BRCA1 NM_007294.4:c.135-1G>T, Splice_Site

Variant summary: The BRCA1 c.135-1G>T variant involves the alteration of a conserved intronic nucleotide located at a canonical splice site. Mutation taster predicts a damaging outcome for this variant along with 5/5 in silico splice site prediction algorithms predicting the loss of the splice acceptor site. These predictions were confirmed by Tesoriero_HM_2005 which demonstrated the variant to result in exon skipping that creates an in-frame deletion of 26 amino acids from exon 5. The variant was found in 1/111484 control chromosomes at a frequency of 0.000009, which does not exceed the estimated maximal expected allele frequency of a pathogenic BRCA1 variant (0.0010005). It was reported in several HBOC patients and in at least one HBOC family it co-segregated with the disease (Tesoriero_HM_2005). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as Pathogenic. Taken together, this variant is classified as a Pathogenic.

The BRCA1 c.135-1G>T variant disrupts a canonical splice-acceptor site and interferes with normal BRCA1 mRNA splicing. In the published literature, this variant has been reported in multiple individuals and families with breast and/or ovarian cancer (PMIDs: 36451132 (2022), 35464868 (2022), 32885271 (2021), 26187060 (2015), 25452441 (2015), 21324516 (2011), 20020529 (2010), 11179017 (2001), 9333265 (1997)) and at least one individual with prostate cancer (PMID: 18445692 (2008)). In a large-scale breast cancer association study, this variant was observed in a breast cancer case (PMID: 33471991 (2021), see also LOVD (http://databases.lovd.nl/shared)). Assessment of experimental analysis yielded inconclusive results regarding the impact of this variant on protein function (PMID: 30209399 (2018)); however, splicing studies have shown that this variant causes an in-frame deletion of exon 5 of the BRCA1 gene (PMIDs: 30101128 (2018), 16211554 (2005)). In addition, this variant has been reported as pathogenic in multifactorial likelihood studies (PMIDs: 31131967 (2019), 20020529 (2010)). The frequency of this variant in the general population (Genome Aggregation Database, http://gnomad.broadinstitute.org) is uninformative in the assessment of its pathogenicity. Based on the available information, this variant is classified as pathogenic.

The c.135-1G>T variant in BRCA1 has been reported in more than 30 individuals with BRCA1-associated cancers and segregated with breast cancer in 10 relatives from 1 family (Shattuck-Eidens 1997, Risch 2001, Tesoriero 2005, Willems 2008, Rashid 2016, Breast Cancer Information Core (BIC)). This variant has been identified in 2/128060 European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs80358158). This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and functional studies have shown it results in an in-frame deletion of 26 amino acids(Tesoriero 2005, Wappenschmidt 2012). In summary, this variant meets criteria to be classified as pathogenic for HBOC in an autosomal dominant manner. ACMG/AMP criteria applied: PS4, PP1_Strong, PM2, PM4.

The c.135-1G>T intronic pathogenic mutation results from a G to T substitution one nucleotide upstream from coding exon 3 of the BRCA1 gene. This mutation has been identified in multiple breast, ovarian and/or prostate cancer families (Zhang S et al. Gynecol. Oncol. 2011 May;121(2):353-7; Rashid MU et al. Int. J. Cancer 2006 Dec;119(12):2832-9; Tesoriero AA et al. Hum. Mutat. 2005 Nov;26(5):495. Risch HA et al. Am. J. Hum. Genet. 2001 Mar;68(3):700-10. Shattuck-Eidens D et al. JAMA 1997 Oct;278(15):1242-50; Willems AJ et al. Clin. Cancer Res. 2008; 14:2953-61). This variant gives rise to an in -frame deletion of coding exon 3 (also known as exon 5 in the literature-Tesoriero AA et al. Hum Mutat. 2005 Nov;26(5):495; Farber-Katz S et al. Front Oncol, 2018 Jul;8:286). One functional study found that this nucleotide substitution is non-functional in a high throughput genome editing haploid cell survival assay (Findlay GM et al. Nature, 2018 10;562:217-222). Of note, this alteration is also designated as IVS3-1G>T and IVS4-1G>T in the published literature. In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation.

This variant causes a G to T nucleotide substitution at the -1 position of intron 3 of the BRCA1 gene. RNA studies have shown that this variant impacts the splicing of exon 4 that partially encodes the RING domain, which is important for BRCA1 function and is noted to have clinically relevant mutations (PMID: 16211554, 22737296, 30101128). A functional study has shown that this variant impacts BRCA1 function in a haploid human cell proliferation assay (PMID: 30209399). This variant has been reported in at least 7 individuals affected with breast and ovarian cancer (PMID: 11179017, 16211554, 21324516, 25452441, 33471991; Leiden Open Variation Database DB-ID BRCA1_000503) and an individual affected with prostate cancer with a family history of breast cancer (PMID: 18445692). This variant also has been reported with a co-segregation likelihood ratio for pathogenicity of 9528 in one pedigree (PMID: 31131967). This variant has been identified in 2/280296 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.