rs80359380
Variant summary
Our verdict is Pathogenic. The variant received 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong
The NM_000059.4(BRCA2):c.3264dupT(p.Gln1089SerfsTer10) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000503 in 1,590,156 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
Consequence
NM_000059.4 frameshift
Scores
Clinical Significance
Conservation
Publications
- breast-ovarian cancer, familial, susceptibility to, 2Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), ClinGen
- Fanconi anemia complementation group D1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen, G2P
- pancreatic cancer, susceptibility to, 2Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
- sarcomaInheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
- hereditary breast ovarian cancer syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Fanconi anemiaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- medulloblastomaInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Pathogenic. The variant received 16 ACMG points.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | ENST00000380152.8 | c.3264dupT | p.Gln1089SerfsTer10 | frameshift_variant | Exon 11 of 27 | 5 | NM_000059.4 | ENSP00000369497.3 | ||
| BRCA2 | ENST00000530893.7 | c.2895dupT | p.Gln966SerfsTer10 | frameshift_variant | Exon 11 of 27 | 1 | ENSP00000499438.2 | |||
| BRCA2 | ENST00000614259.2 | n.3264dupT | non_coding_transcript_exon_variant | Exon 10 of 26 | 2 | ENSP00000506251.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152110Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000258 AC: 6AN: 232856 AF XY: 0.0000238 show subpopulations
GnomAD4 exome AF: 0.00000487 AC: 7AN: 1438046Hom.: 0 Cov.: 33 AF XY: 0.00000421 AC XY: 3AN XY: 713214 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74310 show subpopulations
ClinVar
Submissions by phenotype
not provided Pathogenic:7
The BRCA2 c.3264dupT; p.Gln1089fs variant (rs80359380), also known as 3492insT, is reported in the literature in multiple individuals with a personal or family history of breast and/or ovarian cancer (de Juan 2015, de la Hoya 2002, Fernandez-Lopez 2019, Llort 2002, Plamero 2018). This variant has also been observed in an individual with Fanconi anemia in trans to a second pathogenic BRCA2 variant (Chandrasekharappa 2013). The c.3264dupT variant is found on only six chromosomes in the Genome Aggregation Database, indicating it is not a common polymorphism. This variant causes a frameshift by inserting a single nucleotide, 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 to be pathogenic. References: Chandrasekharappa SC et al. Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia. Blood. 2013 May 30;121(22):e138-48. 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. de la Hoya M et al. Association between BRCA1 and BRCA2 mutations and cancer phenotype in Spanish breast/ovarian cancer families: implications for genetic testing. Int J Cancer. 2002 Feb 1;97(4):466-71. Fernandez-Lopez JC et al. Population and breast cancer patients' analysis reveals the diversity of genomic variation of the BRCA genes in the Mexican population. Hum Genomics. 2019 Jan 10;13(1):3. Llort G et al. Low frequency of recurrent BRCA1 and BRCA2 mutations in Spain. Hum Mutat. 2002 Mar;19(3):307. Palmero EI et al. The germline mutational landscape of BRCA1 and BRCA2 in Brazil. Sci Rep. 2018 Jun 15;8(1):9188. -
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BRCA2: PVS1, PM2 -
The BRCA2 c.3264dup (p.Gln1089Serfs*10) 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 affected with breast and/or ovarian cancer (PMIDs: 20104584 (2010), 30630528 (2019), 34413315 (2021), 35264596 (2022), 35451682 (2022)), pancreatic ductal adenocarcinoma (PMIDs: 29506128 (2018), 30274973 (2018)), prostate cancer (PMID: 30625039 (2019)), lung adenocarcinoma (PMID: 33858029 (2021)), and medulloblastoma (PMID: 29753700 (2018)). The frequency of this variant in the general population, 0.0002 (6/30610 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. -
