ClinVar Miner

Submissions for variant NM_007294.4(BRCA1):c.594-2A>C

gnomAD frequency: 0.00003  dbSNP: rs80358033
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Total submissions: 19
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000031267 SCV000577983 benign Breast-ovarian cancer, familial, susceptibility to, 1 2017-06-29 reviewed by expert panel curation In our experience this variant always co-occurs in cis with c.641A>G. The haplotype of c.[594-2A>C; 641A>G] has been shown to be not pathogenic from comprehensive clinical studies (PMID:27008870). We recommend that if c.594-2A>C is detected in an individual, presence of c.641A>G should be verified. If co-occurrence is confirmed, the combination of the two variants is classified as not pathogenic/benign (see SCV000282252.1). If c.594-2A>G is detected alone, assume clinical significance uncertain in the absence of further evidence.
Labcorp Genetics (formerly Invitae), Labcorp RCV000049067 SCV000077080 uncertain significance Hereditary breast ovarian cancer syndrome 2024-01-21 criteria provided, single submitter clinical testing 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). This variant is present in population databases (rs80358033, gnomAD 0.007%). Disruption of this splice site has been observed on the opposite chromosome (in trans) from a pathogenic variant in BRCA1 in at least one individual (PMID: 25639900; Invitae), which suggests that this variant may not be disease-causing. This variant is generally observed on the same chromosome as a second BRCA1 variant, c.641A>G. Comprehensive clinical validation studies have shown that this BRCA1 haplotype c.[594-2A>C; 641A>G] is not disease causing (PMID: 27008870, 25639900). ClinVar contains an entry for this variant (Variation ID: 37686). Experimental studies have shown that this variant is associated with the activation of an in-frame cryptic acceptor splice site 21 nucleotides upstream of the natural splice site in intron 8 (i21d), exon 8 skipping, exon 9 skipping and exons 8-9 skipping (PMID: 27008870, 26913838, 24212087, Invitae). These alternative splicing events are also observed in controls. 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.
Ambry Genetics RCV000131863 SCV000186918 uncertain significance Hereditary cancer-predisposing syndrome 2024-04-10 criteria provided, single submitter clinical testing The c.594-2A>C intronic variant results from an A to C substitution two nucleotides upstream from coding exon 8 in the BRCA1 gene. This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. This alteration is frequently observed as a haplotype BRCA1 c.[594-2A>C; 641A>G] which is classified as benign (de la Hoya M et al Hum Mol Genet. 2016; Mar). The same study evaluated the splice effect of the haplotype and of each alteration independently in a minigene assay. The independent BRCA1 c.594-2A>G variant produced an in-frame transcript that retains 21 nucleotides of intron 7, r.594-21_594-1ins which was also detected at a low level in the control samples (de la Hoya M et al Hum Mol Genet. 2016; Mar). This isoform is also known as Δ10p 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. However, as this alteration results in an in-frame insertion that is also present in controls, and since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
CSER _CC_NCGL, University of Washington RCV000049067 SCV000190088 likely benign Hereditary breast ovarian cancer syndrome 2016-05-18 criteria provided, single submitter research
GeneDx RCV000159940 SCV000210077 likely benign not specified 2018-01-02 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario RCV000768650 SCV000219194 uncertain significance Breast and/or ovarian cancer 2020-05-06 criteria provided, single submitter clinical testing
University of Washington Department of Laboratory Medicine, University of Washington RCV000049067 SCV000266035 likely benign Hereditary breast ovarian cancer syndrome 2017-07-11 criteria provided, single submitter clinical testing
Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency RCV000159940 SCV000586870 uncertain significance not specified 2017-04-18 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000159940 SCV000699277 likely benign not specified 2023-11-22 criteria provided, single submitter clinical testing Variant summary: BRCA1 c.594-2A>C 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: five predict the variant abolishes a 3 prime acceptor site; one predicts the variant strengthens a cryptic 3 prime acceptor site. In vitro functional studies have shown that the variant in isolation leads to the increased retention of 21 intronic nucleotides immediately upstream exon 10, resulting in a transcript with an in-frame insertion (r.594-21_594-1ins), which is a naturally occurring minor transcript (de la Hoya 2016). However, the variant very frequently, if not always, is found in complex with c.641A>G (located in exon 10), and the two together were shown to cause an out-of-frame exon 10 skipping (likely resulting in NMD), probably driven by the c.641 variant. Notably, though the double mutant allele c.