rs41293511

Positions:

• chr13-32363369-G-A
• chr13-32363369-G-C

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2 PM5 PP3_Strong PP5

The NM_000059.4(BRCA2):​c.8167G>A​(p.Asp2723Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D2723G) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:3 U:2
• Conservation: PhyloP100: 9.60

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 Likely_pathogenic. Variant got 9 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-32363370-A-G is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.977
• PP5: Variant 13-32363369-G-A is Pathogenic according to our data. Variant chr13-32363369-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 485412.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=3, Uncertain_significance=2}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.8167G>A	p.Asp2723Asn	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.8167G>A	p.Asp2723Asn	missense_variant	18/27	5	NM_000059.4	ENSP00000369497	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:3 Uncertain:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary breast ovarian cancer syndrome Pathogenic:2 Uncertain:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 21, 2022	Variant summary: BRCA2 c.8167G>A (p.Asp2723Asn) results in a conservative amino acid change located in the BRCA2, OB1 domain (IPR015187) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251098 control chromosomes (gnomAD). To our knowledge, no occurrence of c.8167G>A in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome has been reported. At least one publication reports experimental evidence evaluating an impact on protein function. Richardson_2021 demonstrated this variant as loss-of-function using HDR assay. Other variants affecting the same codon have been reported as pathogenic by our lab (p.Asp2723His, p.Asp2723Gly). Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classidfied the variant as VUS (n=2) and likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as likely pathogenic. -
Uncertain significance, criteria provided, single submitter	clinical testing	Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center	Dec 14, 2018	This sequence variant is a single nucleotide substitution (G>A) that results in an aspartic acid to asparagine amino acid change at residue 2723 in the BRCA2 protein. This is a previously reported variant (ClinVar) that has not been reported in breast cancer patients in the literature, to our knowledge. However, other amino acid changes at this position (Asp2723His and Asp2723Gly) are well known to be pathogenic for breast cancer susceptibility, and additional changes (Asp2723Val, Asp2723Ala, and Asp2723Glu) have some clinical assertions in the pathogenic spectrum but also those of uncertain clinical significance. The BRCA2 c.8167G>A variant is not observed in control population datasets (ExAC/gnomAD databases). The Asp2723 residue is located in the OB1 functional domain, which is a domain that binds DNA during the homology directed repair of DNA double strand breaks (PMID: 22193408). Within this domain, a subset of residues (2722-2726) are highly conserved in animal and plant kingdoms, and x-ray crystallographic structure indicates that residues Gly2724 and Trp2725, which are immediate neighbors to the variant residue, make direct contact with the BRCA2-stabilizing protein DSS1 (PMID: 12228710). However, studies assessing the effects of this particular variant on BRCA2 function have not been identified. Multiple bioinformatic tools queried predict that this aspartic acid to asparagine amino acid change would be damaging and the aspartic acid at this position is conserved across all mammalian species examined. Although this data supports pathogenicity, it is important to highlight that aspartic acid and asparagine are similar in structural and chemical properties, suggesting that the effect of this substitution may differ greatly from the known pathogenic substitutions to histidine and glycine, which are highly dissimilar to aspartic acid in structure and charge. Despite the evidence that other amino acid changes at this position cause an increased susceptibility to breast cancer, there is insufficient clinical and functional evidence to determine if this particular variant is pathogenic or benign. Therefore, we consider the clinical significance of this variant to be uncertain. -
Uncertain significance, criteria provided, single submitter	curation	German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne	Jan 09, 2024	. According to the ClinGen ENIGMA BRCA2 v1.0.0 criteria we chose these criteria: PS3 (strong pathogenic): Richardson et al. 2021 Deleterious in HRD-Assay, PM2 (supporting pathogenic): not in gnomAD v3.1.2 non cancer, BP4 (supporting benign): BayesDel 0,159, (BayesDel no-AF score ≤ 0.18 AND SpliceAI ≤0.1) -
Likely pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 26, 2021	In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. 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: 11207042, 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt BRCA2 protein function. ClinVar contains an entry for this variant (Variation ID: 485412). This variant has not been reported in the literature in individuals affected with BRCA2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 2723 of the BRCA2 protein (p.Asp2723Asn). -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 11, 2021

The p.D2723N variant (also known as c.8167G>A), located in coding exon 17 of the BRCA2 gene, results from a G to A substitution at nucleotide position 8167. The aspartic acid at codon 2723 is replaced by asparagine, an amino acid with some similar properties. This alteration is located a structural hotspot region of the protein, which is predicted to destabilize the protein and disrupt the native protein-protein (BRCA2-DSS1) interaction when altered (Yang et al. Science. 2002; 297(5588):1837-48). Other amino acid substitutions at this codon (p.D2723G and p.D2723H) have been classified as definitely pathogenic by multifactorial analysis, which integrates the following lines of evidence to produce a quantitative likelihood of pathogenicity: in silico prediction models, segregation with disease, tumor characteristics, mutation co-occurrence, and functional assay results (Easton D et al. Am J Hum Genet. 2007;81:873-883; Vallee M et al. Hum Mutat. 2012 Jan;33(1):22-8). 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 majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.82
BayesDel_addAF	Pathogenic	0.28	D
BayesDel_noAF	Pathogenic	0.16
CADD	Pathogenic	28
DANN	Uncertain	1.0
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.81
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Pathogenic	0.55	D
MetaRNN	Pathogenic	0.98	D;D
MetaSVM	Pathogenic	1.1	D
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.55	T
PROVEAN	Benign	-1.5	N;N
REVEL	Pathogenic	0.82
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Vest4		0.79
MutPred		0.93		Gain of catalytic residue at D2723 (P = 0.1316);Gain of catalytic residue at D2723 (P = 0.1316);
MVP		0.99
MPC		0.17
ClinPred		1.0	D
GERP RS		5.5
gMVP		0.89

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: rs41293511; hg19: chr13-32937506;