NM_000059.4:c.6935A>T

Variant names:

• chr13-32344651-A-T
• rs80358916
• NM_000059.4:c.6935A>T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 1P and 12B. PP3 BP6_Very_Strong BS2

The NM_000059.4(BRCA2):​c.6935A>T​(p.Asp2312Val) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000141 in 1,558,374 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D2312E) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000072 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00015 (4 hom.)
• Consequence: BRCA2 NM_000059.4 missense, splice_region
• Scores: Splicing: ADA: 0.9966
• Clinical Significance: Benign reviewed by expert panel U:1 B:23
• Conservation: PhyloP100: 5.07
• Publications: 26 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: Benign. The variant received -11 ACMG points.

• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.
• BP6: Variant 13-32344651-A-T is Benign according to our data. Variant chr13-32344651-A-T is described in ClinVar as Benign. ClinVar VariationId is 52220.Status of the report is reviewed_by_expert_panel, 3 stars.
• BS2: High Homozygotes in GnomAdExome4 at 4 AD,AR gene

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.6935A>T	p.Asp2312Val	missense splice_region	Exon 12 of 27	NP_000050.3
	BRCA2	NM_001432077.1		c.6935A>T	p.Asp2312Val	missense splice_region	Exon 12 of 27	NP_001419006.1
	BRCA2	NM_001406720.1		c.6935A>T	p.Asp2312Val	missense splice_region	Exon 12 of 27	NP_001393649.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRCA2	ENST00000380152.8	TSL:5 MANE Select	c.6935A>T	p.Asp2312Val	missense splice_region	Exon 12 of 27	ENSP00000369497.3
	BRCA2	ENST00000544455.6	TSL:1	c.6935A>T	p.Asp2312Val	missense splice_region	Exon 12 of 27	ENSP00000439902.1
	BRCA2	ENST00000530893.7	TSL:1	c.6566A>T	p.Asp2189Val	missense splice_region	Exon 12 of 27	ENSP00000499438.2

Frequencies

GnomAD3 genomes AF: 0.0000723 AC: 11 AN: 152100 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000244 AC: 61 AN: 249766 AF XY: 0.000369

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 FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000177

Gnomad OTH exome AF: 0.000165

GnomAD4 exome AF: 0.000149 AC: 209 AN: 1406156 Hom.: 4 Cov.: 27 AF XY: 0.000202 AC XY: 142 AN XY: 702668

African (AFR) AF: 0.0000311 AC: 1 AN: 32162

American (AMR) AF: 0.0000225 AC: 1 AN: 44536

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25722

East Asian (EAS) AF: 0.00 AC: 0 AN: 39298

South Asian (SAS) AF: 0.00209 AC: 178 AN: 85066

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53272

Middle Eastern (MID) AF: 0.000178 AC: 1 AN: 5610

European-Non Finnish (NFE) AF: 0.0000169 AC: 18 AN: 1061946

Other (OTH) AF: 0.000171 AC: 10 AN: 58544

GnomAD4 genome AF: 0.0000723 AC: 11 AN: 152218 Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5 AN XY: 74418

African (AFR) AF: 0.0000241 AC: 1 AN: 41566

American (AMR) AF: 0.00 AC: 0 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0000589 AC: 4 AN: 67966

Other (OTH) AF: 0.00 AC: 0 AN: 2112

Alfa AF: 0.000217 Hom.: 0

Bravo AF: 0.0000567

ExAC AF: 0.000264 AC: 32

Asia WGS AF: 0.000289 AC: 1 AN: 3476

EpiCase AF: 0.00

EpiControl AF: 0.0000593

ClinVar

Significance: Benign

Submissions summary: Uncertain:1 Benign:23

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Uncertain:1 Benign:5

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

Jun 18, 2019

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

Significance: Benign

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 1 based on posterior probability = 0.000027

May 29, 2002

Breast Cancer Information Core (BIC) (BRCA2)

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

May 28, 2019

Mendelics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Mar 02, 2020

BRCAlab, Lund University

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

Jul 29, 2016

Counsyl

Significance: Benign

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.

