rs80359027

chr13-32362693-G-Achr13-32362693-G-Cchr13-32362693-G-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Very_Strong

The NM_000059.4(BRCA2):c.7976G>A(p.Arg2659Lys) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2659G) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense, splice_region
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:28 U:1 O:1
• Conservation: PhyloP100: 9.89

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 Pathogenic. Variant got 16 ACMG points.

• PM1: In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 17 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 chr13-32362692-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 38130.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 13-32362693-G-A is Pathogenic according to our data. Variant chr13-32362693-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 38131.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-32362693-G-A is described in Lovd as [Likely_pathogenic]. Variant chr13-32362693-G-A is described in Lovd as [Pathogenic]. Variant chr13-32362693-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.7976G>A	p.Arg2659Lys	missense_variant, splice_region_variant	17/27	ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.7976G>A	p.Arg2659Lys	missense_variant, splice_region_variant	17/27	5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251134 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135706

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: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000881

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461760 Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1 AN XY: 727176

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Alfa AF: 0.000181 Hom.: 0

Bravo AF: 0.00000378

ExAC AF: 0.00000824 AC: 1

EpiCase AF: 0.000109

EpiControl AF: 0.00

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:28 Uncertain:1 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:10

Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Feb 06, 2024	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 04, 2022	Located at the last nucleotide of the exon and demonstrated to result in abnormal splicing leading to in-frame skipping of the adjacent exon (Yang et al., 2002; Hofmann et al., 2003; Wu et al., 2005; Fraile-Bethencourt et al., 2017); Published functional studies demonstrate a damaging effect: inactivation of BRCA2 function with respect to cellular localization, cell survival, homologous recombination repair, and centrosome regulatory functions (Wu et al., 2005; Farrugia et al., 2008; Zhang et al., 2015); Observed in individuals with BRCA2-related cancers, with evidence of segregation in some cases (Konstantopoulou et al., 2014; Susswein et al., 2016; Pritzlaff et al., 2017; Herold et al., 2018); Multifactorial studies suggest this variant is associated with breast and ovarian cancer (Easton et al., 2007; Lindor et al., 2012); Not observed at a significant frequency in large population cohorts (gnomAD); Also known as 8204G>A; This variant is associated with the following publications: (PMID: 19043619, 21638052, 26300996, 28008555, 29969168, 28277317, 25186627, 23231788, 25525159, 17924331, 26489468, 24010542, 26913838, 26681312, 25447315, 18059333, 28339459, 28454591, 26295337, 17576681, 29541174, 29394989, 31191615, 29446198, 31131967, 12228710, 18451181, 12624152, 15695382, 32885271, 21990134, 30787465, 31360904) -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jan 10, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg	Aug 02, 2023	This variant has been identified by standard clinical testing. Metastatic Breast Cancer Selected ACMG criteria: Pathogenic (III):PP5;PP3;PM5;PM2;PS4 -
Pathogenic, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Dec 01, 2023	BRCA2: PM2, PM5, PS4:Moderate, PP3, PS3:Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Jan 25, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	May 28, 2019	Statistically enriched in patients compared to ethnically matched controls. Predicted to have a damaging effect on the protein. Located in potentially important domain of the protein. Assessment of experimental evidence suggests this variant results in abnormal protein function. -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jun 28, 2023	PP4, PP5, PM2, PM4, PS3 -

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

Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Sep 21, 2015	- -
not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	Variant interpretted as Pathogenic and reported on 12-11-2017 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	May 29, 2002	- -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Sep 21, 2012	- -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Apr 07, 2016	- -

