ClinVar Miner

Submissions for variant NM_007294.3(BRCA1):c.5153-26A>G (rs80358109)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000112532 SCV000784867 likely benign Breast-ovarian cancer, familial 1 2017-01-18 criteria provided, single submitter clinical testing
Cancer Variant Interpretation Group UK, Institute of Cancer Research, London RCV001253796 SCV001429668 uncertain significance Hereditary breast and ovarian cancer syndrome 2020-02-17 criteria provided, single submitter clinical testing Data included in classification: Case control comparison of UK familial cases against ethnically matched population data (7/25,773 in familial UK cases against 0/23,509 NFE controls from GnomAD genome sequencing and UK 100,000 genome project pexact= 0.016) (PS4_strong). 1/8 segregation in one large UK family (PP1_sup). UK Family 1: Homozygous Iranian case (from consanguineous family) with normal phenotype in adulthood (age 34), no cancer and normal chromosome breakage in lymphocytes. Additional studies inc. RNA and skin biopsy were sought from this patient could not be attained. (BS2_strong). Absent from the remainder of the GnomAD population (PM2_sup). Additional data (not included in classification): In silico analysis supports aberration of splicing compared to WT due to experimentally-proven intronic branch site. Functional evidence conflicting: Mini-gene assay: suggestive of incomplete skipping of exon 19. Published RNA analyses: estimated that transcripts lacking exon 19 (41bp) account for 30-40% of all BRCA1 transcripts in blood, inferring that 10-20% of transcripts expressed from the variant allele are of full length. See also: Steffensen et al Eur J Hum Genet 2014, Rosenthal ET et al, Clin Genet 2015, Mercer, Genome Res 2015. Patient-derived RNA assay from UK diagnostic labs demonstrated the variant to cause out of frame deletion of exon 19. This results in a PTC in exon 20. Estimation that transcripts lacking exon 19 account for 30-40% of all BRCA1 transcripts in blood. Haploid yeast saturation genome editing assay shown to be functional (Findlay et al, 2018).
Breast Cancer Information Core (BIC) (BRCA1) RCV000112532 SCV000145354 uncertain significance Breast-ovarian cancer, familial 1 2001-02-15 no assertion criteria provided clinical testing
Brotman Baty Institute,University of Washington RCV000112532 SCV001242236 not provided Breast-ovarian cancer, familial 1 no assertion provided in vitro

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