chr13-32371000-AAG-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.8537_8538del(p.Glu2846GlyfsTer22) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000684 in 1,461,838 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
BRCA2
NM_000059.4 frameshift
NM_000059.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.51
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 13-32371000-AAG-A is Pathogenic according to our data. Variant chr13-32371000-AAG-A is described in ClinVar as [Pathogenic]. Clinvar id is 9328.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32371000-AAG-A is described in Lovd as [Pathogenic]. Variant chr13-32371000-AAG-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| BRCA2 | NM_000059.4 | c.8537_8538del | p.Glu2846GlyfsTer22 | frameshift_variant | 20/27 | ENST00000380152.8 | NP_000050.3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | ENST00000380152.8 | c.8537_8538del | p.Glu2846GlyfsTer22 | frameshift_variant | 20/27 | 5 | NM_000059.4 | ENSP00000369497 | A2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251142Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135704
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GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461838Hom.: 0 AF XY: 0.00000825 AC XY: 6AN XY: 727220
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:25
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:8
| Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 1998 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Oct 02, 2023 | This variant deletes 2 nucleotides in exon 20 of the BRCA2 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, functional studies have not been reported for this variant. This variant has been reported as a recurring pathogenic variant in French Canadian, Sardinian, and Yemenite Jewish populations (PMID: 9792861, 17640379, 23621881, 29086229). This variant has been identified in 3/251142 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 | Sharing Clinical Reports Project (SCRP) | Apr 22, 2013 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Breast Cancer Information Core (BIC) (BRCA2) | May 29, 2002 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Pathway Genomics | Jul 24, 2014 | - - |
| 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, reviewed by expert panel | curation | Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) | Sep 08, 2016 | Variant allele predicted to encode a truncated non-functional protein. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Sep 16, 2016 | - - |
not provided Pathogenic:5
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Feb 17, 2020 | 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; 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 8765delAG and 8765_8766delAG; This variant is associated with the following publications: (PMID: 23929434, 8673090, 16168118, 18489799, 21947752, 23302520, 23621881, 10422801, 15024741, 20694749, 26295337, 30014164, 28918466, 29086229, 29506128, 23199084, 25884701, 19656164, 26656232, 17640379, 25452441, 22798144, 21348412, 27836010, 27603373, 27160020, 25085752, 19619314, 15382066, 11512557, 9792861, 9634522, 21324516, 17591843, 16047344, 29560538, 22401979, 30720243, 30322717, 29625052) - |
| Pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jan 05, 2021 | This frameshift variant causes the premature termination of BRCA2 protein synthesis. In addition, it has been reported in individuals affected with breast cancer, ovarian cancer, and pancreatic cancer in the published literature (PMID: 30322717 (2018), 29625052 (2018), 29506128 (2018), 29086229 (2018), 21324516 (2011)). Based on the available information, this variant is classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | AiLife Diagnostics, AiLife Diagnostics | Jul 23, 2021 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 29, 2022 | - - |
Hereditary breast ovarian cancer syndrome Pathogenic:5
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | This sequence change creates a premature translational stop signal (p.Glu2846Glyfs*22) 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 (rs80359714, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with breast and/or ovarian cancer (PMID: 8673090, 21324516, 22401979). It is commonly reported in individuals of French Canadian, Yemenite Jewish, and Northern Sardinian ancestry (PMID: 9634522, 9792861, 11512557, 15382066, 17640379, 19619314, 27603373). This variant is also known as 8765delAG. ClinVar contains an entry for this variant (Variation ID: 9328). 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 | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 08, 2016 | The p.Glu2846fs variant in BRCA2 is a well-established pathogenic founder varian t for several populations, including French Canadians, Jewish-Yemenites, and Nor thern Sardinian (Tonin 1998, Lerer 1998, Ferla 2007). This variant has been ide ntified in 1/66688 European chromosomes by the Exome Aggregation Consortium (ExA C, http://exac.broadinstitute.org; dbSNP rs80359716). This frequency is low enou gh 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 2846 and leads to a premature termination codon 22 amino acids downstream. This alteratio n is then predicted to lead to a truncated or absent protein. Heterozygous loss of BRCA2 function is an established disease mechanism in HBOC. In summary, this variant meets our criteria to be classified as pathogenic for HBOC in an autosom al dominant manner. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jun 03, 2022 | Variant summary: BRCA2 c.8537_8538delAG (p.Glu2846GlyfsX22) 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 1.2e-05 in 251142 control chromosomes. c.8537_8538delAG has been reported in the literature in many individuals and families affected with Hereditary Breast And Ovarian Cancer Syndrome (example Phelan_1996, Machackova_2008, Ghadirian_2014) including 76 patients from the BIC database. It is commonly reported as a pathogenic variant in French Canadian, Yemenite Jewish, and Northern Sardinian populations (example Lerer_1998, Manning_2001, Palomba_ 2007). These data indicate that the variant is very likely to be associated with disease. Multiple clinical diagnostic laboratories and reputable databases have classified this variant as pathogenic in ClinVar. Based on the evidence outlined above, the variant was classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Department of Pathology and Molecular Medicine, Queen's University | Apr 20, 2017 | - - |
Breast and/or ovarian cancer Pathogenic:3
| Pathogenic, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Jun 16, 2023 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | CZECANCA consortium | Jun 11, 2019 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research | May 11, 2016 | - - |
Hereditary cancer-predisposing syndrome Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 26, 2024 | The c.8537_8538delAG (p.E2846Gfs*22) alteration, located in exon 20 (coding exon 19) of the BRCA2 gene, consists of a deletion of 2 nucleotides from position 8537 to 8538, causing a translational frameshift with a predicted alternate stop codon after 22 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This mutation has been reported in multiple individuals and families with hereditary breast and ovarian cancer (HBOC) syndrome (Foretova, 2004; Palomba, 2005; Machackova, 2008; Zhang, 2011; Abd-Rabbo, 2012; Belanger, 2015; El Ghorayeb, 2016; Carter, 2018; Bernstein-Molho, 2018; Felix, 2018; Lowery, 2018; Breast Cancer Association, 2021) and has also been reported in a family with a history of male breast and prostate cancer (Phelan, 1996). This mutation has also been reported in patients with pancreatic and gastric cancers (Halpern, 2020;Lerner-Ellis, 2021). This alteration is known to be one of the more commonly occurring BRCA2 mutations in several different regions in Europe and North America (Tonin, 1998; Manning, 2001; Palomba, 2007; Janaviius, 2010). Of note, this alteration is also designated as 8535delAG, 8765delAG, c.8764_8765delAG and c.8537_8538del2 in published literature. Based on the available evidence, this alteration is classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | May 31, 2023 | This variant deletes 2 nucleotides in exon 20 of the BRCA2 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, functional studies have not been reported for this variant. This variant has been reported as a recurring pathogenic variant in French Canadian, Sardinian, and Yemenite Jewish populations (PMID: 9792861, 17640379, 23621881, 29086229). This variant has been identified in 3/251142 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. - |
Malignant tumor of breast Pathogenic:1
| Pathogenic, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The BRCA2 p.Glu2846GlyfsX22 variant was identified in 21 of 4958 proband chromosomes (frequency: 0.004) from individuals or families with breast and ovarian cancer (Phelan 1996, Zhang 2011, Machackova 2008, Pruss 2014, Seong M-W 2009, Tung 2016). The variant was also identified in the following databases: dbSNP (ID: rs80359714) as “With Pathogenic allele”, Clinvitae database (classified as pathogenic by ClinVar and Invitae), ARUP Laboratories BRCA Mutations Database (classification), the ClinVar database (classified as pathogenic by Invitae, Ambry genetics, GeneDx, LMMPHPM, QDNISJC, COGR, Pathway Genomics, BIC,OMIM, SCRP), COGR database (classified as pathogenic by a clinical laboratories MESHWCRI, LMM, CHEO, QUEENSU, NYG), the BIC database (76X with clinical importance), and UMD (16X with a causal classification). The variant was also identified in Exome Aggregation Consortium database (August 8, 2016) in the European population in 1 of 121324 chromosomes (freq. 0.000008). The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. The c.8537_8538del variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 2846 and leads to a premature stop codon 22 codons downstream. This alteration is then predicted to result in 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 and is the type of variant expected to cause the disorder. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. - |
Familial cancer of breast Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 07, 2024 | - - |
Computational scores
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