13-32340072-ACT-A
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Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong
The NM_000059.4(BRCA2):c.5722_5723del(p.Leu1908ArgfsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 1,461,602 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★★). Synonymous variant affecting the same amino acid position (i.e. N1906N) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000015 ( 0 hom. )
Consequence
BRCA2
NM_000059.4 frameshift
NM_000059.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.124
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 Pathogenic. Variant got 16 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
Variant 13-32340072-ACT-A is Pathogenic according to our data. Variant chr13-32340072-ACT-A is described in ClinVar as [Pathogenic]. Clinvar id is 9320.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32340072-ACT-A is described in Lovd as [Pathogenic]. Variant chr13-32340072-ACT-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| BRCA2 | NM_000059.4 | c.5722_5723del | p.Leu1908ArgfsTer2 | frameshift_variant | 11/27 | ENST00000380152.8 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | ENST00000380152.8 | c.5722_5723del | p.Leu1908ArgfsTer2 | frameshift_variant | 11/27 | 5 | NM_000059.4 | A2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250888Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135674
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GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461602Hom.: 0 AF XY: 0.0000151 AC XY: 11AN XY: 727094
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:39
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:14
| Pathogenic, reviewed by expert panel | curation | Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) | Apr 22, 2016 | Variant allele predicted to encode a truncated non-functional protein. - |
| Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 21, 1995 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Department of Human Genetics, Hannover Medical School | Jul 02, 2024 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge | Oct 02, 2015 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Sharing Clinical Reports Project (SCRP) | Mar 28, 2013 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet | May 27, 2024 | PVS1; PM5_PTC_Strong - |
| Pathogenic, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Dec 15, 2023 | This variant deletes 2 nucleotides in exon 11 of the BRCA2 gene, creating a frameshift and premature translation stop signal. This variant is also known as 5950delCT, 5946delCT and 5950-5951delCT in the literature. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in at least 12 individuals affected with breast and/or ovarian cancer (PMID: 8665505, 14647210, 19353265, 20683152, 21324516, 24010542, 25136594, 26026974, 27553291, 28724667, 29470806, 30287823, 33471991; Leiden Open Variation Database DB-ID BRCA2_001607) and five individuals affected with pancreatic cancer (PMID: 24963353, 25940717) or prostate cancer (PMID: 20736950, 31214711). This variant also has been reported in families suspected of being affected with hereditary breast and ovarian cancer (PMID: 8524414, 11802209, 15340362, 16234499, 25863477). This variant has been identified in 1/250888 chromosomes 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 Pathogenic. - |
| Pathogenic, no assertion criteria provided | clinical testing | BRCAlab, Lund University | Aug 26, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine | Oct 12, 2018 | This c.5722_5723del (p.Leu1908Argfs*2) variant in the BRCA2 gene is predicted to introduce a premature translation termination codon. This variant has been reported in multiple unrelated individuals with breast cancer or ovarian cancer (PMID 8524414, 20927582, 21324516, 24010542, 25863477, 27553291), pancreatic cancer (PMID 25940717) and prostate cancer (PMID 20736950). This variant is extremely rare in general population database. Therefore, this c.5722_5723del (p.Leu1908Argfs*2) variant in the BRCA2 gene is classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | University of Science and Technology Houari Boumediene, Laboratory of Molecular and Cellular Biology (LBCM) | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Michigan Medical Genetics Laboratories, University of Michigan | Nov 03, 2014 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Breast Cancer Information Core (BIC) (BRCA2) | May 29, 2002 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | May 27, 2015 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Department of Medical Genetics, Oslo University Hospital | Jul 01, 2015 | - - |
not provided Pathogenic:10
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Oct 23, 2020 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Dec 01, 2019 | Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Observed in individuals with a personal or family history consistent with pathogenic variants in this gene (Wooster 1995, Frank 1998, Couch 2007, Cherbal 2010, de Juan 2015, Holter 2015, Johns 2017, Pritzlaff 2017); Not observed at a significant frequency in large population cohorts (Lek 2016); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Also known as c.5950delCT; This variant is associated with the following publications: (PMID: 21324516, 20736950, 25136594, 17301269, 19353265, 28008555, 27553291, 29339979, 29335924, 29752822, 22535016, 20683152, 12181777, 26026974, 24830819, 23028338, 9667259, 17453335, 20104584, 22798144, 16835750, 12112655, 12048272, 14973102, 25863477, 8524414, 25940717, 27836010, 26843898, 25330149, 28454591, 27989354, 29470806, 28724667, 30720863, 30940775, 30078507, 30287823, 30720243, 30702160, 31528241, 31577767, 31447099, 31980526) - |
| Pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jun 12, 2023 | The BRCA2 c.5722_5723del (p.Leu1908Argfs*2) variant alters the translational reading frame of the BRCA2 mRNA and causes the premature termination of BRCA2 protein synthesis. This variant has been reported in the published literature in individuals with breast and/or ovarian cancer (PMID: 30940775 (2019), 32341426 (2020), 34290354 (2021)), including male individuals with breast cancer (PMID: 20927582 (2011), 23028338 (2012)). This variant has also been reported in individuals with prostate cancer (PMID: 20736950 (2010)), and pancreatic cancer (PMID: 25940717 (2015), 31577767 (2019)). The frequency of this variant in the general population, 0.000004 (1/250888 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 24, 2023 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The p.Leu1908ArgfsX2 deletion variant has been previously reported in the literature in at least 4 of 3460 proband chromosomes in individuals with hereditary breast, ovarian or pancreatic cancer and was shown to segregate with disease in one family (Selected publications: Edwards 2010, Heidemann 2012, Kwong 2009, Zhang 2011). In addition, it was reported 17x in the UMD database as causal and 42X in the BIC database as having clinical importance. This DNA alteration leads to a premature stop codon at position 1908, which is predicted to lead to a truncated or absent protein and loss of function. Loss of function variants of the BRCA2 gene are an established mechanism of disease in hereditary breast and ovarian cancer. In summary, this variant is classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 04, 2015 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Clinical Genetics and Genomics, Karolinska University Hospital | Apr 18, 2019 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Apr 28, 2022 | The BRCA2 c.5722_5723delCT; p.Leu1908ArgfsTer2 variant (rs80359530), also known as 5950delCT, has been described in several individuals and families affected with breast, ovarian, prostate, or pancreatic cancers (Cherbal 2010, de Juan 2015, Ding 2011, Edwards 2010, Holter 2015, Kwong 2009, Thompson 2012, Zhang 2011). This variant is reported in ClinVar (Variation ID: 9320) and is classified as pathogenic by an expert panel. This variant is only observed on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. This variant causes a frameshift by deleting 2 nucleotides, so it is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Based on available information, this variant is considered pathogenic. REFERENCES Cherbal F et al. BRCA1 and BRCA2 germline mutations screening in Algerian breast/ovarian cancer families. Dis Markers. 2010;28(6):377-84. PMID: 20683152. de Juan I et al. BRCA1 and BRCA2 mutations in males with familial breast and ovarian cancer syndrome. Results of a Spanish multicenter study. Fam Cancer. 2015 Dec;14(4):505-13. PMID: 26026974. Ding Y et al. Mutations in BRCA2 and PALB2 in male breast cancer cases from the United States. Breast Cancer Res Treat. 2011 Apr;126(3):771-8. PMID: 20927582. Edwards S et al. Prostate cancer in BRCA2 germline mutation carriers is associated with poorer prognosis. Br J Cancer. 2010 Sep 7;103(6):918-24. PMID: 20736950. Holter S et al. Germline BRCA Mutations in a Large Clinic-Based Cohort of Patients With Pancreatic Adenocarcinoma. J Clin Oncol. 2015 Oct 1;33(28):3124-9. PMID: 25940717. Kwong A et al. A BRCA2 founder mutation and seven novel deleterious BRCA mutations in southern Chinese women with breast and ovarian cancer. Breast Cancer Res Treat. 2009 Oct;117(3):683-6. PMID: 19353265. Thompson E et al. Exome sequencing identifies rare deleterious mutations in DNA repair genes FANCC and BLM as potential breast cancer susceptibility alleles. PLoS Genet. 2012 Sep;8(9):e1002894. PMID: 23028338. Zhang S et al. Frequencies of BRCA1 and BRCA2 mutations among 1,342 unselected patients with invasive ovarian cancer. Gynecol Oncol. 2011 May 1;121(2):353-7. PMID: 21324516. - |
| Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | BRCA2: PVS1, PM2, PS4:Moderate - |
| Pathogenic, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Jul 31, 2024 | - - |
Hereditary breast ovarian cancer syndrome Pathogenic:4
| Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | This sequence change creates a premature translational stop signal (p.Leu1908Argfs*2) in the BRCA2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BRCA2 are known to be pathogenic (PMID: 20104584). This variant is present in population databases (rs80359530, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with breast cancer (PMID: 8524414, 20736950, 20927582, 21324516, 22535016, 23028338, 24963353, 25940717, 27553291). It has also been observed to segregate with disease in related individuals. This variant is also known as 5950delCT. ClinVar contains an entry for this variant (Variation ID: 9320). For these reasons, this variant has been classified as Pathogenic. - |
