rs769152395
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_000059.4(BRCA2):c.68-2A>G variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.00000137 in 1,458,660 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
BRCA2
NM_000059.4 splice_acceptor, intron
NM_000059.4 splice_acceptor, intron
Scores
4
2
1
Splicing: ADA: 1.000
2
Clinical Significance
Conservation
PhyloP100: 6.59
Genes affected
BRCA2 (HGNC:1101): (BRCA2 DNA repair associated) Inherited mutations in BRCA1 and this gene, BRCA2, confer increased lifetime risk of developing breast or ovarian cancer. Both BRCA1 and BRCA2 are involved in maintenance of genome stability, specifically the homologous recombination pathway for double-strand DNA repair. The largest exon in both genes is exon 11, which harbors the most important and frequent mutations in breast cancer patients. The BRCA2 gene was found on chromosome 13q12.3 in human. The BRCA2 protein contains several copies of a 70 aa motif called the BRC motif, and these motifs mediate binding to the RAD51 recombinase which functions in DNA repair. BRCA2 is considered a tumor suppressor gene, as tumors with BRCA2 mutations generally exhibit loss of heterozygosity (LOH) of the wild-type allele. [provided by RefSeq, May 2020]
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ACMG classification
Classification made for transcript
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 0.024276104 fraction of the gene. Cryptic splice site detected, with MaxEntScore 7.8, offset of 6, new splice context is: ttttttttaaatggatttAGgac. Cryptic site results in inframe 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;
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | ENST00000380152.8 | c.68-2A>G | splice_acceptor_variant, intron_variant | Intron 2 of 26 | 5 | NM_000059.4 | ENSP00000369497.3 | |||
| BRCA2 | ENST00000530893.7 | c.-302-2A>G | splice_acceptor_variant, intron_variant | Intron 2 of 26 | 1 | ENSP00000499438.2 | ||||
| BRCA2 | ENST00000614259.2 | n.68-2A>G | splice_acceptor_variant, intron_variant | Intron 1 of 25 | 2 | ENSP00000506251.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247642Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134330
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1458660Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 725568
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:5
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:1Uncertain:1
| Likely pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | May 04, 2023 | - - |
Hereditary cancer-predisposing syndrome Uncertain:2
| Uncertain significance, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Sep 02, 2022 | This variant causes an A to G nucleotide substitution at the -2 position of intron 2 of the BRCA2 gene. Splice site prediction tools indicate that this variant may have a significant impact on RNA splicing. RNA studies have confirmed that the variant disrupts splicing of the full-length transcript, however, the predominant product is a 6-basepair deletion in exon 3, resulting in the in-frame deletion of two amino acids p.Asp23_Leu24del, and an increase in the skipping of exon 3 (PMID: 33469799, 35979650; ClinVar accession ID: SCV000218118.6, SCV000831230.5). Functional studies have reported that this variant does not impact BRCA2 function in the complementation of Brca2-deficient mouse embryonic stem cells and in a homology-directed repair assay (PMID: 35979650). A carrier health history analysis for this variant compared against known benign and pathogenic variant carriers has reported that the pathogenicity of this variant was inconclusive but trending towards benign (PMID: 33469799). While a multifactorial analysis has reported likelihood ratios for pathogenicity based on tumor pathology, segregation and family history of 0.57, 0.28 and 0.79, respectively (PMID: 35979650). This variant has been identified in 1/247642 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. - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 23, 2024 | The c.68-2A>G intronic variant results from an A to G substitution two nucleotides before coding exon 2 of the BRCA2 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 and will result in the creation or strengthening of a novel splice acceptor site. RNA studies have demonstrated that this alteration results in substantial expression of multiple abnormal transcripts including a splice variant which is predicted to result in an in-frame loss of two amino acids as well as one that results in skipping of coding exon 2 (also known as exon 3 in the literature) (Ambry internal data; Nix P et al. Fam Cancer, 2021 Jan; personal communication). The loss of coding exon 2 of is strongly associated with hereditary breast and ovarian cancer phenotype based on multifactorial analysis (Caputo SM et al. Oncotarget, 2018 Apr;9:17334-17348); however the functional and clinical impact of the small in-frame loss is unknown. Downstream functional studies showed that this alteration was able to rescue the growth defect in BRCA2-null mouse embryonic stem cells and that these surviving cells maintained partial activity in a homology directed DNA repair assay (personal communication). This alteration is 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). Based on the available evidence, the clinical significance of this variant remains unclear. It cannot yet be ruled out that this variant may be hypomorphic and present with reduced risks and/or biallelic phenotype. - |
not specified Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 03, 2024 | Variant summary: BRCA2 c.68-2A>G 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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing and loss of BRCA2 function. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 3' splicing acceptor site. Two recently published studies report an impact on splicing resulting in a small in-frame transcript as the predominant transcript, while also detecting an in-frame exon 3 deletion (Thomassen_2022, Nix_2022). This finding is consistent with in-house RNA analysis performed at our laboratory demonstrating an activation of a cryptic acceptor 6 nucleotides downstream of the natural splice site resulting in the in-frame-deletion of 2 amino acids (internal data). The variant allele was found at a frequency of 4e-06 in 247642 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.68-2A>G has been reported in the literature in individuals undergoing multigene-panel testing at a commercial laboratory (example, Thomassen_2022). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in good complementation in the mESC (mouse embryonic stem cells) assay and homology directed repair (HDR) activity 70% (Thomassen_2022). The following publications have been ascertained in the context of this evaluation (PMID: 29922827, 33469799, 35979650, 32641407). ClinVar contains an entry for this variant (Variation ID: 187538). Based on the evidence outlined above, the variant was classified as uncertain significance. - |
Hereditary breast ovarian cancer syndrome Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 15, 2024 | This sequence change affects an acceptor splice site in intron 2 of the BRCA2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in the loss of 2 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is present in population databases (rs769152395, gnomAD 0.0009%). Disruption of this splice site has been observed in individual(s) undergoing genetic testing. An analysis comparing the clinical and personal history of variant carriers with that of carriers of known benign or pathogenic variants showed inconclusive results for this variant (PMID: 33469799). ClinVar contains an entry for this variant (Variation ID: 187538). Studies have shown that disruption of this splice site results in the activation of a cryptic splice site in exon 3 (PMID: 33469799; Invitae). 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. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 8
DS_AL_spliceai
Position offset: 2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at