Hereditary breast ovarian cancer syndrome Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	GeneKor MSA	Jan 01, 2020	This variant is a single base substitution at the last nucleotide of exon 17 of the BRCA2 coding sequence which results in a single amino acid change from Arginine to Lysine at amino acid residue 2659 of the BRCA2 gene. The Arginine residue is highly conserved in a functional domain of the protein and there is a small physiochemical difference between Arginine and Lysine (Grantham Score 26). This variant has been reported in the literature in patients with breast and/or ovarian cancer (PMID: 12624152, 24010542, 26681312). This variant is also known as 8204G>A in the international literature and is present in population databases at a low frequency (rs80359027, <0.01%). Nucleotide substitutions within the consensus splice site are relatively common causes of aberrant splicing (PMID: 17576681). RNA analyses of patients carrying this variant have shown that this variant causes aberrant splicing, resulting in skipping of exon 17 and a loss of 57 amino acid residues from the BRCA2 protein. Experimental analysis of the functional effects of this variant showed that results in inactivation of the BRCA2 protein and a cytoplasmic localization (PMID: 15695382). The mutation database ClinVar contains an entry for this variant (Variation ID: 38131). -
Pathogenic, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Dec 17, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency	Apr 18, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 08, 2016	Variant summary: The BRCA2 c.7976G>A (p.Arg2659Lys) variant involves the alteration of a conserved nucleotide located at the end of exon17. 4/5 in silico tools predict a damaging outcome for this variant. One of five splice prediction tools predicts significant impact on normal splicing. Functional studies show that this variant leads to skipping of exon 17, which results in-frame deletion of 57 highly conserved amino acids which constitute a part of OB and helical domains (InterPro). This in-frame deletion has been shown to result in inactivation cellular localization, cell survival, homologous recombination repair, and centrosome regulatory functions. This variant was found in 1/122178 control chromosomes at a frequency of 0.0000082, which does not exceed the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503). It has been widely reported as a pathogenic variant in literature and clinical databases found in several HBOC patients/families. Multifactorial probability models also strongly suggest for pathogenicity. In addition, several clinical diagnostic laboratories/reputable databases have classified this variant as pathogenic. Taken together, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 29, 2023	This sequence change replaces arginine, which is basic and polar, with lysine, which is basic and polar, at codon 2659 of the BRCA2 protein (p.Arg2659Lys). RNA analysis indicates that this missense change induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs80359027, gnomAD 0.0009%). This missense change has been observed in individual(s) with breast and/or ovarian cancer (PMID: 12624152, 24010542, 25186627, 26681312). This variant is also known as 8204G>A. ClinVar contains an entry for this variant (Variation ID: 38131). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a high probability of being pathogenic (PMID: 17924331). Experimental studies have shown that this missense change affects BRCA2 function (PMID: 15695382). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in skipping of exon 17, but is expected to preserve the integrity of the reading-frame (PMID: 12624152, 28339459; Invitae). This variant disrupts the c.7976G nucleotide in the BRCA2 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 16489001, 19043619). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 26, 2022	This missense variant replaces arginine with lysine at codon 2659 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 >= 0.7, PMID: 27666373). RNA studies have shown that this variant causes in-frame skipping of exon 17, resulting in the loss of a functional domain (DNA binding domain) (PMID: 28339459). Functional studies have shown that this variant decreases homology-directed DNA repair activity of the BRCA2 protein (PMID: 15695382, 18451181). This variant has been detected in at least 10 individuals affected with breast or ovarian cancer (PMID: 12624152, 24010542, 26681312, 28008555, 33471991; Leiden Open Variation Database DB-ID BRCA2_000249, 34296289, 34445631, 34680387). This variant has been identified in 1/251134 chromosomes 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. -
Pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	May 29, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 16, 2022	The c.7976G>A pathogenic mutation (also known as p.R2659K), located in coding exon 16 of the BRCA2 gene, results from a G to A substitution at nucleotide position 7976. This change occurs in the last base pair of coding exon 16, which makes it likely to have some effect on normal mRNA splicing. In addition to potential splicing impact, this alteration changes the arginine at codon 2659 to lysine, an amino acid with highly similar properties. Multiple studies have demonstrated that this alteration leads to the skipping of coding exon 16, resulting in an in-frame deletion of 57 amino acids (Ambry internal data; Hofmann W et al. J. Med. Genet. 2003 Mar;40:e23; Fraile-Bethencourt E et al. PLoS Genet. 2017 Mar;13(3):e1006691). In addition to the splicing impact, functional studies have demonstrated that this alteration, which is located in the COOH-terminal DNA binding domain, inactivates BRCA2 protein function (Wu K et al. Cancer Res. 2005 Jan;65:417-26). This alteration has been detected in numerous breast and/or ovarian cancer families (Rebbeck TR et al. Hum. Mutat. 2018 May;39(5):593-620). Based on the available evidence, this alteration is interpreted as a disease-causing mutation. -

