13-32394717-C-G

Position:

• chr13-32394717-C-G

Variant summary

Our verdict is Pathogenic. Variant got 24 ACMG points: 24P and 0B. PS1_Very_Strong PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000059.4(BRCA2):​c.9285C>G​(p.Asp3095Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,362 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 nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D3095G) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:11 U:1
• Conservation: PhyloP100: 1.46

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 24 ACMG points.

• PS1: Transcript NM_000059.4 (BRCA2) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in ClinVar as 252859
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-32394716-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 409512.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.964
• PP5: Variant 13-32394717-C-G is Pathogenic according to our data. Variant chr13-32394717-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 52805.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-32394717-C-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.9285C>G	p.Asp3095Glu	missense_variant	25/27	ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.9285C>G	p.Asp3095Glu	missense_variant	25/27	5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000399 AC: 1 AN: 250672 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135480

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: 0.00000883

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461362 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 726954

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: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:11 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary breast ovarian cancer syndrome Pathogenic:4

Pathogenic, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Jan 31, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 23, 2021	Variant summary: BRCA2 c.9285C>G (p.Asp3095Glu) results in a conservative amino acid change located in the 3rd oligonucleotide binding (OB) fold (IPR015188), which is part of the DNA-binding domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 250672 control chromosomes (gnomAD). c.9285C>G has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (e.g. Maillet_2006, Biswas_2012, Gabaldo_2017). Segregation data in HBOC families was suggestive, but not conclusive of causality (e.g. Biswas_2012). Multiple publications have reported experimental evidence evaluating an impact on protein function. In these functional studies the variant was shown to cause significantly reduced HDR activity, increased aberrant centriole amplification, and reduced cell viability in null-rescue survival assays (example: Farrugia_2008, Biswas_2012, Guidugli_2012, Hart_2018, Mesman_2018, Ikegami_2020). In addition, multifactorial probability models, performing systematic assessments of variants of unknown significance in the BRCA genes, which included analysis of co-occurrence in trans with known deleterious mutations, personal and family history of cancer, tumor pathology and co-segregation with disease in pedigrees, predicted this variant to be (likely) pathogenic (Easton 2007, Karchin_2008, Lindor 2012, Guidugli_2018). Six ClinVar submitters have assessed this variant since 2014: one classified the variant as likely pathogenic and five as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 02, 2023	This sequence change replaces aspartic acid, which is acidic and polar, with glutamic acid, which is acidic and polar, at codon 3095 of the BRCA2 protein (p.Asp3095Glu). This variant is present in population databases (rs80359198, gnomAD 0.0009%). This missense change has been observed in individual(s) with BRCA2-related conditions (PMID: 18451181, 18951446, 22678057). It has also been observed to segregate with disease in related individuals. This variant is also known as 9513C>G. ClinVar contains an entry for this variant (Variation ID: 52805). 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, 22678057, 23108138). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	curation	Cancer Variant Interpretation Group UK, Institute of Cancer Research, London	Oct 10, 2018	Data used in classification: The frequency of this variant is 1/138,632 individuals (gnomAD) (PM2_mod). This variant is predicted deleterious on AlignGVGD (class: C35), SIFT (Deleterious), Polyphen2 HumVar (probably damaging) and CADD (13.74) (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 accredited diagnostic USA laboratories Ambry Genetics and GeneDx (2018) (PP5_sup). This variant produces the same amino acid change as a variant with overall classification on ClinVar as pathogenic (c.9285C>A p.Asp3095Glu) (PS1_strong). Data not used in classification: There are additional reports of this variant in ClinVar (9), BIC (12), and BRCA2 LOVD (6). -

