rs11571833

chr13-32398489-A-T

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP5_Strong BS3 BA1

This summary comes from the ClinGen Evidence Repository: The c.9976A>T variant in BRCA2 is predicted to cause a change in the length of the protein due to the insertion of a terminating codon instead of the usual Lysine at amino acid 3326 (p.Lys3326Ter). The highest non-cancer, non-founder population filter allele frequency in gnomAD v2.1 (exomes only, non-cancer subset, read depth ≥20) or gnomAD v3.1 (non-cancer subset, read depth ≥20) is 0.00813 in the European (non-Finnish) population, which is above the ENIGMA BRCA1/2 VCEP threshold (>0.001) for BA1 (BA1 met). Nonsense variant predicted to cause a premature stop codon that is predicted to escape nonsense mediated decay, and lead to truncation of a region with unknown protein function (sequence up to BRCA2:p.Glu3309 is maintained) (PVS1 not met). Reported by one calibrated study to exhibit protein function similar to benign control variants (PMID:29988080) (BS3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 3.09E-263 (based on Cosegregation LR=0.001; Pathology LR=1.864E-35; Co-occurrence LR=0.0001; Case-Control LR=1.66E-221), below the threshold for Very strong benign evidence (LR <0.00285) (BP5_Very strong met; PMID:18451181, Internal lab contributor).In summary, this variant meets the criteria to be classified as a Benign variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (BA1, BS3, BP5_Very strong). LINK:https://erepo.genome.network/evrepo/ui/classification/CA026350/MONDO:0012933/097

• Frequency:
  • Genomes: 𝑓 0.0060 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0081 (69 hom.)
• Consequence: BRCA2 NM_000059.4 stop_gained
• Clinical Significance: Benign reviewed by expert panel U:1 B:45 O:2
• Conservation: PhyloP100: 0.723

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 Benign. Variant got -16 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.9976A>T	p.Lys3326Ter	stop_gained	27/27	ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.9976A>T	p.Lys3326Ter	stop_gained	27/27	5	NM_000059.4	A2

Frequencies

GnomAD3 genomes AF: 0.00601 AC: 915 AN: 152244 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00116

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.00510

Gnomad ASJ AF: 0.00547

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00683

Gnomad FIN AF: 0.0104

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00849

Gnomad OTH AF: 0.00621

GnomAD3 exomes AF: 0.00660 AC: 1654 AN: 250748 Hom.: 14 AF XY: 0.00683 AC XY: 927 AN XY: 135670

Gnomad AFR exome AF: 0.00118

Gnomad AMR exome AF: 0.00264

Gnomad ASJ exome AF: 0.00397

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00693

Gnomad FIN exome AF: 0.0109

Gnomad NFE exome AF: 0.00895

Gnomad OTH exome AF: 0.00688

GnomAD4 exome AF: 0.00812 AC: 11863 AN: 1461794 Hom.: 69 Cov.: 31 AF XY: 0.00826 AC XY: 6006 AN XY: 727208

Gnomad4 AFR exome AF: 0.00120

Gnomad4 AMR exome AF: 0.00266

Gnomad4 ASJ exome AF: 0.00448

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00650

Gnomad4 FIN exome AF: 0.00985

Gnomad4 NFE exome AF: 0.00901

Gnomad4 OTH exome AF: 0.00725

GnomAD4 genome AF: 0.00600 AC: 914 AN: 152362 Hom.: 3 Cov.: 32 AF XY: 0.00585 AC XY: 436 AN XY: 74506

Gnomad4 AFR AF: 0.00115

Gnomad4 AMR AF: 0.00510

Gnomad4 ASJ AF: 0.00547

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00683

Gnomad4 FIN AF: 0.0104

Gnomad4 NFE AF: 0.00850

Gnomad4 OTH AF: 0.00615

Alfa AF: 0.00705 Hom.: 2

Bravo AF: 0.00539

TwinsUK AF: 0.0113 AC: 42

ALSPAC AF: 0.00934 AC: 36

ESP6500AA AF: 0.00272 AC: 12

ESP6500EA AF: 0.00837 AC: 72

ExAC AF: 0.00701 AC: 851

Asia WGS AF: 0.00231 AC: 8 AN: 3478

EpiCase AF: 0.00862

EpiControl AF: 0.00960

ClinVar

Significance: Benign

Submissions summary: Uncertain:1 Benign:45 Other:2

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Benign:14 Other:1

Benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Feb 22, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Sep 21, 2015	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	Oct 09, 2014	- -
Benign, criteria provided, single submitter	literature only	Counsyl	Jan 02, 2014	- -
Benign, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	May 29, 2002	- -
Benign, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Jul 07, 2023	- -
Benign, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	May 01, 2012	- -
Benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Mar 06, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Michigan Medical Genetics Laboratories, University of Michigan	Nov 03, 2014	- -
Benign, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Oct 06, 2021	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Benign, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Jun 02, 2022	The BRCA2 c.9976A>T variant is classified as Benign (BS2) -
Likely benign, no assertion criteria provided	literature only	Pathway Genomics	Jul 24, 2014	- -

