Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_ModeratePM2PP5_Very_Strong
The NM_007294.4(BRCA1):c.135-1G>A variant causes a splice acceptor change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).
BRCA1 (HGNC:1100): (BRCA1 DNA repair associated) This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1 gene contains 22 exons spanning about 110 kb of DNA. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. [provided by RefSeq, May 2020]
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.013769671 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.1, offset of 28, new splice context is: tgctgaaacttctcaaccAGaag. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-43106534-C-T is Pathogenic according to our data. Variant chr17-43106534-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 245755.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Hereditary breast ovarian cancer syndrome Pathogenic:2
Pathogenic, criteria provided, single submitter
clinical testing
Labcorp Genetics (formerly Invitae), Labcorp
Jan 30, 2019
For these reasons, this variant has been classified as Pathogenic. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BRCA1 are known to be pathogenic (PMID: 20104584). Experimental studies have shown that this variant disrupts mRNA splicing and/or protein function (PMID: 30209399). This variant has not been reported in the literature in individuals with BRCA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 245755). This variant is not present in population databases (ExAC no frequency). This sequence change affects an acceptor splice site in intron 3 of the BRCA1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. -
Pathogenic, criteria provided, single submitter
clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Apr 17, 2023
Variant summary: BRCA1 c.135-1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a canonical 3' splice acceptor site. The variant was absent in 248910 control chromosomes. c.135-1G>A has been reported in the literature in an individual affected with Hereditary Breast And Ovarian Cancer Syndrome (Carter_2018). At least one functional study reports experimental evidence evaluating an impact on protein function and showed a damaging effect of this variant on homology directed repair (HDR) activity (Findlay_2018). HDR assays qualify as a recognized gold standard on the basis of updated guidance provided by the ClinGen Sequence Variant Interpretation (SVI) working group. Three submitters have provided clinical-significance assessments for this variant to ClinVar after 2014, and classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter
clinical testing
GeneDx
Oct 07, 2016
This pathogenic variant is denoted BRCA1 c.135-1G>A or IVS3-1G>A and consists of a G>A nucleotide substitution at the -1 position of intron 3 of the BRCA1 gene. The variant destroys a canonical splice acceptor site and is predicted to cause abnormal gene splicing, leading to an abnormal message that is subject to an abnormal protein product. Although this variant has not, to our knowledge, been published in the literature, another variant at this position, BRCA1 c.135-1G>T has been identified in individuals with breast and ovarian cancer and has been shown to result in skipping of exon 4 resulting in an in frame deletion (Shattuck-Eidens 1997, Risch 2001, Tesoriero 2005, Spurdle 2010). Although this deletion does not result in a frameshift, it does result in the loss of the RING finger functional domain (Paul 2014). Therefore, we consider BRCA1 c.135-1G>A to be pathogenic. -
Likely pathogenic, criteria provided, single submitter
clinical testing
Color Diagnostics, LLC DBA Color Health
Jan 27, 2022
This variant causes a G to A nucleotide substitution at the -1 position of intron 3 of the BRCA1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. RNA studies have shown that a similar variant c.135-1G>T 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 reported that this variant impacts BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). This variant has been reported in at least one individual affected with ovarian cancer (PMID: 31341520). Similar mutations at this position, c.135-1G>A and c.135-1G>T, also have been reported in at least 8 individuals affected with breast and ovarian cancer (PMID: 11179017, 16211554, 16683254, 21324516, 25452441, 26541979, 33471991). This variant has not been identified 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 Likely Pathogenic. -
Breast-ovarian cancer, familial, susceptibility to, 1 Other:1