13-32363370-A-G

Position:

• chr13-32363370-A-G

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000059.4(BRCA2):​c.8168A>G​(p.Asp2723Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,866 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. D2723H) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:14 U:1
• Conservation: PhyloP100: 8.95

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.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-32363369-G-C is described in Lovd as [Likely_pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.98
• PP5: Variant 13-32363370-A-G is Pathogenic according to our data. Variant chr13-32363370-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 38141.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32363370-A-G is described in Lovd as [Pathogenic]. Variant chr13-32363370-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.8168A>G	p.Asp2723Gly	missense_variant	18/27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.8168A>G	p.Asp2723Gly	missense_variant	18/27	5	NM_000059.4	ENSP00000369497	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461866 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 727230

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: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:14 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

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

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)	Oct 29, 2013	- -
Pathogenic, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Aug 10, 2015	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 -
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, criteria provided, single submitter	clinical testing	Counsyl	Oct 23, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jul 11, 2023	This missense variant replaces aspartic acid with glycine at codon 2723 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). Functional studies have shown the mutant protein to exhibit a loss of homology-directed DNA repair function (PMID: 18451181, 20513136, 29394989, 33609447) and a failure to complement BRCA2-deficient mouse cells (PMID: 25146914). The mutant protein has shown inability to interact with its binding partner DSS1 and mislocalization to the cytoplasm instead of the nucleus (PMID: 33978741). In addition to resulting in defective protein function, this variant has been shown to create a new splice donor site that is partially used in mini-gene assays, resulting in the production of a mRNA species lacking 164 nucleotide of exon 18 (PMID: 20215541, 20513136, 21673748). Although a frameshift and premature truncation is predicted for this aberrant mRNA, this mRNA was produced at much lower levels than normal transcript (PMID: 21673748). This variant has been reported in individuals affected with breast cancer (PMID: 17924331, 20513136, 24052750, 25452441, 29088781, 29335924, 34906479; Color internal data). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). A multifactorial likelihood analysis using personal and family health history and computational prediction has determined this variant to be deleterious (PMID: 17924331). Furthermore, different missense variants occurring at the same position, p.Asp2723His and p.Asp2723Val, are known to be disease-causing (ClinVar variation ID: 52515, 140975), indicating that aspartic acid at this position is important for BRCA2 function. Based on the available evidence, this variant is classified as Pathogenic. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Oct 22, 2019	In the published literature, the variant has been reported the variant has been shown to cause defective BRCA2 protein activity and a 164-bp deletion in exon 18 (PMIDs: 28339459 (2017), 27886673 (2016), 21673748 (2011), 20215541 (2010), and 18451181 (2008)). Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 23, 2022	RNA and minigene assays demonstrate abnormal splicing with the primary aberrant transcript resulting in a shortened protein product (Sanz 2010, Walker 2010, Thry 2011, Fraile-Bethencourt 2017); Observed in individuals with BRCA2-related cancers (Couch 2015, Jakimovska 2018, Fernandez-Lopez 2019, Momozawa 2019, Shimmura 2019); Published functional studies demonstrate a damaging effect: defective homologous recombination, centrosome amplification, and cell growth (Farrugia 2008, Walker 2010, Guidugli 2013, Hendriks 2014, Guidugli 2018, Mesman 2018, Hart 2019); Multifactorial studies suggest this variant is associated with breast and ovarian cancer (Lindor 2012); Not observed in large population cohorts (gnomAD); In silico analysis, which includes splice predictors and evolutionary conservation, suggests this variant may impact gene splicing.; In silico analysis supports that this missense variant does not alter protein structure/function; Also known as 8396A>G; This variant is associated with the following publications: (PMID: 22505045, 23348723, 19043619, 24323938, 18451181, 20513136, 25146914, 31214711, 30630528, 20215541, 24052750, 21673748, 25452441, 17924331, 25782689, 28339459, 29335924, 29988080, 29446198, 21990134, 29394989, 29884841, 12228710, 32295079, 31612916, 23108138) -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 14, 2022	This missense variant replaces aspartic acid with glycine at codon 2723 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). Functional studies have shown the mutant protein to exhibit a loss of homology-directed DNA repair function (PMID: 18451181, 20513136, 29394989, 33609447) and a failure to complement BRCA2-deficient mouse cells (PMID: 25146914). The mutant protein has shown inability to interact with its binding partner DSS1 and mislocalization to the cytoplasm instead of the nucleus (PMID: 33978741). In addition to resulting in defective protein function, this variant has been shown to create a new splice donor site that is partially used in mini-gene assays, resulting in the production of a mRNA species lacking 164 nucleotide of exon 18 (PMID: 20215541, 20513136, 21673748). Although a frameshift and premature truncation is predicted for this aberrant mRNA, this mRNA was produced at much lower levels than normal transcript (PMID: 21673748). This variant has been reported in individuals affected with breast cancer (PMID: 17924331, 20513136, 24052750, 25452441, 29088781, 29335924, 34906479; Color internal data). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). A multifactorial likelihood analysis using personal and family health history and computational prediction has determined this variant to be deleterious (PMID: 17924331). Furthermore, different missense variants occurring at the same position, p.Asp2723His and p.Asp2723Val, are known to be disease-causing (ClinVar variation ID: 52515, 140975), indicating that aspartic acid at this position is important for BRCA2 function. Based on the available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jun 07, 2024	The p.D2723G pathogenic mutation (also known as c.8168A>G), located in coding exon 17 of the BRCA2 gene, results from an A to G substitution at nucleotide position 8168. This alteration was shown to create an aberrant splice product (Walker LC et al. Hum. Mutat. 2010 Jun;31(6):E1484-505; Sanz DJ et al. Clin Cancer Res. 2010 Mar 15;16(6):1957-67; Thery JC et al. Eur J Hum Genet. 2011 Oct;19(10):1052-8; Houdayer C et al. Hum. Mutat. 2012 Aug;33(8):1228-38). In addition, in-vitro functional studies demonstrated reduced homologous recombination and increased centrosome amplification (Farrugia DJ et al. Cancer Res. 2008 May 1;68(9):3523-31; Walker LC et al. Hum. Mutat. 2010 Jun;31(6):E1484-505). Furthermore, this alteration could not complement the lethality of BRCA2-deficient mouse-embryonic stem (mES) cells (Hendriks G et al. Hum. Mutat. 2014 Nov;35(11):1382-91). This alteration has been classified as a pathogenic mutation based on a posterior probability model, which integrates evolutionary conservation and multifactorial analysis (including segregation, co-occurrence, family history, and tumor histology) (Easton D et al. Am J Hum Genet. 2007;81:873-883; Lindor NM et al. Hum. Mutat. 2012 Jan;33(1):8-21). Several other pathogenic alterations have also been reported at the same codon (p.D2723H, p.D2723A, p.D2723V) (Vallee M et al. Hum Mutat. 2012 Jan;33(1):22-8; Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the available evidence, this alteration is classified as a pathogenic mutation. -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 17, 2024	This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 2723 of the BRCA2 protein (p.Asp2723Gly). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of BRCA2-related conditions (PMID: 25452441, 27886673). ClinVar contains an entry for this variant (Variation ID: 38141). Advanced modeling performed at Invitae incorporating data from internal and/or published 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: 18451181, 20513136, 21673748, 25146914). RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). This variant disrupts the p.Asp2723 amino acid residue in BRCA2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 15290653, 15695382, 16489001, 18607349, 24013206). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 29, 2018	Variant summary: BRCA2 c.8168A>G (p.Asp2723Gly) variant involves the alteration of a highly conserved nucleotide leading to a missense change in the DNA-binding domain (IPR012340) in the OB1 (oligonucleotide binding) fold (IPR015187, InterPro). Five of five in-silico tools predict a damaging effect of the variant on protein function. Several computational tools also predict a significant impact on normal splicing: four predict the variant creates a cryptic 5 donor splice site. These predictions are corroborated by publications reporting experimental evidence that this variant affects mRNA splicing (Walker 2010, Rodriguez-Balada 2016, Sanz 2010), partly generating an aberrantly spliced transcript encoding a truncated protein, but in part the variant allele becomes also transcribed to a full length transcript encoding a missense protein that was reported to have a reduced function (Farrugia 2008, Walker 2010). The most pronounced variant effect results in 10%-<30% of normal activity. The variant was absent in 247432 control chromosomes. The variant c.8168A>G has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (Walker 2010, Couch 2015, Rodriguez-Balada 2016, Alvarez 2017, Farrugia 2008). Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

CZECANCA consortium

Jun 11, 2019

- -

Gastric cancer Pathogenic:1

Pathogenic, no assertion criteria provided

research

Laboratory for Genotyping Development, RIKEN

Jul 01, 2021

- -

Familial cancer of breast Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Jul 17, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
BayesDel_addAF	Pathogenic	0.56	D
BayesDel_noAF	Pathogenic	0.57
CADD	Pathogenic	30
DANN	Uncertain	1.0
Eigen	Pathogenic	0.83
Eigen_PC	Pathogenic	0.74
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Pathogenic	0.52	D
MetaRNN	Pathogenic	0.98	D;D
MetaSVM	Pathogenic	1.1	D
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	-2.1	N;N
REVEL	Pathogenic	0.94
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Vest4		0.82
MutPred		0.91		Gain of sheet (P = 0.0477);Gain of sheet (P = 0.0477);
MVP		0.99
MPC		0.18
ClinPred		1.0	D
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
gMVP		0.91

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.23		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.23		Position offset: -1

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

Publications

LitVar

Other links and lift over

dbSNP: rs41293513; hg19: chr13-32937507;