| Pathogenic, no assertion criteria provided | research | Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto | Jan 31, 2014 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 02, 2021 | Variant summary: BRCA2 c.5722_5723delCT (p.Leu1908ArgfsX2) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 4e-06 in 250888 control chromosomes. c.5722_5723delCT has been reported in the literature in multiple individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (example, Rebbeck_2018). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Multiple clinical diagnostic laboratories, an expert panel (ENIGMA) and a consortium (CIMBA) have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 23, 2022 | The p.Leu1908ArgfsX2 variant in BRCA2 has been reported in >60 individuals with BRCA2-associated cancers (Kwong 2009 PMID: 19353265, Cherbal 2010 PMID: 20683152, Zhang 2011, Edwards 2010 PMID: 20736950, Rebbeck 2018 PMID: 29446198, Breast Cancer Information Core (BIC) database). It has also been identified in 0.003% (1/30598) of South Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org); however, this frequency is low enough to be consistent with the frequency of hereditary breast and ovarian cancer (HBOC) in the general population. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 1908 and leads to a premature termination codon 2 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Heterozygous loss of function of the BRCA2 gene is an established disease mechanism in HBOC. Additionally, this variant was classified as pathogenic on April 22, 2016 by the ClinGen-approved ENIGMA expert panel (Variation ID 9320). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant HBOC. ACMG/AMP criteria applied: PVS1, PS4, PM2_Supporting. - |
Familial cancer of breast Pathogenic:3
| Pathogenic, criteria provided, single submitter | clinical testing | Eurofins-Biomnis | Oct 25, 2022 | - - |
| Pathogenic, no assertion criteria provided | literature only | Center for Precision Medicine, Meizhou People's Hospital | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 21, 2024 | - - |
Hereditary cancer-predisposing syndrome Pathogenic:3
| Pathogenic, criteria provided, single submitter | curation | Sema4, Sema4 | Feb 16, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Apr 04, 2023 | This variant deletes 2 nucleotides in exon 11 of the BRCA2 gene, creating a frameshift and premature translation stop signal. This variant is also known as 5950delCT, 5946delCT and 5950-5951delCT in the literature. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in at least 12 individuals affected with breast and/or ovarian cancer (PMID: 8665505, 14647210, 19353265, 20683152, 21324516, 24010542, 25136594, 26026974, 27553291, 28724667, 29470806, 30287823, 33471991; Leiden Open Variation Database DB-ID BRCA2_001607) and five individuals affected with pancreatic cancer (PMID: 24963353, 25940717) or prostate cancer (PMID: 20736950, 31214711). This variant also has been reported in families suspected of being affected with hereditary breast and ovarian cancer (PMID: 8524414, 11802209, 15340362, 16234499, 25863477). This variant has been identified in 1/250888 chromosomes 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 Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 21, 2022 | The c.5722_5723delCT pathogenic mutation, located in coding exon 10 of the BRCA2 gene, results from a deletion of two nucleotides at nucleotide positions 5722 to 5723, causing a translational frameshift with a predicted alternate stop codon (p.L1908Rfs*2). This mutation has been reported in multiple hereditary breast and ovarian cancer (HBOC) syndrome cohorts, including individuals with male breast cancer, pancreatic cancer and prostate cancer (Wooster R et al. Nature. 1995 Dec;378:789-92; Edwards SM et al. Br. J. Cancer. 2010 Sep;103:918-24; Cherbal F et al. Dis Markers, 2010;28:377-84; Ding YC et al. Breast Cancer Res. Treat. 2011 Apr;126:771-8; Zhang S et al. Gynecol. Oncol. 2011 May;121(2):353-7; Konstantopoulou I et al. Clin. Genet. 2014 Jan;85:36-42; Johns AL et al. Genome Med. 2014 May;6:42; Ruiz A et al. Biomed Res Int. 2014 Jun;2014:542541; Kang E et al. Breast Cancer Res. Treat. 2015 May;151:157-68; Holter S et al. J. Clin. Oncol. 2015 Oct;33:3124-9; de Juan I et al. Fam. Cancer. 2015 Dec;14:505-13; Rashid MU et al. BMC Cancer. 2016 08;16:673; Na R et al. Eur Urol, 2017 05;71:740-747; Sun J et al. Clin. Cancer Res. 2017 Oct;23:6113-6119; Singh J et al. Breast Cancer Res Treat, 2018 Jul;170:189-196; Momozowa Y et al. Nat Commun. 2018 10;9(1):4083; Wang H et al. Medicine (Baltimore), 2019 Oct;98:e17443; Guo Y et al. Biosci Rep, 2019 04;39; Deng M et al. Int J Cancer, 2019 09;145:1517-1528; De Talhouet S et al. Sci Rep, 2020 04;10:7073; Shao D et al. Cancer Sci, 2020 Feb;111:647-657; Abdel-Razeq H et al. Sci Rep, 2021 07;11:14906). Of note, this mutation is also designated as 5950delCT and c.5718_5719del in published literature. In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. - |
Breast and/or ovarian cancer Pathogenic:2
| Pathogenic, no assertion criteria provided | clinical testing | Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research | May 15, 2015 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Jun 23, 2023 | - - |
Medulloblastoma;C0346153:Familial cancer of breast;C0376358:Malignant tumor of prostate;C1838457:Fanconi anemia complementation group D1;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2;C2751641:Glioma susceptibility 3;C3150546:Pancreatic cancer, susceptibility to, 2;CN033288:Wilms tumor 1 Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 02, 2021 | - - |
Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Department of Molecular Diagnostics, Institute of Oncology Ljubljana | Apr 02, 2020 | - - |
Gastric cancer Pathogenic:1
| Pathogenic, no assertion criteria provided | research | Laboratory for Genotyping Development, RIKEN | Jul 01, 2021 | - - |
Computational scores
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