rs80359772

chr13-32398178-GT-G

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000059.4(BRCA2):c.9666del(p.Cys3222TrpfsTer27) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,602 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. C3222C) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 frameshift
• Clinical Significance: Pathogenic reviewed by expert panel P:16
• Conservation: PhyloP100: 0.301

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 18 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 46 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 13-32398178-GT-G is Pathogenic according to our data. Variant chr13-32398178-GT-G is described in ClinVar as [Pathogenic]. Clinvar id is 52888.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32398178-GT-G is described in Lovd as [Pathogenic]. Variant chr13-32398178-GT-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.9666del	p.Cys3222TrpfsTer27	frameshift_variant	27/27	ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.9666del	p.Cys3222TrpfsTer27	frameshift_variant	27/27	5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000402 AC: 1 AN: 248958 Hom.: 0 AF XY: 0.00000742 AC XY: 1 AN XY: 134744

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: 0.00000885

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1457602 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 725270

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: 9.01e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

EpiCase AF: 0.00

EpiControl AF: 0.0000593

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:16

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Nov 14, 2023	The c.9666del (p.Cys3222Trpfs*27) variant in the BRCA2 gene is located on the exon 27 and is predicted to shift of reading frame that introduces a premature translation termination codon (p.Cys3222Trpfs*27), resulting in an absent or disrupted protein product. The variant has been reported in multiple individuals with breast/ovarian/prostate cancer (PMID: 31567591, 36623239, 29446198). Loss-of-function variants of BRCA2 are known to be pathogenic (PMID: 8988179, 11897832, 29446198). The variant is reported in ClinVar as pathogenic (ID: 52888) and reviewed by the expert panel. The variant is rare in general population according to gnomAD (1/248958). Therefore, the c.9666del (p.Cys3222Trpfs*27) variant of BRCA2 has been classified as pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	-	- -
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. -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 14, 2023	Frameshift variant predicted to result in protein truncation in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Also known as 9894del; This variant is associated with the following publications: (PMID: 11179017, 29446198, 21913181, 11897832, 11802209, 17148771, 21324516, 32885271, 30720243, 28888541, 31567591, 29922827, 17026620, 18593900, 18607349, 26295337, 29053726, 22711857) -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	May 25, 2021	Although this frameshift variant occurs in the terminal exon of BRCA2 and is not expected to undergo nonsense-mediated decay, the variant removes the last 197 residues of the BRCA2 protein including a region functionally important for interaction with the RAD51 protein and is involved in recombination-mediated DNA repair (PMID: 17515903 (2007)). This variant has been reported in multiple individuals and families with breast/ovarian cancer (PMID: 32885271 (2021), 29053726 (2017), 21913181 (2012), 11897832 (2002), 11179017 (2001)). This variant has not been reported in large, multi-ethnic general populations. Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Aug 19, 2020	The BRCA2 c.9666delT; p.Cys3222fs variant (rs80359772) is reported in the literature in multiple individuals with a personal and/or family history of breast and/or ovarian cancer (Hamann 2002, Harter 2017, Risch 2001). This variant is found on a single chromosome in the Genome Aggregation Database (1/248958 alleles), indicating it is not a common polymorphism. This variant causes a frameshift by deleting a single nucleotide in the last exon of the BRCA2 gene. While this may not lead to nonsense-mediated decay, it is expected to create a truncated protein lacking the last 197 residues of the wildtype protein. Further, other truncating variants downstream of c.9666delT are reported in individuals with breast and/or ovarian cancer and are considered disease-causing (Dodova 2015, van der Hout 2006). Based on available information, the c.9666delT variant is considered to be pathogenic. References: Dodova RI et al. Spectrum and frequencies of BRCA1/2 mutations in Bulgarian high risk breast cancer patients. BMC Cancer. 2015;15:523. Hamann U et al. Contribution of BRCA2 germline mutations to hereditary breast/ovarian cancer in Germany. J Med Genet. 2002;39(3):E12. Harter P et al. Prevalence of deleterious germline variants in risk genes including BRCA1/2 in consecutive ovarian cancer patients (AGO-TR-1). PLoS One. 2017;12(10):e0186043. Risch HA et al. Prevalence and penetrance of germline BRCA1 and BRCA2 mutations in a population series of 649 women with ovarian cancer. Am J Hum Genet. 2001;68(3):700-710. van der Hout AH et al. A DGGE system for comprehensive mutation screening of BRCA1 and BRCA2: application in a Dutch cancer clinic setting. Hum Mutat. 2006;27(7):654-666. -

