Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_007294.4(BRCA1):c.594-1G>T variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.000000686 in 1,458,188 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★★).
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 Uncertain_significance. Variant got 4 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.013590844 fraction of the gene. Cryptic splice site detected, with MaxEntScore 6.7, offset of -21, new splice context is: taactagtgtttcttattAGgac. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
PM2
Very rare variant in population databases, with high coverage;
Uncertain significance, criteria provided, single submitter
clinical testing
Ambry Genetics
Jan 15, 2016
The c.594-1G>T intronic variant results from a G to T substitution one nucleotide upstream from coding exon 8 of the BRCA1 gene. 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; however, this alteration occurs at a splice junction that is located at a naturally occurring, alternatively spliced exon and, thus, the degree and effects of abnormal splicing cannot be predicted (Colombo M et al. Hum. Mol. Genet., 2014 Jul;23:3666-80). Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to abolish the native splice acceptor site; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Uncertain significance, criteria provided, single submitter
clinical testing
Color Diagnostics, LLC DBA Color Health
Dec 16, 2019
This variant causes a G>T nucleotide substitution at the -1 position of intron 8 of the BRCA1 gene. While this variant is expected to disrupt the intron 8 splice acceptor site, another canonical splice site variant c.594-2A>C at this splice site was found not to segregate with breast or ovarian cancer (PMID: 25639900, 27008870) and it has been observed in trans with a pathogenic BRCA1 co-variant in an individual who did not have early-developmental phenotype (PMID: 26884819). The naturally-occurring and functional alternative BRCA1 transcript lacking exons 8 and 9 is thought to ameliorate canonical splice site variants in exons 8 and 9 (PMID: 19892845, 27008870). To our knowledge, functional studies have not been performed for this variant nor has it been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 1/249902 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter
clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Sep 01, 2017
The c.594-1G>T variant in BRCA1 has not been previously reported in individuals with BRCA1-associated cancers, but has been identified in 1/14982 South Asian ch romosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute. org; dbSNP rs757781708). This variant occurs in the invariant region (+/- 1,2) o f the splice consensus sequence and is predicted to cause altered splicing leadi ng to skipping of exon 9; however, a BRCA1 isoform that lacks exons 9 and 10 is normally expressed in breast tissue, suggesting that the c.594-1G>T variant may not cause disease (Tesoriero 2005, Rosenthal 2015, de la Hoya 2016, Wong-Brown 2 016). In summary, the clinical significance of the c.594-1G>T variant is uncerta in. -
Hereditary breast ovarian cancer syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter
clinical testing
Labcorp Genetics (formerly Invitae), Labcorp
Jun 02, 2023
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Studies have shown that disruption of this splice site is associated with altered splicing resulting in skipping of exon 8 and 9 (also known as exon 9 and 10). However, an in-frame BRCA1 isoform that skips exons 8 and 9 is expressed in normal blood and breast tissue, suggesting that this isoform may not be deleterious (PMID: 24569164). ClinVar contains an entry for this variant (Variation ID: 440453). Disruption of this splice site has been observed in individual(s) with breast cancer (PMID: 33151324). This variant is present in population databases (rs757781708, gnomAD 0.003%). This sequence change affects an acceptor splice site in intron 8 of the BRCA1 gene. Loss-of-function variants in BRCA1 are expected to be pathogenic (PMID: 20104584). However, an in-frame BRCA1 isoform lacking exons 8 and 9 (also known as exons 9 and 10) is highly expressed in blood from unaffected individuals and in normal breast tissue; this isoform may retain protein function and could functionally rescue loss-of-function variants within exons 8-9 (PMID: 24569164). -