[594-2A>C; 641A>G] did not produce detectable levels of full-length transcripts, it produced normal levels of the delta 9,10 transcripts (a which is a naturally occurring alternative transcript, with an in-frame deletion of exon 9 and 10), predicted to encode a BRCA1 protein with sufficient tumor suppression function to compensate for the lack of full length transcripts (de la Hoya 2016). The variant allele was found at a frequency of 5.1e-05 in 294540 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in BRCA1 causing Hereditary Breast And Ovarian Cancer Syndrome (5.1e-05 vs 0.001), allowing no conclusion about variant significance. The c.594-2A>C variant has been reported in the literature in multiple individuals affected with Hereditary Breast and Ovarian Cancer, in most cases as a complex allele in cis with c.641A>G. However, the variant has also been found to co-occur with other pathogenic BRCA mutations in several cases (Rosenthal 2015, Wong-Brown 2016), leaving the pathogenicity of the variant questionable. In addition, a multifactorial analysis considering largescale case-control, segregation and breast cancer pathology information for the complex allele c.[594-2A>C; 641A>G] predicted the complex variant to be not pathogenic (de la Hoya 2016). The following publications have been ascertained in the context of this evaluation (PMID: 22711857, 20104584, 24569164, 19892845, 21702907, 16912212, 22811390, 29254167, 25366421, 25639900, 10408690, 24667779, 16211554, 23239986, 26884819, 27008870). 12 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Multiple submitters reported the variant with conflicting assessments (pathogenic n=1, benign/likely benign n=6, VUS n=5), including one expert panel classified it as benign. Based on the evidence outlined above, the variant was classified as likely benign.
Color Diagnostics, LLC DBA Color Health RCV000131863 SCV000910719 likely benign Hereditary cancer-predisposing syndrome 2016-07-27 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000588403 SCV002046864 likely benign not provided 2023-06-20 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000131863 SCV002537879 uncertain significance Hereditary cancer-predisposing syndrome 2022-01-14 criteria provided, single submitter curation
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000588403 SCV004565118 uncertain significance not provided 2023-05-11 criteria provided, single submitter clinical testing
Sharing Clinical Reports Project (SCRP) RCV000031267 SCV000053872 not provided Breast-ovarian cancer, familial, susceptibility to, 1 2010-03-15 no assertion provided clinical testing
Breast Cancer Information Core (BIC) (BRCA1) RCV000031267 SCV000145639 pathogenic Breast-ovarian cancer, familial, susceptibility to, 1 2002-05-29 no assertion criteria provided clinical testing
Pathway Genomics RCV000031267 SCV000187727 pathogenic Breast-ovarian cancer, familial, susceptibility to, 1 2014-07-24 no assertion criteria provided literature only
Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto RCV000159940 SCV000587066 uncertain significance not specified 2014-01-31 no assertion criteria provided research
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001354004 SCV000591290 uncertain significance Malignant tumor of breast no assertion criteria provided clinical testing The BRCA1 c.594-2A>C variant was identified in the literature in functional, in silico analysis, segregation studies and reviews (Steffensen 2014, Tesoriero 2005, Hoya 2016, Rosenthal 2015). The variant was also identified in dbSNP (ID: rs80358033) as “With Pathogenic, untested allele”; NHLBI GO Exome Sequencing Project in 1 of 8600 European American alleles; Exome Aggregation Consortium database (August 8, 2016) in 2 of 109096 chromosomes (freq. 0.00001833) in the following populations: European (Non-Finnish) in 2 of 59486 chromosomes (freq. 0.00003362), but was not seen in African, East Asian, European (Finnish), Latino, South Asian and Other populations. ClinVar and Clinvitae databases (uncertain significance by Invitae, Ambry Genetics, GeneDx, Genetics Diagnostic Laboratory-CHEO; as likely benign by CSER CC NCGI University of Washington; as pathogenic by University of Washington, Dept of Medicine, Pathway Genetics, BIC and Sharing Clinical Report Projects of Myriad did not provide a classification );Fanconi Anemia Mutation Database-LOVD (3X neutral, and LOVD-3.0 9X); ARUP Laboratories BRCA Mutations Database (5- definitely pathogenic.); GeneInsight COGR database (pathogenic by MESHWCRI and NYG, as unknown significance by CHEO and CVHTHP); the BIC database (15X with clinical importance). The c.594-2A>C variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. A study by Hoya (Hoya 2016) used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A >C. A recent analysis using family history weighting and co-observation classification modeling indicated that BRCA1 c.594- 2A > C (IVS9-2A > C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenic BRCA1 variant. Data indicate that c.594-2A > C is always in cis with c.641A > G. The spliceogenic effect of c.