chr13-32354859-A-T
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000059.4(BRCA2):c.7008-2A>T variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.000000714 in 1,399,800 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).
Frequency
Consequence
NM_000059.4 splice_acceptor, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | ENST00000380152.8 | c.7008-2A>T | splice_acceptor_variant, intron_variant | Intron 13 of 26 | 5 | NM_000059.4 | ENSP00000369497.3 | |||
| BRCA2 | ENST00000530893.7 | c.6639-2A>T | splice_acceptor_variant, intron_variant | Intron 13 of 26 | 1 | ENSP00000499438.2 | ||||
| BRCA2 | ENST00000614259.2 | n.7008-2A>T | splice_acceptor_variant, intron_variant | Intron 12 of 25 | 2 | ENSP00000506251.1 |
Frequencies
GnomAD3 genomes
GnomAD4 exome AF: 7.14e-7 AC: 1AN: 1399800Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 699986
GnomAD4 genome
ClinVar
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:5
- -
Allele-specific assay on patient-derived mRNA demonstrated that the variant allele produces only predicted non-functional transcripts. Variant allele produces r.7008_7435del, r.7008_7017del, and r.7008_7253del transcripts (encoding predicted non-functional proteins). -
- -
- -
The c.7008-2A>T variant has been previously reported in the literature in 8/64 proband chromosomes of individuals of Italian descent with hereditary breast and/or ovarian cancer. However, no control chromosomes were evaluated to establish the prevalence of the variant in the general population (Colombo 2009, Pensabene 2009, Lowery 2011, Gaildrat 2012, Diez 2009). Interestingly, the authors of the above studies reported that this particular mutation was found to co-exist with another BRCA2 variant, c.631G>A, a co-occurrence that we have also observed in this individual. The c.7008-2A>T variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the -2 position of the splice consensus sequence. Indeed, functional studies have shown that the variant altered the natural splice sites leading to exon skipping due to modification of the 5' splice site (Pensabene 2009, Gaildrat 2012). In-silico or computational prediction software (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predicts a greater than 10% difference in splicing in all 5 programs. The variant has been reported twice in the UMD database as causal, and six times in the BIC database as clinically significant. However, as one of the studies pointed out, the c.7008-2A>T mutation may not contribute to cancer risk in the context of the c.631G>A variant, since it lies downstream of the other mutation identified in this individual that completely abolishes the synthesis of a functional gene product (Colombo 2009). In summary, based on the above information, this variant meets our laboratory's criteria to be classified as pathogenic. -
not provided Pathogenic:3
This variant is located in a canonical splice-acceptor site and interferes with normal BRCA2 mRNA splicing. In the published literature, the variant has been reported in patients with hereditary breast and ovarian cancer, male breast cancer, prostate cancer, and pancreatic cancer (PMIDs: 32854451 (2020), 32338768 (2020), 32058061 (2020), 32438681 (2020), 33287145 (2020), 31512090 (2019), 31336956 (2019), 30014164 (2018), 25980754 (2015), 21934105 (2011), 19179552 (2009), 19423647 (2009)). In functional studies, this variant has been shown to disrupt splicing and lead to exon skipping (PMIDs: 30883759 (2019), 26913838 (2016), 23451180 (2013), 22962691 (2012), 22505045 (2012)). Of note, this variant is frequently reported in cis with BRCA2 c.631G>A (p.Val211Ile), also reported in the literature as c.859G>A (PMIDs: 32338768 (2020), 32058061 (2020), 32438681 (2020), 33287145 (2020), 31336956 (2019), 19423647 (2009), 19179552 (2009), 12960223 (2003)). It has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as pathogenic. -
- -
Canonical splice site variant demonstrated to result in aberrant splicing, producing multiple out-of-frame transcripts in a gene for which loss-of-function is a known mechanism of disease (Pensabene et al., 2009; Colombo et al., 2009; Colombo et al., 2013; Houdayer et al., 2012; Fraile-Bethencourt et al., 2019); Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Also known as 7236-2A>T; This variant is associated with the following publications: (PMID: 30014164, 19179552, 19423647, 21934105, 22962691, 22505045, 27125725, 29446198, 31191615, 32398771, 32438681, 31336956, 31512090, 31209999, 32854451, 33287145, 33810291, 32338768, 25525159, 23451180, 33804961, 35411189, 30613976, 32853339) -
Hereditary cancer-predisposing syndrome Pathogenic:2
