13-32394803-A-T

Variant names:

• chr13-32394803-A-T
• rs28897759
• NM_000059.4:c.9371A>T

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000059.4(BRCA2):​c.9371A>T​(p.Asn3124Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000186 in 1,613,530 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N3124K) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:42 U:1
• Conservation: PhyloP100: 6.06
• Publications: 65 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.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 19 benign, 35 uncertain in NM_000059.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-32394804-C-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 462524.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.966
• PP5: Variant 13-32394803-A-T is Pathogenic according to our data. Variant chr13-32394803-A-T is described in ClinVar as Pathogenic. ClinVar VariationId is 38233.Status of the report is reviewed_by_expert_panel, 3 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.9371A>T	p.Asn3124Ile	missense	Exon 25 of 27	NP_000050.3
	BRCA2	NM_001432077.1		c.9371A>T	p.Asn3124Ile	missense	Exon 25 of 27	NP_001419006.1
	BRCA2	NM_001406720.1		c.9320A>T	p.Asn3107Ile	missense	Exon 25 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.9371A>T	p.Asn3124Ile	missense	Exon 25 of 27	ENSP00000369497.3
	BRCA2	ENST00000544455.6	TSL:1	c.9371A>T	p.Asn3124Ile	missense	Exon 25 of 27	ENSP00000439902.1
	BRCA2	ENST00000530893.7	TSL:1	c.9002A>T	p.Asn3001Ile	missense	Exon 25 of 27	ENSP00000499438.2

Frequencies

GnomAD3 genomes AF: 0.00000659 AC: 1 AN: 151714 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.00000398 AC: 1 AN: 251346 AF XY: 0.00000736

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: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461816 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 727208

African (AFR) AF: 0.00 AC: 0 AN: 33478

American (AMR) AF: 0.00 AC: 0 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26130

East Asian (EAS) AF: 0.00 AC: 0 AN: 39682

South Asian (SAS) AF: 0.00 AC: 0 AN: 86254

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53416

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

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1111976

Other (OTH) AF: 0.00 AC: 0 AN: 60392

GnomAD4 genome AF: 0.00000659 AC: 1 AN: 151714 Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1 AN XY: 74022

African (AFR) AF: 0.00 AC: 0 AN: 41268

American (AMR) AF: 0.00 AC: 0 AN: 15230

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.00 AC: 0 AN: 4794

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10564

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 67910

Other (OTH) AF: 0.00 AC: 0 AN: 2078

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ExAC AF: 0.0000165 AC: 2

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:42 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:14 Uncertain:1

Aug 26, 2022

BRCAlab, Lund University

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

Sep 10, 2024

Department of Human Genetics, Hannover Medical School

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Sep 01, 2023

Department of Medical and Surgical Sciences, University of Bologna

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

PS3(Strong)+PM2(Supporting)+PP4(Very Strong) according to ACMG/AMP classification guidelines specified for BRCA1 & BRCA2 (Classification Criteria V1.0.0 2023-09-08 - https://cspec.genome.network/cspec/ui/svi/affiliation/50087) (PMID: 38160042)

Jul 28, 2017

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

May 28, 2019

Mendelics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Feb 04, 2022

Human Genetics Bochum, Ruhr University Bochum

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG criteria used to clasify this variant: PP3, PS3, PM1, PS4, PM2

Nov 24, 2023

Zotz-Klimas Genetics Lab, MVZ Zotz Klimas

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

Jun 18, 2019

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 20, 2004

Breast Cancer Information Core (BIC) (BRCA2)

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

Jul 16, 2013

Sharing Clinical Reports Project (SCRP)

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

Jun 17, 2016

Counsyl

Significance: Likely 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.

Feb 01, 2016

Genetic Services Laboratory, University of Chicago

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Dec 21, 2021

Institute of Human Genetics Munich, TUM University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Sep 15, 2025

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PP4_VSTR,PS3

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

not provided Pathogenic:13

Jul 07, 2014

Clinical Genetics and Genomics, Karolinska University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

May 28, 2021

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has been reported in individuals and families with breast and/or ovarian cancer in the published literature (PMID: 24728577 (2014), 25085752 (2014), 22729890 (2012) and 11139248 (2001)). In addition, functional studies in the published literature demonstrate that this variant is damaging to BRCA2 protein function (PMID: 32444794 (2020), 23108138 (2013), 22678057 (2012), and 22729890 (2012)). Publications describe this variant as recurrent pathogenic variant in the Polish population (PMID: 28324225 (2017) and 26843898 (2016)). Based on the available information, this variant is classified as pathogenic.