not specified Benign:10 Other:1

Benign, criteria provided, single submitter	clinical testing	Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency	Apr 18, 2017	- -
Benign, criteria provided, single submitter	clinical testing	GeneKor MSA	Nov 01, 2017	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Oct 13, 2015	- -
not provided, no classification provided	reference population	ITMI	Sep 19, 2013	- -
Benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	May 11, 2020	- -
Benign, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Jan 31, 2014	- -
Benign, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	Department of Pathology and Molecular Medicine, Queen's University	Apr 20, 2017	- -

not provided Benign:8

Benign, no assertion criteria provided	research	Biesecker Lab/Clinical Genomics Section, National Institutes of Health	Jul 13, 2012	- -
Likely benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Feb 02, 2017	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	May 01, 2024	BRCA2: BS2 -
Benign, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 12, 2016	Variant summary: The BRCA2 c.9976A>T (p.Lys3326X) variant results in a termination codon at the penultimate exon, predicted to cause a truncation of the last 93 amino acids. This variant is not expected to affect any known domain (InterPro) and no truncations downstream of this position have been reported to be pathogenic in literature and databases. This variant was found in 2327/296226 control chromosomes (including 8 homozygotes) at a frequency of 0.0078555, which is approximately 10 times the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503), suggesting this variant is likely a benign polymorphism. In addition, several clinical diagnostic laboratories/reputable databases have classified this variant as benign (14)/likely benign (1). Available family, co-occurrence and functional data also show that it is not a disease causing variant. Despite these, this variant is found at considerably high frequency, especially in patients with breast and/or ovarian cancer, raising a possibilty that it may be a risk variant. Using weighted logistic regression, Meeks et al 2016 analyzed data from the large iCOGS study including 76637 cancer case patients and 83796 control patients to estimate odds ratios (ORw) and 95% confidence intervals (CIs) for K3326X variant carriers in relation to breast, ovarian, and prostate cancer risks, with weights defined as probability of not having a pathogenic BRCA2 variant. Other adjustments in the study were adjustment for attained age, consortium study site, and principal components of population structure. From the study, weighted ORs for invasive breast cancer and ovarian cancers were 1.28 (confidence interval 1.17-1.4; P-value=3.84x10e-3) and 1.26 (confidence interval 1.1-1.43; P-value=3.84x10e-3), respectively. The authors conclude that this study provides evidence that the K3326X variant is associated with risk of developing breast and ovarian cancers independent of other pathogenic variants in BRCA2. Hence this variant is a risk allele which attributes a significant but a low risk in development of breast or ovarian cancer. In addition, other genetic/lifestyle/environmental factors may also be playing a part in elevation of risk. Taken together, this variant is classified as Benign for HBOC. -
Benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Dec 27, 2016	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 22, 2023	- -

Hereditary breast ovarian cancer syndrome Uncertain:1 Benign:4

Benign, criteria provided, single submitter	research	Genetics Program, Instituto Nacional de Cancer	Nov 01, 2021	- -
Benign, criteria provided, single submitter	research	CSER _CC_NCGL, University of Washington	Mar 11, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	Jul 09, 2015	- -
Uncertain significance, criteria provided, single submitter	clinical testing	National Health Laboratory Service, Universitas Academic Hospital and University of the Free State	Apr 19, 2022	- -

Hereditary cancer-predisposing syndrome Benign:3

Benign, no assertion criteria provided	clinical testing	True Health Diagnostics	Feb 20, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Nov 19, 2014	- -
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. -

Breast and/or ovarian cancer Benign:2

Likely benign, no assertion criteria provided	clinical testing	Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research	Aug 02, 2013	- -
Likely benign, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Dec 19, 2017	- -