This variant is predicted to abolish the intron 13 splice acceptor site of the BRCA2 gene. RNA studies using patient-derived cells have shown that this variant causes skipping of exon 14 and premature truncation but does not completely abolish normal RNA splicing (thus referred to as a "leaky" splice variant) (PMID: 19179552, 19423647, 23451180) and causes aberrant splicing in minigene splicing assay (PMID: 31191615). This variant has been reported in an individual affected with ductal carcinoma in situ (PMID: 30014164). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on available evidence, this variant is classified as Likely Pathogenic. This variant also has been reported to co-occur with a pathogenic splice variant c.631G>A in the BRCA2 gene in at least seven unrelated European individuals affected with breast/ovarian cancer (PMID: 19179552, 19423647, 23451180, 27125725, 31336956) and in an individual affected with pancreatic adenocarcinoma (PMID: 21934105). In six of the individuals affected with breast/ovarian cancer, these variants were reported to occur on the same chromosome (in cis phase) determined in part by retro-transcription analysis or segregation analysis in family studies (PMID: 19179552, 19423647, 22962691, 31336956). For several individuals who carried both variants (PMID: 21934105; Color internal data), the phase of the two variants has not been determined. These two variants have not been reported in trans in the literature. Therefore, although this test cannot distinguish if c.631G>A and c.7008-2A>T variants occur on the same chromosome (in cis) or on opposite chromosomes (in trans), it is likely that these variants are in cis when found together in an individual. -
ONLY INCLUDE IF PT HAS BOTH c.7008-2A>T and c.631G>A (p.V211I) BRCA2 VARIANTS The c.631G>A pathogenic mutation (also known as p.V211I), located in coding exon 6 of the BRCA2 gene, results from a G to A substitution at nucleotide position 631. The amino acid change results in valine to isoleucine at codon 211, an amino acid with highly similar properties; however, this change occurs in the last base pair of coding exon 6, which makes it likely to have some effect on normal mRNA splicing. The c.7008-2A>T intronic pathogenic mutation results from an A to T substitution two nucleotides before coding exon 13 in the BRCA2 gene. The c.631G>A and c.7008-2A>T alterations have been identified in cis in multiple individuals and families with HBOC (Gaildrat PJ et al. Med. Genet. 2012 Oct;49(10):609-17; Pensabene M et al. Ann. Oncol. 2009 May;20(5):874-8; Colombo M et al. Ann. Oncol. 2009 Jun;20(6):1143-4). These alterations have also been identified in cis in one individual with pancreatic adenocarcinoma (Lowery MA et al. Oncologist 2011;16(10):1397-402). Functional studies have demonstrated that the c.631G>A alteration leads to the skipping of coding exon 6, leading to a frameshift and alternate stop in coding exon 8 (Ambry internal data; Pensabene M et al. Ann. Oncol. 2009 May;20(5):874-8; Colombo M et al. Ann. Oncol. 2009 Jun;20(6):1143-4). Functional studies have also demonstrated that the c.7008-2A>T alteration leads to multiple frameshifting aberrant transcripts which may be incomplete (Ambry internal data; Pensabene M et al. Ann. Oncol. 2009 May;20(5):874-8; Colombo M et al. Ann. Oncol. 2009 Jun;20(6):1143-4; Houdayer C et al. Hum. Mutat. 2012 Aug;33(8):1228-38; Colombo M et al. PLoS ONE 2013;8(2):e57173). Of note, c.631G>A and c.7008-2A>T are also designated as 859G>A and IVS13-2A>T, respectively, in published literature. Based on the available evidence, c.631G>A and c.7008-2A>T are classified as a pathogenic haplotype. -
Hereditary breast ovarian cancer syndrome Pathogenic:2
This sequence change affects an acceptor splice site in intron 13 of the BRCA2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with a personal or family history of BRCA2-related conditions. In some cases, this variant occurred on the same chromosome as the c.631G>A (p.Val211Ile) variant (PMID: 19179552, 19423647, 22962691, 25980754, 29446198, 30014164). This variant is also known as IVS13-2A>T. ClinVar contains an entry for this variant (Variation ID: 52246). Studies have shown that disruption of this splice site alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 19179552, 22505045, 23451180, 31191615; Invitae). For these reasons, this variant has been classified as Pathogenic. -
Variant summary: BRCA2 c.7008-2A>T 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 out of four predict the variant abolishes a 3' canonical acceptor site. Multiple studies report experimental evidence that this variant affects mRNA splicing (e..g, Pensabene_2009, Colombo_2009, Houdayer_2012). The variant was absent in 250362 control chromosomes. c.7008-2A>T has been reported in the literature in multiple individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (e.g., Azzollini_2016, Colombo_2009, Diez_2009, Gaildrat_2012, Pensabene_2009, Saied_2021). These data indicate that the variant is very likely to be associated with disease. The variant has been reported in several studies to co-occur with another splice mutation c.631G>A, likely on the same allele. The following publications have been ascertained in the context of this evaluation (PMID: 27062684, 23451180, 19423647, 19542536, 22962691, 22505045, 19179552, 34296289). Nine submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic or likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Breast and/or ovarian cancer Pathogenic:1
- -
Familial cancer of breast Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at