chr13-32363535-T-C

Variant names:

• chr13-32363535-T-C
• rs398122602
• NM_000059.4:c.8331+2T>C

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1_Moderate PM2 PP5_Very_Strong

The NM_000059.4(BRCA2):​c.8331+2T>C variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,457,672 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: BRCA2 NM_000059.4 splice_donor, intron
• Scores: Splicing: ADA: 0.9921
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:17
• Conservation: PhyloP100: 7.67
• Publications: 18 publications found

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]

BRCA2 Gene-Disease associations (from GenCC):

• breast-ovarian cancer, familial, susceptibility to, 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), ClinGen
• Fanconi anemia complementation group D1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen, G2P
• pancreatic cancer, susceptibility to, 2

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• sarcoma

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• hereditary breast ovarian cancer syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Fanconi anemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• medulloblastoma

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Pathogenic. The variant received 12 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.03461051 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.2, offset of 21, new splice context is: ttgGTaaaa. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 13-32363535-T-C is Pathogenic according to our data. Variant chr13-32363535-T-C is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 267692.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000059.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRCA2	NM_000059.4	MANE Select	c.8331+2T>C		splice_donor intron	N/A	NP_000050.3
	BRCA2	NM_001432077.1		c.8331+2T>C		splice_donor intron	N/A	NP_001419006.1
	BRCA2	NM_001406720.1		c.8331+2T>C		splice_donor intron	N/A	NP_001393649.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRCA2	ENST00000380152.8	TSL:5 MANE Select	c.8331+2T>C		splice_donor intron	N/A	ENSP00000369497.3
	BRCA2	ENST00000544455.6	TSL:1	c.8331+2T>C		splice_donor intron	N/A	ENSP00000439902.1
	BRCA2	ENST00000530893.7	TSL:1	c.7962+2T>C		splice_donor intron	N/A	ENSP00000499438.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000206 AC: 3 AN: 1457672 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 725464

African (AFR) AF: 0.00 AC: 0 AN: 33382

American (AMR) AF: 0.00 AC: 0 AN: 44686

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26094

East Asian (EAS) AF: 0.00 AC: 0 AN: 39674

South Asian (SAS) AF: 0.00 AC: 0 AN: 86092

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53386

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1108354

Other (OTH) AF: 0.0000166 AC: 1 AN: 60236

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:17

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:5

Jan 20, 2023

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant disrupts a canonical splice-donor site and interferes with normal BRCA2 mRNA splicing. This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant has been reported in an individual with ovarian cancer (PMID: 24504028 (2014)), and in individuals with breast cancer (PMID: 25186627 (2015), 29487695 (2018), 30130155 (2018), 30702160 (2019), 32854451 (2020), 35464868 (2022)). In large breast cancer association studies, this variant was found in individuals affected with breast cancer as well as unaffected individuals (PMID: 33471991 (2021), https://databases.lovd.nl/shared/variants/BRCA2). Functional splicing assays demonstrate this this variant causes aberrant splicing and skipping of exon 18 and/or partial exon 17 and exon 18, creating a premature stop codon (PMID: 28339459 (2017), 30832263 (2019), 31143303 (2019), 33469799 (2021)). However, production of the normal transcript was also demonstrated (PMID: 30832263 (2019), 32123317 (2020), 33469799 (2021)). Based on the available information, this variant is classified as pathogenic.

Dec 24, 2020

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Canonical splice site variant expected to result in aberrant splicing, however published functional and RNA studies are conflicting showing both aberrant splicing resulting in skipping of exon 18 and normal splicing, as well as both aberrant and wildtype transcript expression (Fraile-Bethencourt 2017, Gelli 2019, Wangensteen 2019, Wai 2020); Not observed in large population cohorts (Lek 2016); Also known as 8559+2T>G; Observed in individuals with a personal and/or family history of breast and/or ovarian cancer referred for genetic testing at GeneDx and in published literature (Cunningham 2014, Tung 2015, Kwong 2018, Fanale 2020, Rumford 2020); This variant is associated with the following publications: (PMID: 29487695, 32123317, 25186627, 28339459, 30832263, 31143303, 24504028, 29339979, 29446198, 30702160, 31131967, 32854451, 32098980, 31209999, 32380732)

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

May 08, 2023

Clinical Genetics Laboratory, Skane University Hospital Lund

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jan 10, 2023

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Aug 26, 2022

BRCAlab, Lund University

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

Oct 02, 2015

Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Nov 12, 2015

Department of Medical Genetics, Oslo University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Oct 05, 2023

All of Us Research Program, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant disrupts a canonical splice site and is predicted to result in abnormal splicing. This prediction has been confirmed by functional studies (PMID: 28339459, 31143303). Aberrant splicing and/or loss of function is an established mechanism of disease. This variant has been reported in multiple individuals with hereditary breast and ovarian cancer syndrome (PMID: 24504028, 29339979, 24728189, 29487695). This variant is absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/).

