13-32356496-C-T

Position:

• chr13-32356496-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP6

The NM_000059.4(BRCA2):​c.7504C>T​(p.Arg2502Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000173 in 1,614,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign 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. R2502H) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.00087 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00010 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:8 B:17
• Conservation: PhyloP100: 0.109

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_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.014025956).
• BP6: Variant 13-32356496-C-T is Benign according to our data. Variant chr13-32356496-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 41563.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=7, Benign=7, Uncertain_significance=4}. Variant chr13-32356496-C-T is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.7504C>T	p.Arg2502Cys	missense_variant	15/27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.7504C>T	p.Arg2502Cys	missense_variant	15/27	5	NM_000059.4	ENSP00000369497	A2

Frequencies

GnomAD3 genomes AF: 0.000874 AC: 133 AN: 152180 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00306

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00143

GnomAD3 exomes AF: 0.000270 AC: 68 AN: 251420 Hom.: 0 AF XY: 0.000206 AC XY: 28 AN XY: 135876

Gnomad AFR exome AF: 0.00338

Gnomad AMR exome AF: 0.000116

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000653

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.0000528

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000101 AC: 148 AN: 1461852 Hom.: 0 Cov.: 31 AF XY: 0.0000935 AC XY: 68 AN XY: 727232

Gnomad4 AFR exome AF: 0.00287

Gnomad4 AMR exome AF: 0.000112

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000464

Gnomad4 FIN exome AF: 0.0000374

Gnomad4 NFE exome AF: 0.0000270

Gnomad4 OTH exome AF: 0.000182

GnomAD4 genome AF: 0.000867 AC: 132 AN: 152298 Hom.: 0 Cov.: 31 AF XY: 0.000846 AC XY: 63 AN XY: 74466

Gnomad4 AFR AF: 0.00303

Gnomad4 AMR AF: 0.0000653

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.000240 Hom.: 0

Bravo AF: 0.00113

ESP6500AA AF: 0.00340 AC: 15

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000296 AC: 36

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:8 Benign:17

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:3 Benign:3

Benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Sep 15, 2022	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 11, 2016	Variant summary: Variant affects a non-conserved nucleotide and results in a replacement of a large size and basic Arginine (R) with a medium size and polar Cysteine (C). 4/5 in silico tools predict the variant to be benign. It was observed in the large and broad cohorts of the ExAC project at an allele frequency of 0.029%. It is most prevalent in the African subpopulation with an observed allele frequency of 0.29% which exceeds the maximal expected allele frequency of a disease causing BRCA2 allele (0.075%) indicating the variant to be benign. The variant was also observed in HBOC spectrum patients, however without strong evidence for pathogenicity. A functional study reported the variant not to have an effect on normal splicing. Moreover, BIC reports co-occurrence with multiple pathogenic BRCA1 variants c.3764_3765insA (p.Asn1255fsX12), and c.5324T>G (p.Met1775Arg) and c. 5074G>A (p.Asp1692Asn) further supporting a benign impact. Clinical diagnostic centers classify variant as Uncertain/Likely Benign/Benign via ClinVar (without evidence to independently evaluate). Considering all evidence, the variant was classified as Benign. -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 05, 2014	- -
Uncertain significance, no assertion criteria provided	research	Biesecker Lab/Clinical Genomics Section, National Institutes of Health	Jul 13, 2012	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2024	BRCA2: BP4, BS1 -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The BRCA2 p.Arg2502Cys variant was identified in 1 of 1144 proband chromosomes (frequency: 0.0.001) from individuals or families with cancer syndromes (Johnston 2012). The variant was also identified by our laboratory in 1 individual with breast cancer. The variant was identified in dbSNP (ID: rs55716624 “With Uncertain significance allele”, with a minor allele frequency of 0.0004 (2/5000 chromosomes tested in 1000 Genomes Project), NHLBI Exome Sequencing Project (Exome Variant Server) in 15 of 4406 African Americans (frequency: 0.0034) and not found in European Americans, Exome Aggregation Consortium database (March 14, 2016) in 36 of 121024 chromosomes (frequency:0.003) from a population of African (30/10322), European (Non-Finnish-4/66524), Latino (1/11538) individuals and not in East Asian , South Asian and European (Finnish) or Other individuals. The p.Arg2502Cys variant was also identified in HGMD, LOVD (2x as unknown), classified as an Uncertain significance variant by 6 separate submitters to the ClinVar database (the Sharing Clinical Reports Project derived from Myriad reports, GeneDX, BIC, Ambry Genetics, CSER_CC_NCGL, Biesecker Laboratory – ClinSeq Project_NHGRI), GeneInsight COGR 1x (classified as uncertain by a clinical laboratory), the BIC database (17x with unknown clinical importance), and UMD (6x as an uncertain variant). Note the variant co-occurred 2x with 2 other variants of unknown significance i.e. c.1798T>C, p.Tyr600His VUS and c.IVS10+9delGT VUS. The p.Arg2502 residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, MutationTaster) do not suggest a high likelihood of impact to the protein. However, this information is not predictive enough to rule out pathogenicity. The p.Arg2502Cys variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In addition, an assessment of 1,433 missense variants of unknown clinical significance, a likelihood ratio was computed based on a hypothesis that the variants were equivalent to an average deleterious mutation compared with neutral with respect to odds risk to other factors such as family history and co-occurrence. The likelihood ratios derived from each component were combined to provide an overall assessment for each VUS. The combined odds ratio for the variant was 21:1 and predicted causal, an odds ratio of 100:1 being neutral (Easton 2007). In another study (Karchin 2008), the authors are in disagreement with the conclusion of the Easton study. They have presented a new computational approach for analyzing the impact of missense changes in the DNA-binding domains of the cancer susceptibility protein BRCA2 that uses information from protein sequence, structure, and sequence conservation. They concluded the 2502Cys variant as neutral. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -

Breast-ovarian cancer, familial, susceptibility to, 2 Uncertain:3 Benign:1

Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	May 29, 2002	- -
Benign, no assertion criteria provided	clinical testing	BRCAlab, Lund University	Feb 02, 2024	- -
Uncertain significance, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Feb 09, 2007	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Apr 12, 2016	- -

not specified Uncertain:1 Benign:3

Likely benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	May 18, 2019	- -
Likely benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Jul 13, 2017	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 30, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 23, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency; ClinVar: 2 LB, 7 VUS -

Hereditary cancer-predisposing syndrome Benign:4

Likely benign, criteria provided, single submitter	curation	Sema4, Sema4	May 17, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Jan 22, 2020	This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Likely benign, no assertion criteria provided	clinical testing	True Health Diagnostics	Jan 05, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	May 24, 2016	- -

Hereditary breast ovarian cancer syndrome Benign:4

Benign, criteria provided, single submitter	curation	German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne	Oct 19, 2023	(BA1, BS3, BP4_strong). According to the ACMG standard criteria we chose these criteria: BP4 (strong benign): Bayes Del noAF (-0.0527), BS3 (strong benign): Richardson et al., 2021: neutral / final classification: benign (BA1, BS3, BP4_strong), BA1 (stand-alone benign): gnomAD: AF AFR: 0.003065 -
Benign, criteria provided, single submitter	clinical testing	Mendelics	Aug 22, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	St. Jude Molecular Pathology, St. Jude Children's Research Hospital	Dec 03, 2020	The BRCA2 c.7504C>T (p.Arg2502Cys) missense change has a maximum subpopulation frequency of 0.32% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/13-32930633-C-T). This frequency is higher than would be expected for a pathogenic variant in BRCA2 (BS1; PMID: 28166811). This variant affects a nucleotide that is not highly conserved and is predicted to be benign by multiple in silico algorithms (BP4). In summary, this variant meets criteria to be classified as likely benign based on the ACMG/AMP criteria: BS1, BP4. -

Breast and/or ovarian cancer Uncertain:1 Benign:1

Uncertain significance, criteria provided, single submitter	research	CSER _CC_NCGL, University of Washington	Jun 01, 2014	Low GERP score may suggest that this variant may belong in a lower pathogenicity class -
Likely benign, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Dec 05, 2022	- -

BRCA2-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 01, 2022

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Uncertain	-0.050
CADD	Benign	8.7
DANN	Benign	0.93
Eigen	Benign	-1.0
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.059	N
M_CAP	Uncertain	0.16	D
MetaRNN	Benign	0.014	T;T
MetaSVM	Benign	-0.76	T
MutationTaster	Benign	1.0	N;N
PrimateAI	Benign	0.18	T
PROVEAN	Benign	-0.92	N;N
REVEL	Uncertain	0.52
Sift	Benign	0.12	T;T
Sift4G	Benign	0.12	T;T
Vest4		0.19
MVP		0.75
MPC		0.022
ClinPred		0.014	T
GERP RS		0.57
gMVP		0.21

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs55716624; hg19: chr13-32930633; COSMIC: COSV66461376;