chr13-32326499-G-C

Position:

chr13-32326499-G-C

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM2PM5PP3PP5_Very_Strong

The NM_000059.4(BRCA2):c.517G>C(p.Gly173Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,449,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 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. G173C) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

BRCA2
NM_000059.4 missense, splice_region

Scores

Splicing: ADA: 0.9958

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:12

Conservation

PhyloP100: 2.04

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 13 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM5

Other missense variant is known to change same aminoacid residue: Variant chr13-32326499-G-T is described in Lovd as [Likely_pathogenic].

PP3

Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.

PP5

Variant 13-32326499-G-C is Pathogenic according to our data. Variant chr13-32326499-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 182177.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-32326499-G-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4 linkuse as main transcript	c.517G>C	p.Gly173Arg	missense_variant, splice_region_variant	7/27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8 linkuse as main transcript	c.517G>C	p.Gly173Arg	missense_variant, splice_region_variant	7/27	5	NM_000059.4	ENSP00000369497	A2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.90e-7

AC:

AN:

1449710

Hom.:

Cov.:

AF XY:

0.00000139

AC XY:

AN XY:

721970

show subpopulations

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:

9.08e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

EpiCase

AF:

0.0000545

EpiControl

AF:

0.00

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:12

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Pathogenic:5

Likely pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Oct 27, 2022	It has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant has been reported in a triple-negative breast tumor tissue specimen (PMID: 24963051 (2014)). In a large scale breast cancer association study, this variant was observed in a breast cancer case and not in unaffected study control individuals (PMID: 33471991 (2021), ). In addition, this variant has been observed in individuals with breast cancer (Quest internal data). Experimental studies report this variant causes aberrant splicing resulting in protein truncation based on cDNA analysis of carrier lymphocytes (PMID: 29280214 (2018)), and impaired DNA repair via a functional ex vivo assay (PMID: 24963051 (2014)). Based on the available information, this variant is classified as likely pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Nov 10, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Dec 01, 2022	PS4_MOD, PM2_SUP, PVS1_STR -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Feb 28, 2023	Exonic splice variant demonstrated to result in abnormal splicing, leading to out-of-frame skipping of exon 7 (Baert et al., 2017); Observed in an individual with breast cancer (Dorling et al., 2021); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Also known as 745G>C; This variant is associated with the following publications: (PMID: 24963051, 22962691, 21702907, 29446198, 28726806, 30139880, 30883759, 33471991, 29280214) -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Sep 11, 2019	DNA sequence analysis of the BRCA2 gene demonstrated a sequence change, c.517G>C, in exon 7 that results in an amino acid change, p.Gly173Arg. In vitro mRNA analysis showed that the c.517G>C variant induces aberrant splicing (skipping of exon 7) due to loss of the natural splice site leading to a frameshift, r.517_631del; p.(Gly173Serfs19) (PMID: 29280214). This change is predicted to result in degradation of the transcript. This sequence change has been previously described in patients with breast cancer in two studies but no additional information was provided (PMIDs: 29446198, 21702907). This sequence change has not been described in the population databases (ExAC and gnomAD). The p.Gly173Arg change affects a poorly conserved amino acid residue located in a domain of the BRCA2 protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL, in silico splice prediction tools) provide contradictory results for the p.Gly173Arg substitution. A different variant affecting the same nucleotide, c.517G>T(p.Gly173Cys), has been reported to lead to abnormal splicing of the BRCA2 gene by functional splicing minigene assay and was predicted to result in a frame shift (p.Gly173Serfs19) (PMID: 22962691). These collective evidences indicate that this sequence change is likely pathogenic. -