[594-2A > C;641A > G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A > C; 641A > G] caused exon 10 skipping, albeit not due to c.594-2A > C impairing the acceptor site but rather by c.641A > G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with a per allele BRCA1 expression profile composed of 70–80% truncating transcripts, and 20–30% of in-frame D 9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function. The study confirms that BRCA1 c.[594-2A > C;641A > G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant in BRCA1 exons 9 or 10, or any other BRCA1 allele that permits 20–30% of tumor suppressor function. More generally, the findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes. A review of the variant by Rosenthal (Rosenthal 2015) detailed the following: The expected classification of BRCA1 c.594-2A >C as pathogenic is based on the predicted impact on mRNA splicing at the intron 9/exon 10 boundary. Splicing analysis algorithms predict that this change disrupts normal mRNA splicing because the consensus splice acceptor sequence at this position is highly conserved. Biochemical studies confirm skipping of exon 10 in transcripts from the BRCA1 c.594-2A >C allele, resulting in the loss of 77 nucleotides and premature truncation of the BRCA1 protein (Steffensen 2014 24667779). They re-evaluated BRCA1 c.594-2A >C following published studies of a BRCA1 variant located at a different splice junction, c.591C > T (p.C197C). This variant is predicted to disrupt splicing at the exon 9/intron 9 boundary, but it has long been classified as clinically insignificant based on multiple lines of evidence, including a high frequency in control populations. Given this benign designation, it is somewhat surprising that this variant results in a significant reduction in the production of full length BRCA1 transcripts and the production of abnormal transcripts missing exon 9. However, this is accompanied by an increase in the proportion of an alternatively spliced transcript lacking both exons 9 and 10. In fact, this Δ (9, 10) isoform is normally present at relatively high levels in breast tissue containing only wild-type BRCA1 and may retain at least some BRCA1 function as the deletion of both exons 9 and 10 results in an in-frame deletion of 41 amino acids in a portion of the protein unrelated to homologous repair. These findings raise the possibility that this alternative transcript can ‘rescue’ variants that disrupt splicing for exons 9 and 10, or possibly even sequence changes within those exons. They subsequently performed a systematic review of available data for c.594-2A >C in their clinical database. As of September 23, 2013, they had detected this variant in 110 apparently unrelated individuals as an outcome of comprehensive sequencing and large arrangement analysis. It has been observed in multiple patients from six families who also have deleterious variants in BRCA2, placing this variant in the benign category using the MCO model. BRCA1 c.594-2A >C also falls within the benign range using the HWA. The family testing outcomes do not demonstrate consistent segregation of the variant with breast or ovarian cancer, although they cannot exclude some contribution of the variant to the familial aggregation of cancer. In the past, it has been believed that embryonic lethality was inevitably associated with homozygosity or compound heterozygosity for pathogenic BRCA1 variants, but recent reports of two patients with two deleterious BRCA1 variants in trans has demonstrated that in rare cases this can lead to a clinical condition similar to FA. They have observed a patient with variant c.594-2A>C in trans with the BRCA1 founder variant exon13ins6kb. This patient does not have reported symptoms consistent with FA, which further contradicts a pathogenic interpretation for this variant. Myriad currently reports BRCA1 c.594-2A >C as a ‘special interpretation’ variant based on the as yet unresolved conflict between the predicted impact on protein sequence and function and the available data. 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.
King Laboratory, University of Washington RCV001171441 SCV001251352 pathogenic Breast-ovarian cancer, familial, susceptibility to, 1; Hereditary breast ovarian cancer syndrome 2019-09-01 no assertion criteria provided research

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