chr13-32379516-G-T

Variant names:

• chr13-32379516-G-T
• rs81002882
• NM_000059.4:c.8953+1G>T

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000059.4(BRCA2):​c.8953+1G>T variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.000000685 in 1,459,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 splice_donor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:19
• Conservation: PhyloP100: 5.38
• Publications: 9 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 18 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, Cryptic splice site detected, with MaxEntScore 4.6, offset of 4, new splice context is: taaGTatgt. Cryptic site results in frameshift 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 13-32379516-G-T is Pathogenic according to our data. Variant chr13-32379516-G-T is described in ClinVar as Pathogenic. ClinVar VariationId is 38198.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.8953+1G>T		splice_donor_variant, intron_variant	Intron 22 of 26	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.8953+1G>T		splice_donor_variant, intron_variant	Intron 22 of 26	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.8584+1G>T		splice_donor_variant, intron_variant	Intron 22 of 26	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.*1011+1G>T		splice_donor_variant, intron_variant	Intron 21 of 25	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.85e-7 AC: 1 AN: 1459830 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 726144

African (AFR) AF: 0.00 AC: 0 AN: 33364

American (AMR) AF: 0.00 AC: 0 AN: 44378

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26070

East Asian (EAS) AF: 0.00 AC: 0 AN: 39632

South Asian (SAS) AF: 0.00 AC: 0 AN: 85818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53228

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5758

European-Non Finnish (NFE) AF: 9.00e-7 AC: 1 AN: 1111274

Other (OTH) AF: 0.00 AC: 0 AN: 60308

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000536 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:19

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:8

May 29, 2002

Breast Cancer Information Core (BIC) (BRCA2)

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jan 03, 2017

Counsyl

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

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. -

Aug 10, 2015

Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 5 based on posterior probability = 1 -

Feb 21, 2012

Sharing Clinical Reports Project (SCRP)

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 02, 2020

BRCAlab, Lund University

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

May 27, 2024

Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PVS1 (RNA); PM2_Supporting; PP4strong -

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 16, 2023

All of Us Research Program, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.8953+1G>T variant in the BRCA2 gene is located at the canonical splice site of intron 22 and is predicted to inflict donor loss (SpliceAI delta score: 0.99), resulting in aberrant splicing and disrupted protein product. The variant has been reported in multiple individuals with breast/ovarian/prostate cancer (PMID: 31209999, 32022259, 32614418, 21394826, 36045058, 18465347). Functional minigene splicing assay and RNA analysis showed aberrant transcripts and negative functional impact (PMID: 25382762, 21394826). Loss-of-function variants of BRCA2 are known to be pathogenic (PMID: 8988179, 11897832, 29446198). The variant is reported in ClinVar as pathogenic (ID: 38198) and reviewed by the expert panel. The variant is absent in the general population database (gnomAD). Therefore, the c.8953+1G>T variant of BRCA2 has been classified as pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:4

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

- -

Feb 08, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.8953+1G>T variant in BRCA2 has been reported in 3 individuals with BRCA2-a ssociated cancers (Borg 2010, Breast Cancer Information Core (BIC) database) and was absent from large population studies. This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and is predicted to cause alte red splicing leading to an abnormal or absent protein. In vitro functional studi es provide some evidence that the c.8953+1G>T variant impacts splicing (Whiley 2 011, Acedo 2015). Heterozygous loss of function of the BRCA2 gene is an establis hed disease mechanism in individuals with hereditary breast and ovarian cancer ( HBOC). In addition, this variant was classified as Pathogenic on August 10, 2015 by the ClinGen-approved ENIGMA expert panel (ClinVar SCV000244490.1). In summar y, the c.8953+1G>T variant meets our criteria to be classified as pathogenic for HBOC in an autosomal dominant manner based upon absence from controls, function al evidence, and the predicted impact to the protein. -