Dec 18, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Observed in individuals with BRCA2-related cancers and described as a recurrent pathogenic variant in the Eastern European population (PMID: 11139248, 21965345, 20383589, 22366370, 24728577, 25452441, 25948282, 26786923, 26843898, 29161300); Published functional studies demonstrate a damaging effect: defective homology-directed DNA break repair, impaired protein structure and stability, and sensitivity to PARP inhibitors (PMID: 22678057, 23108138, 29394989, 29884841, 32444794, 33964450, 33609447, 35736817); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); Also known as 9599A>T; This variant is associated with the following publications: (PMID: 24323938, 21965345, 16284991, 20383589, 11102977, 22366370, 28888541, 29161300, 11139248, 22729890, 21232165, 25782689, 26843898, 25948282, 23108138, 26219265, 25452441, 22678057, 21120943, 26689913, 18724707, 19043619, 23583677, 11452040, 24728577, 26786923, 27153395, 28324225, 28873162, 25085752, 11802209, 28715532, 29387975, 29506128, 29394989, 31131967, 29907814, 29988080, 29446198, 31159747, 29884841, 32444794, 34597585, 34426522, 34399810, 30787465, 30613976, 31360904, 33964450, 33609447, 35665744, 35736817, 35264596, 30040829, 29922827, 32772980, 12228710, 27535533, 21990134)

Oct 01, 2022

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Aug 31, 2017

Eurofins Ntd Llc (ga)

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Oct 23, 2020

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

Nov 03, 2021

Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

Sep 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BRCA2: PS4, PM2, PP1:Moderate, PS3:Moderate

Jun 20, 2025

Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has been identified by standard clinical testing. female patient with ovarian cancer

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Familial cancer of breast Pathogenic:4

Dec 19, 2023

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jan 01, 2020

GeneKor MSA

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces Asparagine with Isoleucine at codon 3124 of the BRCA2 protein. The asparagine residue is highly conserved and is located in the oligonucleotide/oligosaccharide-binding, domain of the protein. There is a large physiochemical difference between asparagine and isoleucine (Grantham Score 149). This variant, also known as 9599A>T using an alternate transcript, has been reported in multiple individuals and families affected by breast and ovarian cancer (PMID: 11102977, 16284991, 18703817, 21120943, 21232165, 21965345, 22366370, 22729890, 25948282) and has been shown in epidemiological studies to be a common cause of breast and ovarian cancer in Poland and Germany (PMID: 11802209, 20383589, 24728577, 25948282). This variant is present in population databases at a low frequency (rs28897759, ExAC 0.003%). The mutation database ClinVar contains multiple entries for this variant (Variation ID: 38233).

Aug 26, 2021

MGZ Medical Genetics Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

May 13, 2024

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PP1_VSTR,PS3

Hereditary breast ovarian cancer syndrome Pathogenic:4

Oct 10, 2018

Cancer Variant Interpretation Group UK, Institute of Cancer Research, London

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

Data used in classification: This variant is predicted deleterious on AlignGVGD (class: C65), SIFT (Deleterious), Polyphen2 HumVar (probably damaging) and CADD (22.4) (PP3_sup). The variant is in the DNA-binding domain of BRCA2 (PM1_sup). In the BRCA2 Homology-Directed Repair Activity assay for the DNA Binding Domain (Guidugli et al Cancer Res 2013;73:265-275,Couch Lab), the variant has a probability of pathogenicity of 1.0 (PS3_strong). This variant is classified on ClinVar as pathogenic by multiple USA accredited diagnostic laboratories (PP5_sup). Data not used in classification: The frequency of this variant is 2/123,053 individuals (gnomAD). There are additional reports of this variant in UMD (6), BIC (17), and BRCA2 LOVD (1).

Dec 17, 2015

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

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

Jan 21, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces asparagine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 3124 of the BRCA2 protein (p.Asn3124Ile). This variant is present in population databases (rs28897759, gnomAD 0.002%). This missense change has been observed in individual(s) with breast and/or ovarian cancer (PMID: 11102977, 16284991, 18703817, 21120943, 21232165, 21965345, 22366370, 22729890, 25948282). It is commonly reported in individuals of Polish and German ancestry (PMID: 11802209, 20383589, 24728577, 25948282). This variant is also known as 9599A>T and p. Asn312lle. ClinVar contains an entry for this variant (Variation ID: 38233). Invitae Evidence Modeling incorporating data from in vitro experimental studies (PMID: 33609447) indicates that this missense variant is expected to disrupt BRCA2 function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects BRCA2 function (PMID: 22678057, 23108138). For these reasons, this variant has been classified as Pathogenic.