Malignant tumor of breast Benign:2

Benign, no assertion criteria provided	research	Center of Medical Genetics and Primary Health Care	Apr 08, 2020	ACMG Guidelines 2015 criteria -
Likely benign, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The BRCA2 p.Lys3326X variant was identified in 1577 of 158144 proband chromosomes (frequency: 0.010) from various ethnicities in multinational cohorts of individuals or families with breast and ovarian cancer and was present in 1414 of 167882 control chromosomes (frequency: 0.008) from healthy individuals (Hadjisavvas 2004 15172753, Wagner 1999 9971877, Borg 2010 20104584, Claes 2003 12759930, Meeks 2016 26586665). The variant was also identified in dbSNP (ID: rs11571833) as “With other allele”, ClinVar (Benign by ENIGMA, DVD CHOP, Michigan Medical Genetics, CSER_CC_NCGL University of Washington Medical Center, Colour Genomics, Prevention Genetics, Invitae, Counsyl, Ambry Genetics, Laboatroy Corporation of America Study Description, Children's Mercy Hospital, Fulgent, Cancer Genetic and Genomic Laboratory BC, EGL Genetic Diagnostics, Queen's University Department of Pathology, ARUP, Women's College Hospital, BIC, SCRP, and Biesecker Lab, as likely benign by Illumina, CHEO, and Pathway Genomics and as pathogenic by GeneReviews.), in ClinVitae (7x as Benign in 4 entries including 3 from ClinVar and 1 from EmyClass, as Conflicting interpretations of pathogenicity from Invitae and ClinVar, and as a polymorphism by kConFab), COSMIC (1x observed in alveolar rhabdomyosarcoma, as neutral), LOVD 3.0 (65x as does not affect function, affect unknown or unclassified), UMD-LSDB (114 entries, classified as neutral and reported as co-occuring with pathogenic BRCA2 and BRCA1 variants), BIC Database (301 entries, classification pending), and ARUP Laboratories (classified as not pathogenic or of no clinical significance). The variant was not identified in MutDB, or the Zhejiang Colon Cancer Database. The variant was also identified by our laboratory in 111 individuals with breast, ovarian, pancreatic, or brain cancer. The variant was identified in control databases in 1782 of 276718 chromosomes (13 homozygous) at a frequency of 0.006 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include African in 35 of 23984 chromosomes (freq: 0.001), Other in 48 of 6448 chromosomes (freq: 0.007), Latino in 95 of 34342 chromosomes (freq: 0.003), European Non-Finnish in 1089 of 126410 chromosomes (freq: 0.009), Ashkenazi Jewish in 41 of 10146 chromosomes (freq: 0.004), European Finnish in 266 of 25780 chromosomes (freq: 0.01), and South Asian in 208 of 30764 chromosomes (freq: 0.007) while the variant was not observed in the East Asian population. The c.9976A>T variant leads to a premature stop codon in the penultimate exon of BRCA2 and is predicted to cause a truncation of the last 93 amino acids. There is conflicting evidence in the literature regarding the significance of this variant. The variant was shown to have a 1.26 fold increase in breast cancer risk (in heterozygous form) or 5.78 increase risk (in homozygous form) (95% confidence interval p=1.2x10-5) and/or is in linkage disequilibrium with higher risk variants in a study looking at SNPs selected on the basis of genome wide association studies, genotyped in 45,290 cases and 41,880 controls from 41 studies (Michailidou 2013 23535729). A more recent study of the c.9976A>T variant identified 852/41081 carriers of the variant in women with breast cancer, and 322/14514 with ovarian cancer. They determined an odds ratio of adjusted for the probability of carrying a pathogenic BRCA1/2 variant of 1.28 for the breast cancer group, 1.52 for the triple negative breast cancer group and 1.46 for the serous ovarian cancer group (Meeks 2016 26586665). A posterior probability model integrating causality models based on prior probability derived from evolutionary conservation and likelihoods of causality, indicate that this variant is not pathogenic (Lindor_2012_21990134). However, in vitro splicing assays on 31 BRCA2 variants showed this variant to be pathogenic despite not being pathogenic ba -

Fanconi anemia complementation group D1 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Mar 06, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -

BRCA2-related cancer predisposition Benign:1

Benign, reviewed by expert panel

curation

ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen

Jun 11, 2024

The c.9976A>T variant in BRCA2 is predicted to cause a change in the length of the protein due to the insertion of a terminating codon instead of the usual Lysine at amino acid 3326 (p.Lys3326Ter). The highest non-cancer, non-founder population filter allele frequency in gnomAD v2.1 (exomes only, non-cancer subset, read depth >=20) or gnomAD v3.1 (non-cancer subset, read depth >=20) is 0.00813 in the European (non-Finnish) population, which is above the ENIGMA BRCA1/2 VCEP threshold (>0.001) for BA1 (BA1 met). Nonsense variant predicted to cause a premature stop codon that is predicted to escape nonsense mediated decay, and lead to truncation of a region with unknown protein function (sequence up to BRCA2:p.Glu3309 is maintained) (PVS1 not met). Reported by one calibrated study to exhibit protein function similar to benign control variants (PMID: 29988080) (BS3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 3.09E-263 (based on Cosegregation LR=0.001; Pathology LR=1.864E-35; Co-occurrence LR=0.0001; Case-Control LR=1.66E-221), below the threshold for Very strong benign evidence (LR <0.00285) (BP5_Very strong met; PMID: 18451181, Internal lab contributor). In summary, this variant meets the criteria to be classified as a Benign variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (BA1, BS3, BP5_Very strong). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.026	T
BayesDel_noAF	Pathogenic	0.27
CADD	Pathogenic	34
DANN	Uncertain	0.97
Eigen	Benign	0.0040
Eigen_PC	Benign	-0.30
FATHMM_MKL	Benign	0.044	N
MutationTaster	Benign	1.0	A;D
Vest4		0.64
GERP RS		0.16

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs11571833; hg19: chr13-32972626; COSMIC: COSV66337127; COSMIC: COSV66337127;