13-32370992-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PP3_Moderate PP5

The NM_000059.4(BRCA2):c.8524C>T(p.Arg2842Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000397 in 1,613,762 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2842H) has been classified as Benign.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000043 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:10 B:1
• Conservation: PhyloP100: 4.63

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 3 ACMG points.

• PP3: MetaRNN computational evidence supports a deleterious effect, 0.89
• PP5: Variant 13-32370992-C-T is Pathogenic according to our data. Variant chr13-32370992-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 52610.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=9, Likely_pathogenic=3, Pathogenic=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.8524C>T	p.Arg2842Cys	missense_variant	20/27	ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.8524C>T	p.Arg2842Cys	missense_variant	20/27	5	NM_000059.4	A2

Frequencies

GnomAD3 genomes AF: 0.00000658 AC: 1 AN: 151944 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000656

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: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00000796 AC: 2 AN: 251106 Hom.: 0 AF XY: 0.0000147 AC XY: 2 AN XY: 135698

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: 0.0000462

Gnomad NFE exome AF: 0.00000882

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000431 AC: 63 AN: 1461818 Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32 AN XY: 727208

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.0000522

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.00000658 AC: 1 AN: 151944 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74174

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000656

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000508 Hom.: 0

Bravo AF: 0.0000151

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:10 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

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

Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Dec 18, 2023	This missense variant replaces arginine with cysteine at codon 2842 of the BRCA2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Splice site prediction tools and RNA studies suggest that this variant may not impact RNA splicing (PMID: 24123850). Experimental functional studies have demonstrated partial or intermediate effects on homology directed repair (HDR; PMID: 23108138, 24323938, 29884841, 29394989, 29988080, 32354836, 32482800) and intermediate sensitivity to mitomicin C (MMC) or PARP inhibitors (PMID: 32354836), but normal sensitivity to cisplatin and normal complementation of a BRCA2-null cell lethal phenotype (PMID: 29988080). It has also been shown to be defective in replication fork protection of stalled replication forks during interstrand crosslink (ICL) repair, but without an increase in chromosomal breakage (PMID: 32354836). This variant has been reported in compound heterozygous state in 2 siblings diagnosed with atypical Fanconi anemia, and in compound heterozygous state in 1 unrelated individual diagnosed with Fanconi anemia; all 3 individuals with no evidence of bone marrow failure or malignancy at time of reporting despite family history of cancer (PMID: 32354836, ClinVar: SCV000897864.1). The variant was also reported in homozygous state in an individual with primary ovarian insufficiency without any personal or family history of BRCA2-associated cancer (PMID: 32482800). Cells homozygous for this variant showed intermediate defects compared with cells from non-carriers and cells from individuals with Fanconi anemia, in terms of MMC-induced chromosomal breaks, cell proliferation rate and radiation-induced RAD51 foci formation (PMID: 32482800). This variant has been detected in two breast cancer case-control studies in 0/2575 cases and 1/2809 unaffected individuals (PMID: 28993434) and in 3/60466 cases and 2/53461 unaffected individuals (PMID: 33471991; Leiden Open Variation Database DB-ID BRCA2_000340). This variant has also been reported in an individual considered at-risk for hereditary breast cancer (PMID: 31851867) and in two individuals affected with BRCA2-associated cancers and/or relevant family history (Color internal data). Lastly, it was also found to co-occur with a BRCA1 pathogenic variant in an individual in the BIC database (PMID: 10923033). This variant has been identified in 3/282388 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Although there is evidence of a hypomorphic role for this variant in an autosomal recessive, atypical Fanconi Anemia phenotype, the available evidence is insufficient to conclusively determine the role in autosomal dominant hereditary cancer. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Likely benign, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Feb 09, 2011	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Mar 22, 2023	- -
Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	Dec 23, 2003	- -

