NM_000059.4:c.7975A>G

Variant names:

• chr13-32362692-A-G
• rs80359026
• NM_000059.4:c.7975A>G

Variant summary

Our verdict is Pathogenic. The variant received 15 ACMG points: 15P and 0B. PM1 PM2 PM5 PP3 PP5_Very_Strong

The NM_000059.4(BRCA2):​c.7975A>G​(p.Arg2659Gly) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000684 in 1,461,794 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 Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2659T) 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 reviewed by expert panel P:11 U:3
• Conservation: PhyloP100: 5.92
• Publications: 25 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 15 ACMG points.

• PM1: In a hotspot region, there are 8 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 7 benign, 31 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 chr13-32362693-G-C is described in ClinVar as Pathogenic. ClinVar VariationId is 52455.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 13-32362692-A-G is Pathogenic according to our data. Variant chr13-32362692-A-G is described in ClinVar as Pathogenic. ClinVar VariationId is 38130.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.7975A>G	p.Arg2659Gly	missense_variant, splice_region_variant	Exon 17 of 27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.7975A>G	p.Arg2659Gly	missense_variant, splice_region_variant	Exon 17 of 27	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.7606A>G	p.Arg2536Gly	missense_variant, splice_region_variant	Exon 17 of 27	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.*33A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 16 of 26	2		ENSP00000506251.1
BRCA2	ENST00000614259.2	n.*33A>G		3_prime_UTR_variant	Exon 16 of 26	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461794 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 727200

African (AFR) AF: 0.00 AC: 0 AN: 33476

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: 39688

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

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53408

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

European-Non Finnish (NFE) AF: 8.99e-7 AC: 1 AN: 1111962

Other (OTH) AF: 0.00 AC: 0 AN: 60388

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:11 Uncertain:3

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:2 Uncertain:3

Mar 02, 2020

BRCAlab, Lund University

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Laboratoire de Biologie et Génétique du Cancer, Centre François Baclesse

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Oct 28, 2009

Sharing Clinical Reports Project (SCRP)

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jul 10, 1998

Breast Cancer Information Core (BIC) (BRCA2)

Significance: Uncertain significance

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 = 0.999975 -

not provided Pathogenic:4

Aug 21, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Observed in individuals with a personal and/or family history consistent with Hereditary Breast and Ovarian Cancer, and has been found to segregate with disease in multiple affected individuals (Pinto et al., 2016; Apessos et al., 2018; Jakimovska et al., 2018; Zuntini et al., 2018; Li et al., 2019; Parsons et al., 2019; Barbosa et al., 2020; Huang et al., 2020; Gao et al., 2020; Caputo et al., 2021); Protein-based functional studies demonstrate a damaging effect: impaired homology-directed repair activity and sensitivity to PARP inhibitors (Guidugli et al., 2018; Hart et al., 2019; Ikegami et al., 2020; Iversen et al., 2022); Splicing functional studies are inconclusive demonstrating 3% - 26% abnormal transcript (Davy et al., 2017; Fraile-Bethencourt et al., 2017); In silico analysis supports that this missense variant does not alter protein structure/function; Not observed in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; Also known as 8203A>G; This variant is associated with the following publications: (PMID: 23108138, 24323938, 25348012, 21523855, 19043619, 21120943, 28339459, 22505045, 27553368, 27060066, 28905878, 29335924, 29752822, 29310832, 32444794, 31131967, 30254663, 29394989, 33008098, 33194720, 29884841, 35665744, 12228710, 31825140, 34597585) -

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

- -

Oct 09, 2023

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The BRCA2 c.7975A>G (p.Arg2659Gly) variant has been reported in the published literature in affected individuals with breast and/or ovarian cancer, as well as other BRCA2 related cancers (PMIDs: 27553368 (2016), 29335924 (2018), 29752822 (2018), and 34597585 (2021)). Functional studies demonstrated that this variant resulted in partial in frame skipping of exon 17 (PMIDs: 21120943 (2011) and 28339459 (2017)), as well as reduced activity in a homology-directed DNA repair (HDR) assay (PMID: 24323938 (2014)). A multifactorial analysis considered this variant to have a high probability of pathogenicity (PMID: 31131967 (2019)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as pathogenic. -

Jan 20, 2021

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The BRCA2 c.7975A>G; p.Arg2659Gly variant (rs80359026) is reported in the literature in several individuals affected with suspected hereditary breast and/or ovarian cancer syndrome (Apessos 2018, Caux-Moncoutier 2011, Li 2019). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. Multifactorial likelihood analyses, incorporating personal and family history of cancer, co-occurrence with pathogenic variants, and co-segregation with disease, suggest the p.Arg2659Gly variant is highly likely to be disease-causing (Parsons 2019). The arginine at codon 2659 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.871). Consistent with these predictions, functional assays of homology-directed repair suggest the variant protein has significantly reduced activity (Guidugli 2013). Further, this variant occurs in the penultimate nucleotide of exon 17, and splicing analyses suggest a low level of exon skipping in cells expressing the variant (Fraile-Bethencourt 2017, Houdayer 2019). Based on available information, this variant is considered to be likely pathogenic. References: Apessos et al. Comprehensive BRCA mutation analysis in the Greek population. Experience from a single clinical diagnostic center. Cancer Genet. 2018 Jan;220:1-12. Caux-Moncoutier V et al. EMMA, a cost- and time-effective diagnostic method for simultaneous detection of point mutations and large-scale genomic rearrangements: application to BRCA1 and BRCA2 in 1,525 patients. Hum Mutat. 2011 Mar;32(3):325-34. Fraile-Bethencourt et al. Functional classification of DNA variants by hybrid minigenes: Identification of 30 spliceogenic variants of BRCA2 exons 17 and 18. PLoS Genet. 2017 Mar 24;13(3):e1006691. Guidugli L et al. A classification model for BRCA2 DNA binding domain missense variants based on homology-directed repair activity. Cancer Res. 2013 Jan 1;73(1):265-75. Houdayer C et al. Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants. Hum Mutat. 2012 Aug;33(8):1228-38. Li et al. Germline mutations in 40 cancer susceptibility genes among Chinese patients with high hereditary risk breast cancer. Int J Cancer. 2019 Jan 15;144(2):281-289. Parsons MT et al. Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification. Hum Mutat. 2019 Sep;40(9):1557-1578. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Jun 16, 2023

