SCV000699265 likely benign not specified 2021-04-10 criteria provided, single submitter clinical testing Variant summary: BRCA1 c.548-9delA alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 2.4e-05 in 250442 control chromosomes, predominantly at a frequency of 0.00038 within the African or African-American subpopulation in the gnomAD database. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.548-9delA has been reported in the literature in individuals affected with breast and/or ovarian cancer (example, Cheng_2017, Diaz-Zabala_2018, Judkins_2005, Fackenthal_2012). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and a predominant consensus as likely benign (n=5)/benign(n=1). Based on the evidence outlined above, the variant was classified as likely benign.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000588280 SCV000702258 uncertain significance not provided 2016-10-03 criteria provided, single submitter clinical testing
Color Health, Inc RCV000776096 SCV000910902 likely benign Hereditary cancer-predisposing syndrome 2016-04-07 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000588280 SCV001469399 likely benign not provided 2019-10-11 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001286028 SCV001472546 likely benign none provided 2019-12-12 criteria provided, single submitter clinical testing
Sharing Clinical Reports Project (SCRP) RCV000031259 SCV000053863 benign Breast-ovarian cancer, familial 1 2009-11-04 no assertion criteria provided clinical testing
Breast Cancer Information Core (BIC) (BRCA1) RCV000031259 SCV000145626 uncertain significance Breast-ovarian cancer, familial 1 2002-06-20 no assertion criteria provided clinical testing
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research RCV000735565 SCV000863703 benign Breast and/or ovarian cancer no assertion criteria provided clinical testing

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