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 the heterozygous state in individuals with a personal or family history consistent with pathogenic variants in this gene (PMID: 19941167, 20033483, 23479189, 23233716, 28477318, 29506128); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Also known as 3492dupT; This variant is associated with the following publications: (PMID: 12955716, 20033483, 19941167, 23233716, 24259538, 23613520, 23479189, 12845657, 29907814, 30630528, 30720243, 34413315, 29922827, 28888541, 33858029, 18176857, 22426013, 11857748, 16758124, 26026974, 12655567, 19530235, 25371446, 25628955, 27842325, 26681312, 24123850, 28477318, 28985766, 28680148, 28127413, 29387975, 11802208, 29506128, 21548014, 30274973, 30322717, 31447099, 31589614, 32719484, 30787465, 30625039, 35264596, 29753700, 35451682) -
PP5, PM3, PS4_moderate, PVS1 -
Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:6
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Variant allele predicted to encode a truncated non-functional protein. -
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This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com. -
This variant inserts a single nucleotide causing a frameshift at position 1089 which leads to a premature stop codon. This variant is predicted to result in a loss of protein function, which is a well-established mechanism of disease for the BRCA2 gene (Borg 2010). This variant has been observed in many families with breast and/or ovarian cancer, especially families with Spanish ancestry (Diez 2010, de Sanjose 2003, Esteban Cardenosa 2010, Weitzel 2005), and in an individual with Fanconi anemia (Chandrasekharappa 2013). Based on this information, we consider this variant to be pathogenic. PS4-moderate; PVS1 -
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Hereditary cancer-predisposing syndrome Pathogenic:4
This variant inserts 1 nucleotide in exon 11 of the BRCA2 gene, creating a frameshift and premature translation stop signal. This variant is also known as 3492insT, 3492dupT, 3492_3493insT and c.3264_3265insT 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 ten individuals affected with breast, ovarian and uterine cancer (PMID: 11843247, 12655567, 12845657, 12955716, 20104584, 30630528, 33471991; Leiden Open Variation Database DB-ID BRCA2_000667; Color internal data) and two individuals affected with pancreatic cancer (PMID: 29506128, 30274973) and is a recurrent mutation detected in suspected hereditary breast and ovarian cancer families of Latin American, Caribbean and Spanish origins (PMID: 19241424, 19941167, 20033483, 23233716, 23479189). This variant also has been detected in trans with two different BRCA2 pathogenic mutations in two individuals who had clinical features consistent with Fanconi anemia (PMID: 23613520, 29753700). This variant has been identified in 6/232856 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. -
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The c.3264dupT pathogenic mutation, located in coding exon 10 of the BRCA2 gene, results from a duplication of T at nucleotide position 3264, causing a translational frameshift with a predicted alternate stop codon (p.Q1089Sfs*10). This alteration has been reported as a pathogenic mutation in numerous Spanish and Mexican breast and/or ovarian cancer kindreds (Llort G et al. Hum. Mutat. 2002 Mar;19:307; Weitzel JN et al. J. Clin. Oncol. 2013 Jan;31:210-6; Susswein LR et al. Genet Med. 2016 Aug;18(8):823-832; Gabaldo Barrios X et al. Fam. Cancer. 2017 Oct;16(4):477-489). This alteration has also been observed in Fanconi anemia patients (Myers K et al. Pediatr. Blood Cancer. 2012 Mar;58:462-5; Chandrasekharappa SC et al. Blood 2013 May;121:e138-48) and in a patient with pancreatic cancer (Lowery MA et al. J. Natl. Cancer Inst. 2018 Oct;110(10):1067-1074). Of note, this alteration is also designated as 3492insT 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. -
PVS1, PM5_PTC_Strong, BS1_Supporting c.3264dup, located in exon 11 of the BRCA2 gene, consists in the duplication of 1 nucleotide, causing a translational frameshift with a predicted alternate stop codon p.(Gln1089Serfs*10). This alteration is expected to result in loss of function by premature protein truncation and nonsense-mediated mRNA decay (PVS1, PM5_PTC_Strong). It was found in 6/30278 alleles, with a filter allele frequency of 0.0085% at 95% confidence, within the Admixed American population in the gnomAD v2.1 (non-cancer, exome only subset) (BS1_Supporting). No effect is predicted on splicing by computational tools. This variant has been reported in the ClinVar database (9x pathogenic, 1x likely pathogenic) and in LOVD database (12x pathogenic, 2x uncertain significance) and classified as a pathogenic variant in BRCA Exchange database (“2016-09-08: Variant allele predicted to encode a truncated non-functional protein”). Based on currently available information, the variant c.3264dup is classified as a pathogenic variant according to ClinGen-BRCA1 and BRCA2 Guidelines version 1.0.0. -