Hereditary cancer-predisposing syndrome Benign:5

Jul 11, 2016

Color Diagnostics, LLC DBA Color Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jul 12, 2017

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

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Dec 16, 2021

Sema4, Sema4

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: curation

Nov 19, 2014

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

Jan 15, 2025

Molecular Diagnostics Laboratory, Catalan Institute of Oncology

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BA1, BS3, PP3 c.6935A>T, located in exon 12 of the BRCA2 gene, is predicted to result in the in the substitution of aspartic acid by valine at codon 2312, p.(Asp2312Val). This position is outside a (potentially) clinically important functional but the SpliceAI algorithm predicts a slight effect on the splicing donor site of intron 12 (deltascore=0.22; ALT score=0.73) and activates a cryptic splice donor site: one nucleotide upstream (deltascore=0.14, ALT score=0.14)(PP3). This missense variant shown to alter splicing, functional data considered only from assays that measure effect via mRNA and protein. Reported by two calibrated studies incorporating mRNA splicing effect to affect function similar to benign control variants (PMID:29988080, 33293522) (BS3) The variant allele was found in 58/30450 alleles, with a filter allele frequency of 0.14% at 99% confidence in the gnomAD v2.1.1 database (South Asian exome non-cancer data set)(BA1). This variant has been reported in ClinVar (1x uncertain significance, 10x likely benign, 9x benign) and LOVD (5x uncertain significance, 6x benign, 3x not classified) databases and in BRCA Exchange database as benign (“IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on posterior probability = 0.000027”). Based on currently available information, the variant c.6935A>T is classified as a benign variant according to ClinGen- BRCA1 and BRCA2 Guidelines version 1.0.0.

not provided Benign:4

Feb 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BRCA2: BP1, BP2, BS3:Supporting, BS1

Sep 08, 2023

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jun 27, 2016

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

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: The BRCA2 c.6935A>T (p.Asp2312Val) variant involves the alteration of a non-conserved nucleotide. 5/5 in silico tools predict damaging outcome for this variant. This variant is only three nucleotides away from the nearest exon-intron boundary and is thus predicted to affect normal splicing. 3/5 splice prediction tools predict a significant impact on normal splicing. But in vitro studies show that this variant does not significantly affect normal splicing (Houdayer_2011, Brandao_2011). This variant was found in 32/113924 control chromosomes (including one homozygote), predominantly observed in the South Asian, subpopulation at a frequency of 0.0016915 (27/15962). This frequency is about 2 times higher than the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503), suggesting this is likely a benign polymorphism found primarily in the populations of South Asian. This variant has been reported in several instances in HBOC patients and/or individuals undergoing BRCA1/2 testing including co-occurrence with another deleterious variant (p.Lys1026Ter) in the same gene, strongly supporting for the benign outcome. Multifactorial probability-based models are also consistent with the benign outcome. Multiple clinical labs have classified this variant as benign/likely benign. Taken together, this variant is currently classified as Likely Benign.