Hereditary breast ovarian cancer syndrome Pathogenic:4

Sep 28, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change affects a donor splice site in intron 18 of the BRCA2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BRCA2 are known to be pathogenic (PMID: 20104584). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with clinical features of hereditary breast and ovarian cancer syndrome (PMID: 24504028, 25186627, 29339979, 29446198, 29487695). ClinVar contains an entry for this variant (Variation ID: 267692). Studies have shown that disruption of this splice site alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 20104584). For these reasons, this variant has been classified as Pathogenic.

Jan 31, 2014

Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

Oct 14, 2019

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.8331+2T>C variant in BRCA2 has been reported in at least 2 probands with BRCA2-related cancer (Cunningham 2014, Tung 2015). It was absent from large population studies, but has been reported in ClinVar (Variation ID: 267692). This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. In vitro functional studies confirm that this variant leads to abnormal splicing (Fraile-Bethencourt 2017). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant hereditary breast and ovarian cancer (HBOC). ACMG/AMP Criteria applied: PVS1, PM2, PS4_Supporting.

Nov 16, 2021

National Health Laboratory Service, Universitas Academic Hospital and University of the Free State

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Hereditary cancer-predisposing syndrome Pathogenic:3

Dec 05, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes a T>C nucleotide substitution at the +2 position of intron 18 splice donor site of the BRCA2 gene. RNA studies have shown that this variant results in the production of several aberrant transcripts that lack (i) exon 18, (ii) exon 17 and 18, or (iii) partial exon 17 and exon 18 (PMID: 28339459, 30832263, 33469799). These transcripts are not expected to produce a functional protein, however, it was noted that the slicing defect may be incomplete (PMID: 30832263, 33469799; ClinVar SCV001178672.2). This variant has been reported in over ten individuals affected with breast and/or ovarian cancer (PMID: 18779604, 24728189, 25186627, 28339459, 30832263, 31131967, 33469799, 35464868; communication with an external laboratory). This variant has not been identified 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. Incomplete splicing defect attributed to this variant suggests that this variant may be associated with reduced penetrance.

Apr 05, 2021

Sema4, Sema4

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

May 01, 2025

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.8331+2T>C intronic variant results from a T to C substitution two nucleotides after coding exon 17 in the BRCA2 gene. This alteration has been reported in multiple hereditary breast and/or ovarian cohorts (Cunningham JM et al. Sci Rep, 2014 Feb;4:4026; Song H et al. Hum. Mol. Genet. 2014 Sep;23(17):4703-9; Kwong A et al. Oncotarget 2018 Jan;9(8):7832-7843; Heramb C et al. Hered Cancer Clin Pract 2018 Jan;16:3). This nucleotide position is highly conserved in available vertebrate species. Several variants at this splice donor site demonstrated substantial but incomplete abnormal splicing in multiple different RNA analyses (Ambry internal data; Fraile-Bethencourt E et al. PLoS Genet, 2017 Mar;13:e1006691; Gelli E et al. Cancers (Basel), 2019 Mar;11; Wangensteen T et al. Hered Cancer Clin Pract, 2019 May;17:14; Nix P et al. Fam Cancer, 2022 Jan;21:7-19). However, at least one recent RNA study has reported no aberrant splicing in association with this variant (Wai HA. Genet Med. 2020 Jun;22(6):1005-1014). In addition, this alteration was observed in individuals who collectively do not present with a clinical history seen in typical high-risk hereditary breast and ovarian cancer (HBOC) variant carriers (Nix P et al. Fam Cancer, 2022 Jan;21:7-19). However, these data cannot rule out the possibility of a hypomorphic variant with atypical risks. Based on the majority of available evidence to date, this variant is likely to be pathogenic. However, 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.

Familial cancer of breast Pathogenic:1

Apr 12, 2021

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.38	D
BayesDel_noAF	Pathogenic	0.31
CADD	Pathogenic	29
DANN	Uncertain	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.97
FATHMM_MKL	Pathogenic	1.0	D
PhyloP100		7.7
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.99
dbscSNV1_RF	Benign	0.66
Splicevardb		3.0
SpliceAI score (max)		0.93		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.93		Position offset: -2

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

Other links and lift over

dbSNP: rs398122602; hg19: chr13-32937672;