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.R2659G pathogenic mutation (also known as c.7975A>G), located in coding exon 16 of the BRCA2 gene, results from an A to G substitution at nucleotide position 7975. The arginine at codon 2659 is replaced by glycine, an amino acid with dissimilar properties. This alteration, along with close-match alteration BRCA2 c.7976G>A (p.R2659K) are located near a canonical splice donor site and result in in-frame, exon 16 skipping (Fraile-Bethencourt E et al. PLoS Genet. 2017 Mar;13:e1006691; Caux-Moncoutier V et al. Hum. Mutat. 2011 Mar;32:325-34; Houdayer C et al. Hum. Mutat. 2012 Aug;33:1228-38; Hofmann W et al. J Med Genet. 2003 Mar;40(3):e23). Both of these alterations are also non-functional in protein-based homology-directed DNA repair (HDR) assay (Guidugli L et al. Am. J. Hum. Genet. 2018 Jan; Wu K et al. Cancer Res. 2005 Jan;65:417-26; Guidugli L et al. Cancer Res. 2013 Jan;73:265-75). This alteration is considered pathogenic by multifactorial analysis that considers cosegregation, tumor pathology, co-occurrence with pathogenic mutation, family history and case-control data. Of note, the co-segregation likelihood ratio was particularly strong for this variant in this study (Parsons MT et al. Hum. Mutat., 2019 09;40:1557-1578). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Internal structural analysis suggests the arginine at codon 2659 closely interacts with other amino acids where other pathogenic substitutions have been identified. Further, the presence of a glycine at codon 2659 is likely to disrupt DNA binding (Ambry internal data). Based on the majority of available evidence to date, this alteration is interpreted as a disease-causing mutation. -

Jun 27, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces arginine with glycine at codon 2659 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). Functional studies have shown that this variant impacts BRCA2 function in a homology-directed repair assay and increases sensitivity to PARP inhibitors in mammalian cells (PMID: 23108138, 29394989, 32444794). RNA studies using patient-derived RNA and minigene assays have shown this variant causes partial in-frame skipping of exon 17 (PMID: 22505045, 28339459, 28905878, 31191615). This variant has been reported in at least seven individuals affected with breast or ovarian cancer (PMID: 29335924, 29752822, 30254663, 32850417, 33008098, 33801055, 31131967, 34597585). This variant has been reported in two multifactorial analyses with segregation likelihood ratios for pathogenicity of 1950.0 and 1,114.89 (PMID: 31131967, 34597585). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -

Familial cancer of breast Pathogenic:2

Jun 07, 2022

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 04, 2022

Mendelics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary breast ovarian cancer syndrome Pathogenic:1

Jul 15, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 2659 of the BRCA2 protein (p.Arg2659Gly). RNA analysis indicates that this missense change induces altered splicing and likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast and/or ovarian cancer (PMID: 21120943, 27553368, 29335924, 29752822, 30254663). This variant is also known as 8204G>A. ClinVar contains an entry for this variant (Variation ID: 38130). 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: 31131967). Experimental studies have shown that this missense change affects BRCA2 function (PMID: 15695382, 23108138, 29884841). 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, 22505045, 28339459). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
BayesDel_addAF	Pathogenic	0.44	D
BayesDel_noAF	Pathogenic	0.40
CADD	Uncertain	25
DANN	Uncertain	1.0
Eigen	Pathogenic	0.74
Eigen_PC	Pathogenic	0.67
FATHMM_MKL	Uncertain	0.95	D
M_CAP	Pathogenic	0.72	D
MetaRNN	Pathogenic	0.94	D;D
MetaSVM	Pathogenic	0.90	D
PhyloP100		5.9
PrimateAI	Uncertain	0.63	T
PROVEAN	Benign	-1.9	N;N
REVEL	Pathogenic	0.87
Sift	Pathogenic	0.0	D;D
Sift4G	Uncertain	0.0070	D;D
Vest4		0.85
MutPred		0.78		Loss of MoRF binding (P = 0.0132);Loss of MoRF binding (P = 0.0132);
MVP		0.97
MPC		0.18
ClinPred		0.99	D
GERP RS		4.5
gMVP		0.89
Mutation Taster		=2/98	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
Splicevardb		3.0
SpliceAI score (max)		0.51		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.51		Position offset: 1

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

Other links and lift over

dbSNP: rs80359026; hg19: chr13-32936829;