ClinVar Miner

Submissions for variant NM_007294.3(BRCA1):c.81-13C>G (rs56328013)

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Total submissions: 15
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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) RCV000031282 SCV000244412 benign Breast-ovarian cancer, familial 1 2015-08-10 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 = 0.000301. Also class 1 based on frequency >1% in an outbred sampleset. Frequency 0.0122 (African), derived from 1000 genomes (2012-04-30).
Counsyl RCV000031282 SCV000154032 likely benign Breast-ovarian cancer, familial 1 2014-04-05 criteria provided, single submitter literature only
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000723932 SCV000202276 uncertain significance not provided 2014-03-17 criteria provided, single submitter clinical testing
GeneDx RCV000723932 SCV000209900 likely benign not provided 2021-06-17 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 26287763, 21523855, 22034289, 22505045, 16267036, 21673748, 17924331, 21990134, 23893897, 25556971, 30209399, 31143303)
Invitae RCV001080468 SCV000261618 benign Hereditary breast and ovarian cancer syndrome 2020-12-07 criteria provided, single submitter clinical testing
Baylor Genetics RCV000474249 SCV000540979 benign Familial cancer of breast 2017-02-23 criteria provided, single submitter clinical testing
Color Health, Inc RCV000579728 SCV000683364 benign Hereditary cancer-predisposing syndrome 2015-10-09 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000152870 SCV000806984 benign not specified 2016-10-03 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000031282 SCV001287537 likely benign Breast-ovarian cancer, familial 1 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Sharing Clinical Reports Project (SCRP) RCV000031282 SCV000053887 benign Breast-ovarian cancer, familial 1 2008-07-29 no assertion criteria provided clinical testing
Breast Cancer Information Core (BIC) (BRCA1) RCV000031282 SCV000144221 uncertain significance Breast-ovarian cancer, familial 1 2002-05-29 no assertion criteria provided clinical testing
Brotman Baty Institute,University of Washington RCV000031282 SCV001237811 not provided Breast-ovarian cancer, familial 1 no assertion provided in vitro
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001357880 SCV001553474 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The BRCA1 c.81-13C>G variant was identified in the literature but a frequency in an affected population was not provided. The variant was determined by multiple studies, using RNA analysis and a posterior probability model, to be likely neutral (Easton 2007, Houdayer 2012, Lindor 2012). The variant was also identified in dbSNP (ID: rs56328013) as "With Likely benign, other allele", ClinVar (classified as benign by ENIGMA expert panel, Invitae, SCRP and three other submitters; as likely benign by GeneDx; and as uncertain significance by two submitters), and in LOVD 3.0 (11x). The variant was not identified in UMD-LSDB. The variant was identified in control databases in 63 of 272198 chromosomes (1 homozygous) at a frequency of 0.0002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 54 of 23680 chromosomes (freq: 0.002, increasing the likelihood this could be a low frequency benign variant), Latino in 6 of 33822 chromosomes (freq: 0.0002), European in 1 of 124238 chromosomes (freq: 0.000008), and South Asian in 2 of 29862 chromosomes (freq: 0.00007), while the variant was not observed in the Other, Ashkenazi Jewish, East Asian, or Finnish populations. The variant occurs outside of the splicing consensus sequence and 2 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000152870 SCV001927764 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000152870 SCV001951651 benign not specified no assertion criteria provided clinical testing

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