Aug 29, 2023

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: BRCA2 c.8953+1G>T is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5' splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing. These predictions have been confirmed by functional studies that showed variant lead to exon 22 skipping (Whiley_2011 and Acedo_2014). The variant was absent in 248098 control chromosomes. c.8953+1G>T has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (eg. Borg_2010, Thomassen_2008, Whiley_2011, Nielsen_2017, Sharma_2015, Euhus_2002, etc). These data indicate that the variant is likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 21990134, 20104584, 21394826, 18465347, 12048272, 25382762, 26360800, 26004055). 11 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Aug 12, 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 22 of the BRCA2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or altered protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with breast cancer (PMID: 2010458, 21394826, 26187060). This variant is also known as 9181+1G>T and IVS22+1G>T. ClinVar contains an entry for this variant (Variation ID: 38198). An algorithm developed specifically for the BRCA2 gene suggests that this missense change is likely to be deleterious (PMID: 21990134). Studies have shown that disruption of this splice site results in skipping of exon 22 and activation of a cryptic splice site, which introduces a premature termination codon (PMID: 21394826; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:3

Apr 30, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The BRCA2 c.8953+1G>T variant disrupts a canonical splice-donor site and interferes with normal BRCA2 mRNA splicing. This variant has been reported in the published literature in individuals with prostate cancer (PMID: 26360800 (2016), 36045058 (2023)) and breast and/or ovarian cancer (PMID: 20104584 (2010), 26004055 (2016), 32022259 (2020), 32939053 (2020)). In vitro splicing assays demonstrated that this variant results in aberrant BRCA2 mRNA splicing (PMID: 21394826 (2011) and 25382762 (2015)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as pathogenic. -

Jul 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BRCA2: PVS1, PM2 -

Apr 20, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Observed in individuals with BRCA2-related cancers (Borg 2010, Whiley 2011, Sharma 2016, Roed Nielsen 2016); Published functional studies demonstrate a damaging effect: multiple aberrant transcripts, with skipping of exon 22 being the most prevalent (Whiley 2011, Acedo 2015); Multifactorial studies suggest this variant is associated with breast and ovarian cancer (Lindor 2012); Considered pathogenic by a well-established clinical consortium and/or database; Not observed at significant frequency in large population cohorts (gnomAD); Also known as BRCA2 9181+1G>T; This variant is associated with the following publications: (PMID: 20104584, 29922827, 32022259, 21990134, 26004055, 25382762, 26360800, 29164420, 21394826, 29446198, 31209999, 31263571) -

Hereditary cancer-predisposing syndrome Pathogenic:3

Oct 12, 2021

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes a G to T nucleotide substitution at the +1 position of intron 22 of the BRCA2 gene. RNA studies have shown that this variant causes out-of-frame splicing, resulting in premature termination (PMID: 21394826, 25382762). This variant is expected to result in an absent or non-functional protein product. This variant has been reported in at least three individuals affected with breast or ovarian cancer (PMID: 29164420, 32022259; Color internal data), an individual affected with prostate cancer (PMID: 26360800) and suspected hereditary cancer families (PMID: 21394826, 31209999). 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. -

Jan 16, 2018

Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 01, 2022

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.8953+1G>T intronic pathogenic mutation results from a G to T substitution one nucleotide after coding exon 21 of the BRCA2 gene. Multiple RNA studies with patient material and with a minigene assay have identified skipping of coding exon 21 (also known as Exon 22 in the literature) as the major event produced by this alteration (Ambry internal data; Acedo A et al. Hum Mutat, 2015 Feb;36:210-21; Whiley P et al. Hum Mutat. 2011 Jun;32(6):678-87). This alteration has been reported in a woman with asynchronous contralateral breast cancer; an individual with prostate cancer, and an individual with metachronous early onset breast cancer and tubulovillous adenoma of the papilla of Vater (Borg A et al. Hum Mutat. 2010 Mar;31(3):E1200-40;Roed Nielsen H et al. Acta Oncol, 2016 Sep;55:38-44; Sharma MB et al. Acta Oncol, 2016 May;55:377-81). This alteration has been classified as pathogenic (p>0.96) by multifactorial analysis, which integrates the following lines of evidence to produce a quantitative likelihood of pathogenicity: in silico prediction models, segregation with disease, tumor characteristics, mutation co-occurrence, and functional assay results (Lindor NM et al. Hum Mutat. 2012;33(1):8-21). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -

Familial cancer of breast Pathogenic:1

Dec 19, 2022

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.080
CADD	Pathogenic	34
DANN	Uncertain	0.99
Eigen	Pathogenic	0.98
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Pathogenic	0.99	D
PhyloP100		5.4
GERP RS		5.3
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.84
Splicevardb		3.0
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.59		Position offset: 3
DS_DL_spliceai		0.99		Position offset: -1

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

Other links and lift over

dbSNP: rs81002882; hg19: chr13-32953653;