Hereditary breast ovarian cancer syndrome Pathogenic:3

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	Jul 25, 2021	Variant summary: BRCA2 c.9666delT (p.Cys3222TrpfsX27) 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 248958 control chromosomes (gnomAD). c.9666delT has been reported in the literature in multiple individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (Risch_2001, Hamann_2002, Litton_2012, 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. Eight ClinVar submitters (evaluation after 2014), including one expert panel (ENIGMA), cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Oct 22, 2023	This sequence change creates a premature translational stop signal (p.Cys3222Trpfs*27) in the BRCA2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 197 amino acid(s) of the BRCA2 protein. This variant is present in population databases (rs80359772, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with BRCA2-related conditions. This variant is also known as 9894delT. ClinVar contains an entry for this variant (Variation ID: 52888). 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. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Apr 21, 2023	The c.9666delT pathogenic mutation, located in coding exon 26 of the BRCA2 gene, results from a deletion of one nucleotide at nucleotide position 9666, causing a translational frameshift with a predicted alternate stop codon (p.C3222Wfs*27). This alteration occurs at the 3' terminus of theBRCA2 gene, is not expected to trigger nonsense-mediated mRNA decay, and impacts the last 197 amino acids of the protein. However, premature stop codons are typically deleterious in nature and the impacted region is critical for protein function (Ambry internal data). This mutation has been identified in multiple breast and/or ovarian cancer families to date (Litton, JK et al. Cancer. 2012 Jan 15;118(2):321-5; Hamann, U et al. J Med Genet. 2002 Mar;39(3):E12; Risch, HA et al. Am J Hum Genet. 2001 Mar;68(3):700-10). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Nov 20, 2023	This variant deletes 1 nucleotide in exon 27 of the BRCA2 gene creating a frameshift and premature translation stop signal in the last exon. Although this variant is not predicted to trigger nonsense-mediated decay, it causes the loss of the RAD51 binding domain (PMID: 9126738, 9192668) and the nuclear localization signals (PMID: 10570174) and is expected to result in a non-functional protein product. This variant has been reported in individuals affected with breast and ovarian cancer (PMID: 11179017, 11897832, 17148771, 21324516, 21913181, 29053726, 32885271). This variant has been identified in 1/248958 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. -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

May 17, 2022

- -

Neoplasm of ovary Pathogenic:1

Pathogenic, no assertion criteria provided

research

German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne

Dec 01, 2018

- -

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.Cys3222TrpfsX27 variant was identified in 4 of 5034 proband chromosomes (frequency: 0.0008) from Canadian, American and German individuals or families with breast and ovarian cancers (Hamann 2002, Risch 2001, Risch 2006, Zhang 2011, Meindl 2002, Litton 2011). The variant was also identified in dbSBP (ID: rs80359772) “With Pathogenic allele”, ClinVar (classified pathogenic, reviewed by an expert panel; submitters: ENIGMA, CIMBA, Ambry Genetics, BIC, Invitae and Quest Diagnostics Nichols Institute San Juan Capistrano), Clinvitae (2X), BIC Database (1X, with clinical importance, classification pending), ARUP Laboratories (classified definitely pathogenic), and in in control databases in 1 of 244146 chromosomes at a frequency of 0.000004 increasing the likelihood that this may be a low frequency benign variant in certain populations of origin (Genome Aggregation Consortium Feb 27, 2017), identified in European (Non-Finnish) in 1 of 111064 chromosomes (frequency: 0.000009). The variant was not identified in Cosmic, MutDB, LOVD 3.0, UMD-LSDB, and Zhejiang Colon Cancer Database. The variant was also identified by our laboratory in 1 individual with breast cancer. The variant was not identified in the 1000 Genomes Project, and the NHLBI GO Exome Sequencing Project. The c.9666del variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 3222 and leads to a premature stop codon 27 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

Jul 03, 2023

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs80359772; hg19: chr13-32972315;