13-32326502-C-T

Variant names:

• chr13-32326502-C-T
• rs41293469
• NM_000059.4:c.520C>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000059.4(BRCA2):​c.520C>T​(p.Arg174Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,453,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:13
• Conservation: PhyloP100: 0.282

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.520C>T	p.Arg174Cys	missense_variant	Exon 7 of 27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.520C>T	p.Arg174Cys	missense_variant	Exon 7 of 27	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.151C>T	p.Arg51Cys	missense_variant	Exon 7 of 27	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.520C>T		non_coding_transcript_exon_variant	Exon 6 of 26	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251366 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135852

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: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000344 AC: 5 AN: 1453724 Hom.: 0 Cov.: 30 AF XY: 0.00000415 AC XY: 3 AN XY: 723698

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: 0.00000453

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Alfa AF: 0.0000233 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:13

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

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

May 01, 2012

Sharing Clinical Reports Project (SCRP)

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Nov 20, 2023

All of Us Research Program, National Institutes of Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces arginine with cysteine at codon 174 of the BRCA2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). A functional RNA study reported this variant causes partial exon 7 skipping in minigene splicing assay and confirmed in patient RNA (PMID: 21673748). This variant has been reported in an individual affected with early-onset breast cancer and strong family history of disease (PMID: 21673748) and also in two unaffected controls in a breast cancer case-control study (PMID: 30287823). This variant has been identified in 1/251366 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Sep 01, 2023

Department of Medical and Surgical Sciences, University of Bologna

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

PM2(Supporting)+PP3(Supporting)+BP5(Supporting) according to ACMG/AMP classification guidelines specified for BRCA1 & BRCA2 (Classification Criteria V1.0.0 2023-09-08 - https://cspec.genome.network/cspec/ui/svi/affiliation/50087) (PMID: 38160042) -

Hereditary breast ovarian cancer syndrome Uncertain:3

Jul 02, 2024

German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: curation

Functional data from RNA-Analysis inconclusive; According to the ClinGen ENIGMA BRCA2 v1.1.0 criteria we chose this criterion: PP3 (supporting pathogenic): SpliceAI: 0,274; ClinGen: Apply PP3 for predicted splicing (SpliceAI ≥0.2) for silent, missense/in-frame (irrespective of location in clinically important functional domain) and for intronic variants outside of donor and acceptor 1,2 sites. -

Aug 28, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 174 of the BRCA2 protein (p.Arg174Cys). This variant is present in population databases (rs41293469, gnomAD 0.0009%). This missense change has been observed in individual(s) with breast or ovarian cancer (PMID: 21673748, 31907386). ClinVar contains an entry for this variant (Variation ID: 51818). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt BRCA2 protein function with a negative predictive value of 95%. Studies have shown that this missense change is associated with inconclusive levels of altered splicing (internal data). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Feb 18, 2020

Cancer Variant Interpretation Group UK, Institute of Cancer Research, London

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Data included in classification: Case control comparison of UK matched against ethnically matched population data (3/25,773) in familial cases against 1/56,837 GNOMAD NFE controls pexact= 0.093 (PS4_mod). Absent from the remainder of the gnomAD population (0/68,846) (PM2_mod). Assays reported by Thery 2011, Gaildrat 2012, Di Giacomo 2013 (PMID: 21673748, PMID: 22962691, PMID: 2398314) show 60-70% exon 7 skipping likely due to disruption of ESE. ESE prediction tools predict enhancer site. (PS3_mod). Variant reported in the homozygous form (1) and heterozygous form (1) on the BRCA2 Fanconi database from the Japanese Biobank. Homozygote age 60 years without personal or family history of cancer but had other complex disease (not specified). (BS2_sup). Additional data (not included in classification): The variant has also been observed in at least 2 additional UK families, 5 families tested by Ambry and is reported an additional 4 times on ClinVar. Variable segregation in UK families. None strong. Other classifications: Ambry VUS 2018; Gene Dx VUS 2017; Color VUS 2017; Invitae VUS 2017. In silico predictions mixed. -

not provided Uncertain:2

Nov 03, 2021

Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 27, 2021

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at a significant frequency in large population cohorts (Lek 2016); In silico analysis supports that this missense variant does not alter protein structure/function; Observed in at least two individuals with early-onset familial breast cancer (Thery 2011); RNA and minigene assays demonstrate partial exon 7 skipping, producing both full-length and truncated mRNA transcripts in varying proportions (Gaildrat 2012, Di Giacomo 2013). Exon 7 skipping has been reported to create a frameshift ultimately causing a premature nonsense codon, resulting in a truncated protein product that appears to undergo nonsense-mediated mRNA decay (Pyne 2000); This variant is associated with the following publications: (PMID: 32072338, 32486089, 32170000, 32123317, 30287823, 26761715, 11185744, 23983145, 22962691, 21673748) -