Hereditary breast ovarian cancer syndrome;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:1

Pathogenic, no assertion criteria provided

research

King Laboratory, University of Washington

Sep 01, 2019

- -

Neoplasm of ovary Pathogenic:1

Pathogenic, no assertion criteria provided

research

German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne

Dec 01, 2018

- -

BRCA2-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 20, 2023

The BRCA2 c.7976G>A variant is predicted to result in the amino acid substitution p.Arg2659Lys. In the literature this variant is also referred to as 8204G>A and R2569K. Functional studies have demonstrated that this variant results in skipping of exon 17 and the in-frame deletion of 171 bases (Hofmann et al. 2003. PubMed ID: 12624152; Table S3, Fraile-Bethencourt et al. 2017. PubMed ID: 28339459). Loss of BRCA2 exon 17 is deleterious for BRCA2 function in cells (Hofmann et al. 2003. PubMed ID: 12624152; Wu et al. 2005. PubMed ID: 15695382; Farrugia et al. 2008. PubMed ID: 18451181). This variant has been reported as causative in multiple patients with autosomal dominant hereditary breast, ovarian, or prostate cancers (Easton et al. 2007. PubMed ID: 17924331; Konstantopoulou et al. 2014. PubMed ID: 24010542; Susswein et al. 2016. PubMed ID: 26681312; Pritzlaff et al. 2017. PubMed ID: 28008555; Herold et al. 2018. PubMed ID: 29541174). This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD and is reported in the ClinVar database as pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/38131/). This variant is interpreted as pathogenic. -

Malignant tumor of breast Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The BRCA2 p.Arg2659Lys variant was identified in 4 of 6566 proband chromosomes (frequency: 0.0006) from individuals or families with pancreatic, prostate, breast or ovarian cancer (Johns 2017, Konstantopoulou 2014, Pritzlaff 2016, Tung 2015). The variant was also identified in dbSNP (ID: rs80359027 as "With Pathogenic allele"), ClinVar (classified as pathogenic by Invitae, Ambry Genetics, GeneDx and eleven other submitters), and LOVD 3.0 (28x as pathogenic). The variant was not identified in UMD-LSDB. The variant was identified in control databases in 1 of 245888 chromosomes at a frequency of 0.000004 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the European population in 1 of 111412 chromosomes (freq: 0.000009), but not in the African, Other, Latino, Ashkenazi Jewish, East Asian, Finnish, or South Asian populations. RT-PCR analysis of the variant showed an in-frame deletion of 171 bp, resulting in a deletion of 57 amino acids (Hofman 2003, Farrugia 2008). In addition, one study showed that this variant abolished the interaction between the oligosaccharide binding folds of BRCA2 and PAR (Poly ADP-ribose; Zhang 2015). The p.Arg2659 residue is conserved across mammals and other organisms, and four out of five 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.Arg2659Lys variant occurs in the last three bases 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 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

Familial cancer of breast Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Oct 04, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.84
BayesDel_addAF	Pathogenic	0.32	D
BayesDel_noAF	Pathogenic	0.23
Cadd	Pathogenic	30
Dann	Uncertain	1.0
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.99
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Pathogenic	0.29	D
MetaRNN	Pathogenic	0.88	D;D
MetaSVM	Pathogenic	0.92	D
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	-0.80	N;N
REVEL	Pathogenic	0.71
Sift	Pathogenic	0.0	D;D
Sift4G	Uncertain	0.034	D;D
Vest4		0.69
MutPred		0.83		Gain of methylation at R2659 (P = 0.0287);Gain of methylation at R2659 (P = 0.0287);
MVP		0.97
MPC		0.16
ClinPred		0.94	D
GERP RS		5.7
gMVP		0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.82		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.82		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs80359027; hg19: chr13-32936830;