13-32344651-A-T

Position:

• chr13-32344651-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. 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 (★★★).

• 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:20
• Conservation: PhyloP100: 5.07

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP6: Variant 13-32344651-A-T is Benign according to our data. Variant chr13-32344651-A-T is described in ClinVar as [Benign]. Clinvar id is 52220.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32344651-A-T is described in Lovd as [Benign].
• BS2: High Homozygotes in GnomAdExome4 at 4 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.6935A>T	p.Asp2312Val	missense_variant, splice_region_variant	12/27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.6935A>T	p.Asp2312Val	missense_variant, splice_region_variant	12/27	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.6566A>T	p.Asp2189Val	missense_variant, splice_region_variant	12/27	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.6935A>T		splice_region_variant, non_coding_transcript_exon_variant	11/26	2		ENSP00000506251.1

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

GnomAD3 exomes AF: 0.000244 AC: 61 AN: 249766 Hom.: 1 AF XY: 0.000369 AC XY: 50 AN XY: 135340

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: 0.00190

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

Gnomad4 AFR exome AF: 0.0000311

Gnomad4 AMR exome AF: 0.0000225

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00209

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000169

Gnomad4 OTH exome AF: 0.000171

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

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000589

Gnomad4 OTH AF: 0.00

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:20

Revision: reviewed by expert panel

Submissions by phenotype

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

Benign, no assertion criteria provided	clinical testing	BRCAlab, Lund University	Mar 02, 2020	- -
Benign, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Jun 18, 2019	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 -
Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	May 29, 2002	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	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. -
Benign, criteria provided, single submitter	clinical testing	Counsyl	Jul 29, 2016	- -
Likely benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -

Hereditary cancer-predisposing syndrome Benign:4

Likely benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jul 11, 2016	- -
Likely benign, criteria provided, single submitter	clinical testing	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	Jul 12, 2017	- -
Benign, criteria provided, single submitter	curation	Sema4, Sema4	Dec 16, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Nov 19, 2014	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. -

not specified Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 07, 2017	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. -
Benign, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

not provided Benign:3

Likely benign, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	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 -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 27, 2016	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. -
Benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Sep 08, 2023	- -

Hereditary breast ovarian cancer syndrome Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 28, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	Jul 10, 2015	- -

Medulloblastoma;C0346153:Familial cancer of breast;C0376358:Malignant tumor of prostate;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

Likely benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

May 04, 2022

- -

Fanconi anemia complementation group D1 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

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

Likely benign, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Sep 23, 2024

- -

Computational scores

Source: dbNSFP v4.3

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;T
MetaSVM	Uncertain	0.52	D
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-2.1	N;N
REVEL	Pathogenic	0.89
Sift	Pathogenic	0.0	D;D
Sift4G	Uncertain	0.0020	D;D
Vest4		0.52
MutPred		0.41		Loss of ubiquitination at K2316 (P = 0.022);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

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

Publications

LitVar

Other links and lift over

dbSNP: rs80358916; hg19: chr13-32918788;