rs80359773

chr13-32398184-T-TA

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1 PP5_Very_Strong

The NM_000059.4(BRCA2):c.9672dup(p.Tyr3225IlefsTer30) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,610,772 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: BRCA2 NM_000059.4 frameshift
• Clinical Significance: Pathogenic reviewed by expert panel P:26
• Conservation: PhyloP100: 0.127

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]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 45 pathogenic variants in the truncated region.
• PP5: Variant 13-32398184-T-TA is Pathogenic according to our data. Variant chr13-32398184-T-TA is described in ClinVar as [Pathogenic]. Clinvar id is 126217.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.9672dup	p.Tyr3225IlefsTer30	frameshift_variant	27/27	ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.9672dup	p.Tyr3225IlefsTer30	frameshift_variant	27/27	5	NM_000059.4	A2

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152228 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00000401 AC: 1 AN: 249592 Hom.: 0 AF XY: 0.00000741 AC XY: 1 AN XY: 135040

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000883

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000343 AC: 5 AN: 1458544 Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2 AN XY: 725722

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000450

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152228 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74370

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000756

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:26

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:9

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, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	Oct 10, 2014	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Feb 24, 2023	This variant inserts 1 nucleotide in codon 3225 in exon 27 of the BRCA2 gene, creating a frameshift and premature translation stop signal in the last coding exon. This variant is also known as 9900insA and c.9672_9673insA in the literature. This mutant transcript is predicted to escape nonsense-mediated decay and be expressed as a truncated protein. This variant is expected to disrupt the RAD51 binding domain that has been reported to be essential for homologous recombination and DNA repair (PMID: 17515903). Cell lines that are compound heterozygous for this variant and a known pathogenic BRCA2 truncation variant produced a truncated protein consistent with truncation in exon 27 (PMID: 12065746) and exhibited hypersensitivity to mitomycin C and other DNA damaging agents (PMID: 12065746, 16920162). This variant also has been reported in multiple individuals with personal or family history of breast and/or ovarian cancer (PMID: 16683254, 24156927, 25452441, 27153395, Color internal data). This variant has also been reported in three individuals who are compound heterozygous with a pathogenic BRCA2 covariant and affected with Fanconi anemia (PMID: 12065746, 22720145, 26740091). An external laboratory has reported the associated cancer histories of multiple carriers of this variant are inconsistent with known BRCA2 pathogenic variants (https://myriad-web.s3.amazonaws.com/publications/74925948-ACMG%202017%20Mundt%20variant%20classification%20Presented.pdf). This variant has been identified in 1/249592 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this rare variant has been observed in multiple individuals and families affected with BRCA2-related phenotypes. Although additional studies are necessary to determine the role of this variant in disease and penetrance conclusively, this variant is classified as Likely Pathogenic based on the available evidence. -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Sep 21, 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	MGZ Medical Genetics Center	Nov 15, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	May 29, 2002	- -
Pathogenic, criteria provided, single submitter	clinical testing	Michigan Medical Genetics Laboratories, University of Michigan	Nov 03, 2014	- -