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

The BRCA2 p.Asp2312Val variant was identified in 3 of 4718 proband chromosomes (frequency: 0.0006) from Brazilian, German and Other individuals or families at high risk of breast and ovarian cancers, and was present in 1 of 230 control chromosomes (frequency: 0.004) from healthy elderly Croatian women (Fernandes 2016, Trujillano_2015, Brandao 2011). The variant was identified by Brandao (2011) in an individual from a high-risk breast and/or ovarian cancer family and RT-PCR transcript analysis of lymphocytes from this individual showed an increase in exon12 skipping as compared to normal controls; however, the BRCA2 exon 12 deletion isoform is naturally occurring and the c.6935T allele expressed full-length transcript at similar expression levels compared with the wild-type (WT) allele and control alleles suggesting the variant is likely to be neutral. Li (2009) studied a different variant in this region which was also shown to increase exon 12 skipping, and functional results from this study did not detect any difference between this variant and wild type, suggesting that exon 12 is functionally redundant and missense changes in this region are likely to be neutral. In addition, Li (2009) notes that the peptide encoded by exon 12 does not contain any known important functional motifs; however, this region may have a role in processes that were not assessed. An in silico likelihood-ratio study by Easton (2007) suggests that this variant is neutral. In addition, a splice study using 6 in silico models, with predictions compared to transcript analysis showed the variant does not effect change on splicing (Houdayer 2012). The variant was also identified in dbSNP (ID: rs80358916), ClinVar (with conflicting interpretations of pathogenicity; classified as benign by Ambry Genetics, Counsyl, Invitae; likely benign by Prevention Genetics, Div of Genomic Diagnostics - Children's Hospital of Philadelphia, Illumina Clinical Services, GeneDx; and uncertain significance by BIC), Clinvitae (5X), LOVD 3.0 (4x), UMD-LSDB (10X, 1-neutral), and the BIC Database (5x, clinical importance unknown, classification pending). The variant was not identified in the COGR, Cosmic, ARUP Laboratories, and Zhejiang Colon Cancer Databases. The variant was also identified in control databases in 64 (1 homozygous) of 276074 chromosomes at a frequency of 0.0002 in the following populations: other in 1 of 6424 chromosomes (freq. 0.00016), European in 2 of 126058 chromosomes (freq. 0.000016), Ashkenazi Jewish in 1 of 10110 chromosomes (freq. 0.0001), South Asian in 60 of 30712 chromosomes (freq. 0.0002), increasing the likelihood this could be a low frequency variant (Genome Aggregation Consortium Feb 27, 2017). The variant was also identified by our laboratory in 3 individuals with breast and ovarian cancer. The p.Asp2312 residue is conserved in mammals but not in more distantly related organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The p.Asp2312Val variant occurs in the 3rd last base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In addition, 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign

not specified Benign:3

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Dec 07, 2017

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

Hereditary breast ovarian cancer syndrome Benign:2

Jul 10, 2015

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jan 26, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Medulloblastoma;C0346153:Familial cancer of breast;C0376358:Prostate cancer;C1838457:Fanconi anemia complementation group D1;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2;C2751641:Glioma susceptibility 3;C3150546:Pancreatic cancer, susceptibility to, 2;CN033288:Wilms tumor 1 Benign:1

May 04, 2022

Fulgent Genetics, Fulgent Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Fanconi anemia complementation group D1 Benign:1

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

BRCA2-related cancer predisposition Benign:1

Sep 23, 2024

All of Us Research Program, National Institutes of Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Inherited ovarian cancer (without breast cancer) Benign:1

Nov 06, 2024

Genomics and Molecular Medicine Service, East Genomic Laboratory Hub, NHS Genomic Medicine Service

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.27
BayesDel_addAF	Benign	-0.059	T
BayesDel_noAF	Pathogenic	0.14
CADD	Pathogenic	32
DANN	Uncertain	0.99
Eigen	Uncertain	0.64
Eigen_PC	Uncertain	0.60
FATHMM_MKL	Uncertain	0.95	D
M_CAP	Uncertain	0.28	D
MetaRNN	Benign	0.084	T
MetaSVM	Uncertain	0.52	D
PhyloP100		5.1
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-2.1	N
REVEL	Pathogenic	0.89
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0020	D
Vest4		0.52
MutPred		0.41		Loss of ubiquitination at K2316 (P = 0.022)
MVP		0.97
MPC		0.18
ClinPred		0.24	T
GERP RS		5.0
gMVP		0.44
Mutation Taster		=53/47	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.89
SpliceAI score (max)		0.22		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.22		Position offset: 2

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

Other links and lift over

dbSNP: rs80358916; hg19: chr13-32918788;