Mar 03, 2021

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.9371A>T (p.Asn3124Ile) results in a non-conservative amino acid change located in the BRCA2, OB3 domain (IPR015188) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.9e-06 in 257878 control chromosomes (gnomAD and publication data). c.9371A>T has been reported in the literature in multiple individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (Biswas_2012, Surowy_2014, Rebbeck_2018). Additionally, the single largest study of families presenting with this variant reports the suggestive co-segregation (20 families tested; variant present in 7 unaffected family members and variant absent in 3 affected family members) and provides likelyhood ratio data that is suggestive, but not entirely conclusive, of pathogenicity (Biswas_2012). These data indicate that the variant is very likely to be associated with disease. One co-occurrence with another pathogenic variant has been reported (BRCA1 c.5209A>T, p.Arg1737Ter, BIC database). Functional studies show the variant to disrupts BRCA2 homology-directed DNA break repair activity, and that it is unable to rescue the phenotype in BRCA2 null (Guidugli_2012, Biswas_2012, Ikegami_2020). Another study showed no accumulation of increased chromosomal damage in lymphocytes from a carrier after irradiation (Becker_2012). 20 ClinVar submitters (evaluation after 2014) cite the variant pathogenic (n=12) and likely pathogenic (n=8) , including one expert panel (ENIGMA) classified this variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:2

Apr 02, 2020

Department of Molecular Diagnostics, Institute of Oncology Ljubljana

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Mar 04, 2025

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PP4_VSTR,PS3

Hereditary cancer-predisposing syndrome Pathogenic:2

Aug 26, 2024

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.N3124I pathogenic mutation (also known as c.9371A>T), located in coding exon 24 of the BRCA2 gene, results from an A to T substitution at nucleotide position 9371. The asparagine at codon 3124 is replaced by isoleucine, an amino acid with dissimilar properties. This alteration has been predicted to be pathogenic based on cell-based functional assays (Biswas K et al. Hum. Mol. Genet. 2012 Sep;21:3993-4006; Guidugli L et al. Cancer Res. 2013 Jan;73:265-75). This alteration has been described in several high risk breast and ovarian cancer families and in cohorts of individuals with ovarian cancer (Grzybowska E et al. Hum. Mutat. 2000 Dec;16:482-90; Kwiatkowska E et al. Hum. Mutat. 2001;17:73; Pal T et al. Cancer. 2005 Dec;104:2807-16; Balabas A et al. Fam. Cancer. 2010 Sep;9:267-74; Stegel V et al. BMC Med. Genet. 2011 Jan;12:9; Akbari MR et al. J. Med. Genet. 2011 Nov;48:783-6; Surowy HM et al. Breast Cancer Res. Treat. 2014 Jun;145:451-60; Couch FJ et al. J. Clin. Oncol. 2015 Feb;33:304-11; Kluska A et al. BMC Med Genomics 2015 May;8:19; Wojcik P et al. Hered. Cancer Clin. Pract. 2016 Feb;14:5; Thompson ER et al. J. Clin. Oncol. 2016 May;34:1455-9; Alemar B et al. PLoS One, 2017 Nov;12:e0187630; Meisel C et al. Arch Gynecol Obstet. 2017 May;295(5):1227-1238; Goidescu IG et al. Clujul Med, 2018 Apr;91:157-165; Kowalik A et al. PLoS One, 2018 Jul;13:e0201086; Lowery MA et al. J Natl Cancer Inst, 2018 10;110:1067-1074; Rebbeck TR et al. Hum Mutat, 2018 05;39:593-620). Of note, this alteration is also designated as 9599A>T in published literature. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this variant is interpreted as a disease-causing mutation.

Apr 07, 2025

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces asparagine with isoleucine at codon 3124 in the DNA binding domain of the BRCA2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function. Functional studies have shown that the variant impacts BRCA2 activities in homology-directed DNA repair assays (PMID: 22678057, 23108138, 29394989, 29988080, 33609447, 35736817), in sensitivity assays to PARP inhibitors, cisplatin and carboplatin (PMID: 32444794, 37922907) and in a haploid cell proliferation assay (PMID: 39779857). This variant has been reported in more than 20 individuals affected with breast cancer and ovarian cancer (PMID: 11102977, 11139248, 11802209, 20383589, 21232165, 21965345, 22366370, 24728577, 26786923, 26843898, 27616075, 30040829, 34399810). This variant has shown a significant association with breast cancer in a large case-control study conducted by the BRIDGES consortium (14/60466 cases, 1/53461 controls; OR=12.381 (95%CI 1.628 to 94.157); p-value=0.001; Leiden Open Variation Database DB-ID BRCA2_000450). Multifactorial analyses have reported likelihood ratios for pathogenicity based on segregation, tumor pathology, co-occurrence with a pathogenic variant and personal and family history for 8 carriers that resulted in a combined LR well in excess of 1,000 (PMID: 31131967, 31853058). This variant has been identified in 1/251346 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.

