ClinVar Miner

Submissions for variant NM_007294.3(BRCA1):c.4097-10G>A (rs80358057)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000112252 SCV001161514 benign Breast-ovarian cancer, familial 1 2019-06-18 reviewed by expert panel curation IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on posterior probability = 0.000573
GeneDx RCV000159886 SCV000209968 benign not specified 2014-09-17 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.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000724122 SCV000225366 uncertain significance not provided 2014-07-09 criteria provided, single submitter clinical testing
Invitae RCV001080607 SCV000289792 benign Hereditary breast and ovarian cancer syndrome 2020-12-03 criteria provided, single submitter clinical testing
Counsyl RCV000112252 SCV000489057 likely benign Breast-ovarian cancer, familial 1 2016-08-09 criteria provided, single submitter clinical testing
Color Health, Inc RCV000580105 SCV000683150 likely benign Hereditary cancer-predisposing syndrome 2015-07-30 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000724122 SCV000887686 likely benign not provided 2018-04-15 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000159886 SCV001360562 benign not specified 2020-11-12 criteria provided, single submitter clinical testing Variant summary: BRCA1 c.4097-10G>A alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. Consistent with this, one study report that the variant had no apparent effect on mRNA splicing (Rodriguez-Balada_2016). The variant allele was found at a frequency of 1.6e-05 in 243770 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.4097-10G>A has been reported in the literature in individuals undergoing genetic testing (Judkins_2005, Rodriguez-Balada_2016). However, these reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer. Five other ClinVar submitters including an expert panel (ENIGMA) classified the variant as likely benign or benign. Based on the evidence outlined above, the variant was classified as benign.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001289733 SCV001477711 likely benign none provided 2020-04-01 criteria provided, single submitter clinical testing
Breast Cancer Information Core (BIC) (BRCA1) RCV000112252 SCV000144973 uncertain significance Breast-ovarian cancer, familial 1 2002-05-29 no assertion criteria provided clinical testing

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