Hereditary cancer-predisposing syndrome

Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	May 17, 2023	This variant changes the first nucleotide in exon 7 of the BRCA2 gene and is predicted to impact RNA splicing. This variant is also known as p.Gly173Arg based on predicted change at the protein level. An RNA study using peripheral blood cells from a carrier has shown that this variant results in out-of-frame skipping of exon 7, causing a frameshift and premature translation stop signal (PMID: 29280214). This variant has been reported in an individual affected with breast cancer (Leiden Open Variation Database DB-ID BRCA2_001018; PMID: 33471991). This variant has not been identified 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 Likely Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 26, 2023	The c.517G>C variant (also known as p.G173R) is located in coding exon 6 of the BRCA2 gene. This variant results from a G to C substitution at nucleotide position 517. The glycine at codon 173 is replaced by arginine, an amino acid with dissimilar properties. This change occurs in the first base pair of coding exon 6. This nucleotide position is highly conserved in available vertebrate species. This variant has been detected in breast cancer cohorts (Tung N et al. Cancer, 2015 Jan;121:25-33; Dorling et al. N Engl J Med. 2021 02;384:428-439). In silico splice site analysis predicts that this alteration may weaken the native splice acceptor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data; Baert A et al. Hum. Mutat. 2017 Dec). Another nucleotide substitution at the same position (BRCA2 c.517G>T) was also shown to have a similar severe splice defect in multiple minigene assays (Gaildrat P et al. J. Med. Genet. 2012 Oct;49:609-17; Fraile-Bethencourt E et al. J Pathol, 2019 08;248:409-420). Yet another close-match alteration at this same acceptor site, BRCA2 c.517-2A>G, has been identified in a compound heterozygous and homozygous state in patients with Fanconi Anemia (Leach M et al. Practical Flow Cytometry in Hematology: 100 worked examples. 321-324; 2015; Muramatsu H et al. Genet. Med., 2017 07;19:796-802). BRCA2 c.517-2A>G also demonstrates an intermediate effect in a mouse embryonic stem cell survival and subsequent homology-directed DNA repair assays. Clinical and functional data collectively support BRCA2 c.517-2A>G as a likely hypomorphic variant (Mesman RLS et al. Genet Med, 2020 08;22:1355-1365). BRCA2 c.517-2A>G has a similar splice defect as this variant (Ambry internal data; Houdayer C et al. Hum Mut. 2012; 33:1228–38; Fraile-Bethencourt E et al. J. Pathol. 2019 08;248(4):409-420). Based on the majority of available evidence to date, this variant is likely to be pathogenic. However, because a variant with a similar splicing profile as this variant is functionally hypomorphic and has been identified in multiple patients with Fanconi Anemia it may be similarly hypomorphic and thus, carriers of this variant and their families may present with reduced risks, and not with the typical clinical characteristics of a high-risk pathogenic BRCA2 alteration. As risk estimates are unknown at this time, clinical correlation is advised. -

Breast and/or ovarian cancer

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

May 27, 2020

- -

Breast-ovarian cancer, familial, susceptibility to, 2

Pathogenic: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

- -

Malignant tumor of breast

Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

The p.Gly173Arg variant was not identified in the literature however it is listed in dbSNP (rs397507768) as pathogenic/uncertain significance, but no frequency information was provided, thus the prevalence of this variant in the general population could not be determined. This variant was also identified by ClinVar (4 submissions, Pathogenic 1x by CIMBA, and Uncertain significance 3x, by GeneDx, Genetics Diagnostic, Ambry Genetics), Clinvitae (3x as Uncertain significance, 2 x Pathogenic) and GeneInsight - COGR database (as Unknown significance, by CHEO). This variant was not identified in any of the following databases: UMD, LOVD, BIC, COSMIC, the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project and The Exome Aggregation Consortium database (August 8, 2016). The p.Gly173 residue is conserved in mammals but it is not conserved across other organisms. Computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The c.517G>C variant occurs in the first base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing, this is not very predictive of pathogenicity. Although the p.Gly173Arg variant was not identified in the literature, a different amino acid change at this position, c.517G>T, p.Gly173Cys, has been shown to alter the natural splice site (Gaildrat 2014). The study performed splicing minigene assays and analyses of patient RNA showed that the c.517G>T variant induced total exon skipping (RNA r.517_631del), a defect that results in a frame shift (p.Gly173SerfsX19). In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic. -

Familial cancer of breast

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Mar 02, 2023

- -

Hereditary breast ovarian cancer syndrome

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 23, 2023

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 173 of the BRCA2 protein (p.Gly173Arg). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with BRCA2-related conditions. ClinVar contains an entry for this variant (Variation ID: 182177). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Studies have shown that this missense change results in skipping of exon 7 and introduces a premature termination codon (PMID: 29280214; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. 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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.33

BayesDel_addAF

Benign

-0.012

BayesDel_noAF

Benign

-0.25

CADD

Benign

DANN

Pathogenic

1.0

Eigen

Uncertain

0.48

Eigen_PC

Uncertain

0.42

FATHMM_MKL

Uncertain

0.90

M_CAP

Benign

0.031

MetaRNN

Benign

0.39

T;T

MetaSVM

Benign

-0.97

MutationTaster

Benign

0.51

N;N

PrimateAI

Benign

0.44

PROVEAN

Benign

-1.6

N;N

REVEL

Benign

0.090

Sift

Uncertain

0.0020

D;D

Sift4G

Benign

0.12

T;T

Vest4

0.36

MutPred

0.24

Gain of solvent accessibility (P = 0.0037);Gain of solvent accessibility (P = 0.0037);

MVP

0.92

MPC

0.17

ClinPred

0.88

GERP RS

4.6

gMVP

0.23

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.88

SpliceAI score (max)

0.41

Details are displayed if max score is > 0.2

DS_AL_spliceai

0.41

Position offset: 0

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over