13-32325186-T-C
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_000059.4(BRCA2):c.425+2T>C variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.000000725 in 1,379,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000059.4 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRCA2 | ENST00000380152.8 | c.425+2T>C | splice_donor_variant, intron_variant | Intron 4 of 26 | 5 | NM_000059.4 | ENSP00000369497.3 | |||
BRCA2 | ENST00000530893.7 | c.56+2T>C | splice_donor_variant, intron_variant | Intron 4 of 26 | 1 | ENSP00000499438.2 | ||||
BRCA2 | ENST00000614259.2 | n.425+2T>C | splice_donor_variant, intron_variant | Intron 3 of 25 | 2 | ENSP00000506251.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 7.25e-7 AC: 1AN: 1379436Hom.: 0 Cov.: 26 AF XY: 0.00000145 AC XY: 1AN XY: 690408
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Hereditary breast ovarian cancer syndrome Pathogenic:2
Variant summary: BRCA2 c.425+2T>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: Three predict the variant abolishes the canonical 5' splicing donor site. One predict the variant weakens the canonical 5' splicing donor site. However, to our knowledge, these predictions have yet to be confirmed by published peer-reviewed functional studies. However, at-least two well recognized peers within the data sharing community have reported a splicing impact. The variant was absent in 247740 control chromosomes. To our knowledge, this variant has not been reported as a single germline variant in isolation in an individual affected with Breast and/or Ovarian Cancer. c.425+2T>C has been reported in the literature as a germine variant that was transmitted in double heterozygosity with a different BRCA1 variant, c.3756_3759delGTCT (p.Ser1253Argfs*10) in a 36 year old female with Ovarian Cancer (Vietri_2020, overlaping citations in Santonocito_2020, Franzese_2020, De Falco_2020) (Vietri_2020). The proband's mother who also harbored the double heterozygous genotype was unaffected at age 70 and her maternal male cousin also harboring the same double heterozygous genotype was affected with colorectal cancer at age 37. Double heterozygosity in BRCA1 and BRCA2 genes, although extremely rare, have been reported (cited in Vietri_2020). At-least one additional co-occurrence with another pathogenic BRCA1 variant(s) has been observed at our laboratory (BRCA1 c.5266dup, p.Gln1756fs). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 33057101, 32234730, 31850198, 32438681, 33287145). ClinVar contains an entry for this variant (Variation ID: 234487). Based on the evidence outlined above, the variant was classified as likely pathogenic. -
This sequence change affects a donor splice site in intron 4 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 breast and/or ovarian cancer (PMID: 32438681, 33287145). ClinVar contains an entry for this variant (Variation ID: 234487). Studies have shown that disruption of this splice site results in skipping of exon 4 and introduces a premature termination codon (Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Hereditary cancer-predisposing syndrome Pathogenic:1Uncertain:1
This variant causes a T>C nucleotide substitution at the +2 position of intron 4 of the BRCA2 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. Although this prediction has not been confirmed in published RNA studies, this variant is expected to result in an absent or disrupted protein product. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic. -
The c.425+2T>C intronic variant results from a T to C substitution two nucleotides after coding exon 3 in the BRCA2 gene. This alteration has been identified in an individual diagnosed with breast and/or ovarian cancer (Santonocito C et al. Cancers (Basel), 2020 May;12:). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). RNA studies of a close-match alteration, BRCA2 c.425G>T, have demonstrated that it results in complete abnormal splicing in the set of samples tested (Ambry internal data; Brandão R et al. Breast Cancer Res. Treat. 2011 Oct;129(3):971-82; Nix P et al. Fam Cancer, 2021 Jan). BRCA2 c.425G>T, which has the same splicing profile as this alteration (Ambry internal data), was able to rescue the growth defect in BRCA2-null mouse embryonic stem cells and these surviving cells maintained partial activity in a homology directed DNA repair functional assay (Mesman R et al. Genet Med 2020 Aug;22(8):1355-1365). BRCA2 c.425G>T was also identified in patients who collectively have a phenotype that is not consistent with a high risk BRCA2 pathogenic variant (Nix P et al. Fam Cancer, 2021 Jan). Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -
Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:1
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Familial cancer of breast Pathogenic:1
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not provided Uncertain:1
Canonical splice site variant with an unclear effect on protein function, as an exonic splice variant at this splice junction, c.425G>T, results in the production of multiple transcripts, including potentially functional in-frame transcripts (Brandao 2011, Mesman 2020, Nix 2021); Observed in a woman with ovarian cancer who also harbored a BRCA1 pathogenic variant (Vietri 2020); Not observed at significant frequency in large population cohorts (Lek 2016); Also known as 653+2T>C; This variant is associated with the following publications: (PMID: 33287145) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at