ClinVar Miner

Submissions for variant NM_007294.3(BRCA1):c.80+7C>T (rs80358098)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000111710 SCV000489149 likely benign Breast-ovarian cancer, familial 1 2016-08-30 criteria provided, single submitter clinical testing
Invitae RCV000936794 SCV001082566 likely benign Hereditary breast and ovarian cancer syndrome 2020-08-24 criteria provided, single submitter clinical testing
Color Health, Inc RCV001176121 SCV001339970 likely benign Hereditary cancer-predisposing syndrome 2019-03-29 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001193744 SCV001362812 uncertain significance not specified 2019-06-06 criteria provided, single submitter clinical testing Variant summary: BRCA1 c.80+7C>T 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 4e-06 in 250986 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.80+7C>T has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (Judkins_2005). This report does not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cite variant as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance.
Breast Cancer Information Core (BIC) (BRCA1) RCV000111710 SCV000144213 uncertain significance Breast-ovarian cancer, familial 1 2003-12-23 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001354623 SCV001549284 uncertain significance Malignant tumor of breast no assertion criteria provided clinical testing The BRCA1 c.80+7C>T variant was not identified in the literature nor was it identified in the Cosmic, MutDB, LOVD 3.0, UMD-LSDB, BIC Database, ARUP Laboratories, or Zhejiang Colon Cancer Database. The variant was identified in dbSNP (ID: rs80358098) as “With Likely benign, other allele”, ClinVar (as uncertain significance by BIC and likely benign by Counsyl), and Clinvitae databases. The variant was identified in control databases in 1 of 245756 chromosomes at a frequency of 0.000004 (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include Latino in 1 of 33580 chromosomes (freq: 0.00003), while the variant was not observed in the African, Other, European (Non-Finnish), Ashkenazi Jewish, East Asian, European (Finnish), and South Asian populations. The variant occurs outside of the splicing consensus sequence and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) 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. This variant is classified as a variant of uncertain significance.

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