not provided Pathogenic:7

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 31, 2022	Frameshift variant predicted to result in protein truncation in a gene for which loss of function is a known mechanism of disease; Published functional studies demonstrate a damaging effect: cell line with this variant exhibited sensitivity to MMC exposure, increased IR induction of foci (present in both cytoplasm and nucleus) and absent FANCD2/BRCA2 complex in chromatin (Wang 2004); Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants are considered pathogenic by a well-established clinical consortium and/or database.; Also known as c.9900dupA; This variant is associated with the following publications: (PMID: 24301060, 28152038, 24156927, 14559878, 16683254, 16115142, 25447315, 25452441, 15689453, 24312913, 11597388, 15645491, 22921157, 26846091, 26740091, 22720145, 29922827, 29446198, 29753700, 30720243, 30291343, 32341426, 30787465, 31076742, 35216584, 12065746, 15199141, 10733923, 9126738) -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jun 17, 2022	The BRCA2 c.9672dup (p.Tyr3225Ilefs*30) frameshift variant (also known as c.9672_9673insA and 9900insA) alters the translational reading frame of the BRCA2 mRNA and is predicted to cause the premature termination of BRCA2 protein synthesis. Although it is located in the last exon of BRCA2 and is not expected to undergo nonsense-mediated decay, the variant removes the last 194 residues of the BRCA2 protein including the RAD51-interaction region involved in recombination-mediated DNA repair (PMID: 17515903 (2007)). The frequency of this variant in the general population, 0.000004 (1/249592 chromosomes, http://gnomad.broadinstitute.org), is consistent with pathogenicity. In the published literature, the variant has been reported in individuals with breast and/or ovarian cancer (PMIDs: 32341426 (2020), 25452441 (2015), 25103822 (2014), 24156927 (2014)), as well as Fanconi anemia (PMIDs: 26740091 (2016), 22720145 (2012), 12065746 (2002)). Based on the available information, this variant is classified as pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Jun 17, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 10, 2023	The BRCA2 c.9672dup; p.Tyr3225IlefsTer30 variant (rs80359773), also known as 9900insA, is reported in multiple individuals and families with hereditary breast and ovarian cancer syndrome and found compound heterozygous in at least one individual with Fanconi anemia (de Jonge 2019, Howlett 2002, Verhoog 2001). This variant is classified as pathogenic by an expert panel in the ClinVar Database (Variation ID: 126217). It is only found on one allele in the Genome Aggregation Database (v2.1.1), 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. This variant results in a premature termination codon in the last exon of the BRCA2 gene. While this may not lead to nonsense-mediated decay, it is expected to create a truncated BRCA2 protein. Based on available information, this variant is considered to be pathogenic. References: de Jonge MM et al. Germline BRCA-Associated Endometrial Carcinoma Is a Distinct Clinicopathologic Entity. Clin Cancer Res. 2019 Dec 15;25(24):7517-7526. PMID: 31492746. Howlett NG et al. Biallelic inactivation of BRCA2 in Fanconi anemia. Science. 2002 Jul 26;297(5581):606-9. PMID: 12065746. Verhoog LC et al. Large regional differences in the frequency of distinct BRCA1/BRCA2 mutations in 517 Dutch breast and/or ovarian cancer families. Eur J Cancer. 2001 Nov;37(16):2082-90. PMID: 11597388. -

Hereditary cancer-predisposing syndrome Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Oct 20, 2022	This variant inserts 1 nucleotide in codon 3225 in exon 27 of the BRCA2 gene, creating a frameshift and premature translation stop signal in the last coding exon. This variant is also known as 9900insA and c.9672_9673insA in the literature. This mutant transcript is predicted to escape nonsense-mediated decay and be expressed as a truncated protein. This variant is expected to disrupt the RAD51 binding domain that has been reported to be essential for homologous recombination and DNA repair (PMID: 17515903). Cell lines that are compound heterozygous for this variant and a known pathogenic BRCA2 truncation variant produced a truncated protein consistent with truncation in exon 27 (PMID: 12065746) and exhibited hypersensitivity to mitomycin C and other DNA damaging agents (PMID: 12065746, 16920162). This variant also has been reported in multiple individuals with personal or family history of breast and/or ovarian cancer (PMID: 16683254, 24156927, 25452441, 27153395, Color internal data). This variant has also been reported in three individuals who are compound heterozygous with a pathogenic BRCA2 covariant and affected with Fanconi anemia (PMID: 12065746, 22720145, 26740091). An external laboratory has reported the associated cancer histories of multiple carriers of this variant are inconsistent with known BRCA2 pathogenic variants (https://myriad-web.s3.amazonaws.com/publications/74925948-ACMG%202017%20Mundt%20variant%20classification%20Presented.pdf). This variant has been identified in 1/249592 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this rare variant has been observed in multiple individuals and families affected with BRCA2-related phenotypes. Although additional studies are necessary to determine the role of this variant in disease and penetrance conclusively, this variant is classified as Likely Pathogenic based on the available evidence. -
Pathogenic, criteria provided, single submitter	clinical testing	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	May 23, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Feb 23, 2022	The c.9672dupA pathogenic mutation, located in coding exon 26 of the BRCA2 gene, results from a duplication of A at nucleotide position 9672, causing a translational frameshift with a predicted alternate stop codon (p.Y3225Ifs*30). This alteration has been reported in multiple individuals and families with breast and/or ovarian cancer (van der Hout AH et al. Hum. Mutat. 2006 Jul;27:654-66; Reitsma W et al. Eur. J. Cancer 2013 Jan;49(1):132-41; Tea MK et al. Maturitas 2014 Jan;77(1):68-72; De Talhouet S et al. Sci Rep, 2020 04;10:7073). Further, this alteration was reported in trans with a likely pathogenic BRCA2 missense variant in a patient diagnosed with Fanconi anemia at 2 months of age, who later died of metastatic glioblastoma multiforme at age 4 (Dodgshun AJ et al. Cancer Genet. 2016 209(1-2):53-6). This alteration has also been detected in conjunction with another BRCA2 mutation in cells derived from a patient with Fanconi anemia (Howlett NG et al. Science 2002 Jul;297(5581):606-9; Feng Z et al. Proc. Natl. Acad. Sci. U.S.A. 2011 Jan;108(2):686-91). Of note, this alteration is also designated as 9900insA 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. As such, this alteration is interpreted as a disease-causing mutation. However, because this variant is identified in one or more patients with Fanconi Anemia it may be hypomorphic and thus, carriers of this variant and their families may present with reduced risks, and not with the typical clinical characteristics of a high-risk pathogenic BRCA2 alteration. As risk estimates are unknown at this time, clinical correlation is advised. -