Breast and/or ovarian cancer Pathogenic:1

Jun 11, 2019

CZECANCA consortium

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

BRCA2-related cancer predisposition Pathogenic:1

Mar 25, 2024

All of Us Research Program, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces asparagine with isoleucine at codon 3124 in the DNA binding domain of the BRCA2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have shown that this variant results in the loss of homology-directed repair activity of the BRCA2 protein (PMID: 22678057, 23108138, 29394989, 29988080, 33609447, 33964450). This variant has been reported in more than 20 individuals affected with breast cancer and ovarian cancer (PMID: 11102977, 11139248, 11802209, 20383589, 21232165, 21965345, 22366370, 24728577, 26786923, 26843898, 27616075, 30040829, 34399810). This variant has shown a significant association with breast cancer in a large case-control study conducted by the BRIDGES consortium (14/60466 cases, 1/53461 controls; OR=12.381 (95%CI 1.628 to 94.157); p-value=0.001; Leiden Open Variation Database DB-ID BRCA2_000450). This variant has been identified in 1/251346 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.

Malignant tumor of breast Pathogenic:1

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The p.Asn3124Ile variant was identified in 10 of 5262 proband chromosomes (frequency: 0.002) from individuals or families with hereditary breast and/or ovarian cancer (HBOC), and was not identified in 1500 control chromosomes from healthy individuals (Akbari 2011, Balabas 2010, Biswas 2012, Grzybowska 2000, Guidugli 2013, Karchin 2008, Levanat 2012, Meindl 2002, Rajasekaran 2008, Stegel 2011). The variant was identified in dbSNP as “with pathogenic allele” (ID: rs28897759), in Exome Aggregation Consortium (ExAC) database in 2 of 66670 alleles in the European (non-Finnish) population. It was also found in HGMD, LOVD, the ClinVar database (classified as Pathogenic variant by the Sharing Clinical Reports Project; classified as pathogenic by ambry Genetics; classified as Uncertain significance by BIC and classification not provided by Invitae). In GeneInsight through the COGR (http://opengenetics.ca/) the variant was identified 1x classified as “unknown” by a clinical laboratory, in the BIC database classified as 17x with unknown clinical importance, and in UMD 6x as an unknown variant. The p.Asn3124 residue is conserved across mammals and lower organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the p.Asn3124Ile may impact the protein. In one study (Biswas 2012), which examined co-segregation likelihood ratios, the data was suggestive, but not conclusive, of causality or pathogenicity (LR variant = 36.95) for the p.Asn3124Ile. In addition, in vitro functional studies showed the p.Asn3124Ile variant compromised BRCA2 function (Biswas 2012, Guidugli 2013). In silico structural studies predict the missense change to disrupt the structural integrity of the protein (Biswas 2012, Levanat 2012), and multifactorial likelihood-ratio models showed higher odds in favor of causality for this variant (Karchin 2008), increasing the likelihood this variant may have clinical significance. In one study (Surowy 2014), reviewing all evidence on p.Asn3124Ile variant, the authors investigated the potential pathogenic nature of the p.Asn3124Ile variant. The authors detected the variant in seven families with high-risk familial breast and other related cancers. The absence of this variant in more than 3,000 control individuals of the same geographical region, its absence in individuals with breast cancer with pathogenic BRCA1/2 mutations, its co-segregation with breast and ovarian cancer in one first degree relative in one family, and consistent results of in silico prediction analyses confirm the strong association with high breast cancer risk and underline that the BRCA2 p.Asn3124Ile variant is most likely a pathogenic mutation. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.91
BayesDel_addAF	Pathogenic	0.30	D
BayesDel_noAF	Pathogenic	0.21
CADD	Pathogenic	26
DANN	Uncertain	0.99
Eigen	Pathogenic	0.81
Eigen_PC	Pathogenic	0.78
FATHMM_MKL	Uncertain	0.96	D
M_CAP	Pathogenic	0.43	D
MetaRNN	Pathogenic	0.97	D
MetaSVM	Pathogenic	0.89	D
PhyloP100		6.1
PrimateAI	Benign	0.48	T
PROVEAN	Uncertain	-2.6	D
REVEL	Pathogenic	0.83
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Vest4		0.94
MutPred		0.86		Loss of disorder (P = 0.0481)
MVP		0.98
MPC		0.18
ClinPred		0.99	D
GERP RS		5.9
gMVP		0.76
Mutation Taster		=6/94	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs28897759; hg19: chr13-32968940; COSMIC: COSV105932290;