Hereditary cancer-predisposing syndrome Uncertain:2

Jul 06, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces arginine with cysteine at codon 174 of the BRCA2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). A functional RNA study reported this variant causes partial exon 7 skipping in minigene splicing assay and confirmed in patient RNA (PMID: 21673748). This variant has been reported in an individual affected with early-onset breast cancer and strong family history of disease (PMID: 21673748) and also in two unaffected controls in a breast cancer case-control study (PMID: 30287823). This variant has been identified in 1/251366 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Aug 21, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.R174C variant (also known as c.520C>T), located in coding exon 6 of the BRCA2 gene, results from a C to T substitution at nucleotide position 520. The arginine at codon 174 is replaced by cysteine, an amino acid with highly dissimilar properties. Multiple splicing assays have confirmed that the BRCA2 c.520C>T induces incomplete skipping of coding exon 6-also called exon 7 in published literature (Ambry internal data; Di Giacomo D et al, Hum. Mutat. 2013 Nov; 34(11):1547-57; Gaildrat P, et al. J Med Genet. 2012;49:609-617; Th&eacute;ry JC, et al. Eur J Hum Genet. 2011;19:1052-1058). In addition to this exon skipping event being incomplete, the molecular and clinical impact of loss of coding exon 6 is unclear (Mesman RLS et al. Genet. Med., 2020 May). This amino acid position is well conserved in primates, however, lower organisms do not have a reference at this position on multiple sequence alignment. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

not specified Uncertain:1

Apr 20, 2018

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: BRCA2 c.520C>T (p.Arg174Cys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. Though 5/5 computational tools predict no significant impact on normal splicing, one in silico study predicted potential effects by using 3 ESR-dedicated approaches (Soukarieh 2016). In vitro and in vivo studies indicated that the variant of interest induces partial exon 7 skipping (Thery 2011, Gaildrat 2012, DiGiacomo 2013). Exon 7 skipping is predicted to result in a frameshift, resulting in a truncated protein (that is subject to NMD), however, the in vivo consequence of partial exon 7 skipping is not known. Additionally, when transcribed properly, this variant results in a full length transcript with a missense alteration that could compound the in vivo consequence of this variant. The variant allele was found at a frequency of 4.1e-06 in 246130 control chromosomes. c.520C>T has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (Thery 2011, Gaildrat 2012). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer. Four 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 uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -

Hereditary cancer Uncertain:1

Feb 26, 2025

Mendelics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The available evidence is insufficient to conclusively determine the role of this variant. Therefore, it is classified as a Variant of Uncertain Significance. -

Familial cancer of breast Uncertain:1

Oct 25, 2023

Baylor Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.073
BayesDel_addAF	Benign	-0.070	T
BayesDel_noAF	Benign	-0.34
CADD	Benign	14
DANN	Benign	0.77
Eigen	Benign	-0.51
Eigen_PC	Benign	-0.53
FATHMM_MKL	Uncertain	0.84	D
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.16	T;T
MetaSVM	Benign	-0.86	T
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-0.42	N;N
REVEL	Benign	0.19
Sift	Benign	0.18	T;T
Sift4G	Benign	0.18	T;T
Vest4		0.36
MutPred		0.32		Gain of ubiquitination at K178 (P = 0.0582);Gain of ubiquitination at K178 (P = 0.0582);
MVP		0.81
MPC		0.13
ClinPred		0.30	T
GERP RS		0.93
gMVP		0.27

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.27		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.27		Position offset: -3

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

Publications

LitVar

Other links and lift over

dbSNP: rs41293469; hg19: chr13-32900639; COSMIC: COSV66463658;