Hereditary breast ovarian cancer syndrome Pathogenic:4
This sequence change creates a premature translational stop signal (p.Gln1089Serfs*10) 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 (rs777107618, gnomAD 0.02%). This premature translational stop signal has been observed in individual(s) with breast and/or ovarian cancer and Fanconi anemia (PMID: 12845657, 16030099, 19941167, 20033483, 22426013, 23613520, 24123850, 25136594). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It is commonly reported in individuals of Spanish and American individuals of Latin American descent ancestry (PMID: 16030099, 19941167). This variant is also known as 3492insT and 3492_3493insT. ClinVar contains an entry for this variant (Variation ID: 37830). For these reasons, this variant has been classified as Pathogenic. -
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Variant summary: The BRCA2 c.3264dupT (p.Gln1089Serfs) variant results in a premature termination codon, predicted to cause a truncated or absent BRCA2 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant of interest was not found in controls (ExAC, 1000 Gs or ESP) and has been reported in multiple affected individuals by publications. Multiple reputable databases/clinical laboratories cite the variant as "pathogenic." Therefore, taking all available lines of evidence into consideration, the variant of interest has been classified as Pathogenic. -
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Breast-ovarian cancer, familial, susceptibility to, 2;C3150546:Pancreatic cancer, susceptibility to, 2 Pathogenic:1
The c.3264dup variant in the BRCA2 gene is a loss of function variant predicted to undergo nonsense mediated decay, and loss of function variants have been described as a causing mechanism for the gene (PVS1). The variant has a low frecuency in the gnomAD 3.1 non-cancer database (AF=0.000006763) (PM2). The variant has been described in multiple affected independent families with several affected individuals specially in spanish families (PMID:19241424, 19941167, 20033483, 23233716, 23479189) (PS4_Moderate). With all the available evidence, the variant is classified as pathogenic. -
BRCA2-related cancer predisposition Pathogenic:1
This variant inserts 1 nucleotide in exon 11 of the BRCA2 gene, creating a frameshift and premature translation stop signal. This variant is also known as 3492insT, 3492dupT, 3492_3493insT and c.3264_3265insT in the literature. 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 in at least ten individuals affected with breast, ovarian and uterine cancer (PMID: 11843247, 12655567, 12845657, 12955716, 20104584, 30630528, 33471991; Leiden Open Variation Database DB-ID BRCA2_000667; Color internal data) and two individuals affected with pancreatic cancer (PMID: 29506128, 30274973) and is a recurrent mutation detected in suspected hereditary breast and ovarian cancer families of Latin American, Caribbean and Spanish origins (PMID: 19241424, 19941167, 20033483, 23233716, 23479189). This variant also has been detected in trans with two different BRCA2 pathogenic mutations in two individuals who had clinical features consistent with Fanconi anemia (PMID: 23613520, 29753700). This variant has been identified in 6/232856 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. -
Medulloblastoma;C0346153:Familial cancer of breast;C1838457:Fanconi anemia complementation group D1;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2;C2751641:Glioma susceptibility 3;C2931456:Familial prostate cancer;C3150546:Pancreatic cancer, susceptibility to, 2;CN033288:Wilms tumor 1 Pathogenic:1
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Familial cancer of breast Pathogenic:1
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Ovarian neoplasm Pathogenic:1
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Hereditary breast ovarian cancer syndrome;C1838457:Fanconi anemia complementation group D1 Other:1
Variant interpreted as Pathogenic and reported on 02-02-2021 by Lab or GTR ID 500110. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at