Hereditary breast ovarian cancer syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 12, 2021	Variant summary: BRCA2 c.9672dupA (p.Tyr3225IlefsX30) 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 249832 control chromosomes (gnomAD and publication). c.9672dupA has been reported in the literature in multiple individuals affected with breast cancer and/or ovarian cancer (Couch_2015, Rebbeck_2018, BIC database). 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. 11 ClinVar submitters, including one expert panel (ENIGMA), (evaluation after 2014) cite the variant as pathogenic (n=10) and likely pathogenic (n=1). 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	Oct 28, 2016	The p.Tyr3225fs variant in BRCA2 has been reported in the heterozygous state in >30 individuals with BRCA2-associated cancers and in the compound heterozygous s tate in 1 individual with Fanconi anemia (Howlett 2002, Tea 2014, Hout 2006, Dru sedau 2013, Karami 2013, Breast Cancer Information Core (BIC) database). This va riant was absent from large population studies. This variant is predicted to cau se a frameshift, which alters the protein?s amino acid sequence beginning at pos ition 3225 and leads to a premature termination codon 30 amino acids downstream. Heterozygous loss of function of the BRCA2 gene is an established disease mecha nism in hereditary breast and ovarian cancer (HBOC). In summary, this variant me ets criteria to be classified as pathogenic for HBOC in an autosomal dominant ma nner. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 05, 2023	This sequence change creates a premature translational stop signal (p.Tyr3225Ilefs*30) in the BRCA2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 194 amino acid(s) of the BRCA2 protein. This variant is present in population databases (rs80359773, gnomAD 0.0009%). This premature translational stop signal has been observed in individual(s) with breast and/or ovarian cancer, medulloblastoma, and Fanconi anemia (PMID: 12065746, 16683254, 24156927, 29753700). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as 9900insA. ClinVar contains an entry for this variant (Variation ID: 126217). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects BRCA2 function (PMID: 12065746). This variant disrupts a region of the BRCA2 protein in which other variant(s) (p.Tyr3308*) have been determined to be pathogenic (PMID: 17026620, 18593900, 18607349, 22711857). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

BRCA2-related condition Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 20, 2023

The BRCA2 c.9672dupA variant is predicted to result in a frameshift and premature protein termination (p.Tyr3225Ilefs*30). This variant has been reported in the heterozygous state in multiple individuals with breast and/or ovarian cancer (van der Hout et al. 2006. PubMed ID: 16683254; Karami et al. 2013. PubMed ID: 24312913; Tea et al. 2014. PubMed ID: 24156927; Couch et al. 2014. PubMed ID: 25452441; Rebbeck et al. 2018. PubMed ID: 29446198; Haer-Wigman et al. 2019. PubMed ID: 30291343). This variant has also been reported in the compound heterozygous or homozygous state in individuals with Fanconi anemia (Howlett et al. 2002. PubMed ID: 12065746; Barber et al. 2005. PubMed ID: 16115142). This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/13-32972321-T-TA) and is interpreted as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/126217/). Frameshift variants in BRCA2 are expected to be pathogenic. This variant is interpreted as pathogenic. -

Fanconi anemia complementation group D1 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jul 26, 2002

- -

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.Tyr3225IlefsX30 variant was identified in individuals with hereditary breast and ovarian cancer (Karami 2013, Vos 2014) in the Netherlands populations and in Fanconi Anemia patients (Barber 2005, Howlett 2002, Lee 2014, Offit 2003, Reid 2005¬, Wang 2004), although no frequency data was given. The variant was also identified in dbSNP (ID: rs80359773) as “With Pathogenic allele”, Clinvitae database (pathogenic, Invitae), ARUP Laboratories BRCA Mutations Database (as definitely pathogenic), the ClinVar database (pathogenic, by multiple submitters), GeneInsight COGR database (unclassified) the BIC database (4x with unknown clinical importance), and UMD (3x with a “causal” classification). The c.9672dupA variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 3225 and leads to a premature stop codon at position 3254. 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

Aug 11, 2023

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs80359773; hg19: chr13-32972321;