Hereditary cancer-predisposing syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	May 26, 2021	The p.D3095E pathogenic mutation (also known as c.9285C>G), located in coding exon 24 of the BRCA2 gene, results from a C to G substitution at nucleotide position 9285. The aspartic acid at codon 3095 is replaced by glutamic acid, an amino acid with highly similar properties. This alteration has been classified as a likely pathogenic alteration 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, and mutation co-occurrence (Easton DF et al. Am. J. Hum. Genet. 2007 Nov;81:873-83; Lindor NM et al. Hum. Mutat. 2012 Jan;33:8-21; Vallee MP et al. Hum. Mutat. 2012 Jan;33:22-8). The p.D3095E alteration was not able to perform complementation in mouse ES cell-based assays (Biswas K et al. Hum Mol Genet. 2012 Sep 15;21(18):3993-4006; Mesman RLS et al. Genet Med 2019 02;21(2):293-302). A homology-directed DNA repair (HDR) assay has demonstrated this variant to be non-functional (Guidugli L et al. Am J Hum Genet 2018 02;102(2):233-248; Hart SN et al. Genet Med, 2019 01;21:71-80; Richardson ME et al. Am J Hum Genet 2021 03;108(3):458-468).This alteration has been reported in multiple families with hereditary breast and ovarian cancer, including at least two families with a history of male breast cancer, as well as cohorts of prostate and pancreatic cancer patients (Biswas K et al. Hum Mol Genet. 2012 Sep 15;21(18):3993-4006; Gabaldo Barrios X et al. Fam. Cancer 2017 Oct;16(4):477-489; Antonarakis ES et al. Eur. Urol. 2018 08;74:218-225; Wong W et al. Cancer. 2019 05;125:1441-1448; Isaacsson Velho P et al. Prostate. 2018 04;78:401-407). Of note, this alteration is also designated as 9513C>G in published literature. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as a pathogenic mutation. -
Pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	Mar 24, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Feb 07, 2020	This missense variant replaces aspartic acid with glutamic acid at codon 3095 of the BRCA2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. Functional studies have shown that this variant disrupts homology-directed DNA repair activity (PMID: 18451181, 23108138, 29884841) and fails to complement cell lethality phenotype induced by loss of BRCA2 in mouse embryonic stem cell-based assays (PMID: 24323938, 29988080). This variant has been reported in many individuals affected with breast cancer (PMID: 16875939, 18951446, 28477318, 30728895) and prostate cancer (PMID: 29368341, 29439820, 29983880, 30293905). In addition, several multifactorial likelihood models using health history, in silico, and experimental data have suggested this variant have a high probability of being pathogenic (PMID: 17924331, 19043619, 21990134, 25085752, 29394989). This variant has been identified in 1/250672 chromosomes in the general population by the Genome Aggregation Database (gnomAD). 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	Jan 21, 2023	The frequency of this variant in the general population, 0.000004 (1/250672 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals with breast cancer (PMID: 16875939 (2006), 28477318 (2017), 8640235 (1996)) and prostate cancer (PMID: 29983880 (2018), 29439820 (2018)). Published functional studies have shown that this variant results in a deleterious effect on BRCA2 protein function (PMID: 22678057 (2012), 29394989 (2018), 29988080 (2018)). 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. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 10, 2023	Observed in individuals with a personal or family history consistent with pathogenic variants in this gene (Plon et al., 2008; Gabald Barrios et al., 2017; Wong et al., 2019; Lotan et al., 2021); Published functional studies demonstrate a damaging effect: reduced homology-directed repair (HDR) activity, aberrant centriole amplification, failure to rescue lethality of Brca2 null ES cells (Farruguia et al., 2008; Biswas et al., 2012; Guidugli et al., 2013; Ikegami et al., 2020; Richardson et al., 2021); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Also known as 9513C>G; This variant is associated with the following publications: (PMID: 25085752, 29439820, 28277317, 30293905, 17924331, 22678057, 18451181, 21990134, 17899372, 19043619, 24323938, 18951446, 28477318, 25447315, 16875939, 21990165, 29394989, 29988080, 30787465, 32719484, 29884841, 29368341, 29922827, 32444794, 31948886, 33609447, 32906206, 33462368, 30620386, 35665744, 12228710, 23108138) -

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

Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Mar 30, 2010	- -
Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	May 29, 2002	- -

Familial cancer of breast Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Feb 19, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.84
BayesDel_addAF	Pathogenic	0.40	D
BayesDel_noAF	Pathogenic	0.34
CADD	Benign	16
DANN	Uncertain	0.99
Eigen	Benign	0.19
Eigen_PC	Benign	0.085
FATHMM_MKL	Uncertain	0.78	D
M_CAP	Uncertain	0.28	D
MetaRNN	Pathogenic	0.96	D;D
MetaSVM	Uncertain	0.66	D
MutationTaster	Benign	0.99	D;D
PrimateAI	Uncertain	0.50	T
PROVEAN	Benign	-1.2	N;N
REVEL	Pathogenic	0.69
Sift	Pathogenic	0.0	D;D
Sift4G	Uncertain	0.023	D;D
Vest4		0.68
MutPred		0.96		Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);
MVP		0.96
MPC		0.16
ClinPred		0.96	D
GERP RS		3.5
gMVP		0.71

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: rs80359198; hg19: chr13-32968854;