not provided Pathogenic:1 Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Nov 05, 2020	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2023	Observed in the heterozygous state in individuals with personal or family history of breast cancer, but also in healthy controls (Wen et al., 2018; Peker Eyuboglu et al., 2020; Dorling et al., 2021; Guindalini et al., 2022); 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 8752C>T; This variant is associated with the following publications: (PMID: 27378171, 28664449, 11309337, 28726806, 32042831, 23108138, 27194814, 27176796, 24323938, 11948123, 24123850, 29988080, 12228710, 10923033, 29394989, 28993434, 19043619, 30455982, 32482800, 31851867, 32354836, 29884841, 33054725, 33807840, 33150793, 33977503, 32719484, 31825140, 35665744, 36106376, 36754117, Sflomos2023[article], 36721989, 33471991, 35264596, Bahsi2020[case report]) -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 13, 2023	The BRCA2 c.8524C>T; p.Arg2842Cys variant (rs80359104) is reported in the literature in individuals affected with breast cancer (Bhai 2021, Gao 2020, Guindalini 2022), but also in healthy controls (Wen 2018). Additionally, this variant is reported in the homozygous state in an individual with no cancer or Fanconi anemia traits (Caburet 2020), and in the compound heterozygous state in two siblings with atypical Fanconi anemia (Rickman 2020). This variant is reported in ClinVar (Variation ID: 52610), and is found in the general population with an overall allele frequency of 0.0011% (3/282388 alleles) in the Genome Aggregation Database. Computational analyses predict that this variant is deleterious (REVEL: 0.843). Functional analyses of the variant protein show intermediate homology-directed repair activity (Caburet 2020, Guidugli 2018, Mesman 2019, Rickman 2020). Due to conflicting information, the clinical significance of this variant is uncertain at this time. References: Bhai P et al. Analysis of Sequence and Copy Number Variants in Canadian Patient Cohort With Familial Cancer Syndromes Using a Unique Next Generation Sequencing Based Approach. Front Genet. 2021 Jul 13;12:698595. PMID: 34326862. Caburet S et al. Homozygous hypomorphic BRCA2 variant in primary ovarian insufficiency without cancer or Fanconi anaemia trait. J Med Genet. 2020 Jun 1:jmedgenet-2019-106672. PMID: 32482800. Gao X et al. Comprehensive profiling of BRCA1 and BRCA2 variants in breast and ovarian cancer in Chinese patients. Hum Mutat. 2020 Mar;41(3):696-708. PMID: 31825140. Guidugli L et al. Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches. Am J Hum Genet. 2018 Feb 1;102(2):233-248. PMID: 29394989. Guindalini RSC et al. Detection of germline variants in Brazilian breast cancer patients using multigene panel testing. Sci Rep. 2022 Mar 9;12(1):4190. PMID: 35264596. Mesman RLS et al. The functional impact of variants of uncertain significance in BRCA2. Genet Med. 2019 Feb;21(2):293-302. PMID: 29988080. Rickman KA et al. Distinct roles of BRCA2 in replication fork protection in response to hydroxyurea and DNA interstrand cross-links. Genes Dev. 2020 Jun 1;34(11-12):832-846. PMID: 32354836. Wen WX et al. Inherited mutations in BRCA1 and BRCA2 in an unselected multiethnic cohort of Asian patients with breast cancer and healthy controls from Malaysia. J Med Genet. 2018 Feb;55(2):97-103. PMID: 28993434. -

Hereditary cancer-predisposing syndrome Pathogenic:1 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Oct 13, 2023	The p.R2842C variant (also known as c.8524C>T), located in coding exon 19 of the BRCA2 gene, results from a C to T substitution at nucleotide position 8524. The arginine at codon 2842 is replaced by cysteine, an amino acid with highly dissimilar properties. In a study with breast cancer patients and healthy controls, this alteration was not detected in 2575 breast cancer patients but was detected in 1/2809 controls (Wen WX et al. J. Med. Genet. 2018 Feb;55(2):97-103). In another study, this variant was reported in 3/60,466 breast cancer cases and in 2/53,461 controls (Dorling et al. N Engl J Med. 2021 02;384:428-439). This alteration has been identified in two independent sets of siblings with Fanconi anemia confirmed in trans with two different truncating BRCA2 variants, and one set is described as having a milder presentation (Rickman KA et al. Genes Dev, 2020 06;34:832-846; Ambry internal data). In addition, this alteration has been observed as homozygous in a Turkish woman who presented with primary ovarian insufficiency and who did not have overt clinical features of Fanconi anemia or personal or family history of cancer but who did demonstrate intermediate molecular effects including chromosomal breaks, cell proliferation and RAD51 foci formation (Caburet S et al. J Med Genet, 2020 Jun;). A mouse embryonic stem cell survival assay and multiple homology-directed DNA repair (HDR) assays also demonstrated an intermediate functional effect for p.R2842C (Guidugli L et al. Cancer Res. 2013 Jan 1;73(1):265-75; Guidugli L et al. Am. J. Hum. Genet. 2018 02;102(2):233-248; Mesman RLS et al. Genet. Med. 2019 02;21:293-302). Of note, this alteration is also designated as 8752C>T in published literature. 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. However, because this variant is identified in one or more patients with Fanconi anemia as well as in a homozygous patient without Fanconi anemia, it is likely to be 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 09, 2023	This missense variant replaces arginine with cysteine at codon 2842 of the BRCA2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Splice site prediction tools and RNA studies suggest that this variant may not impact RNA splicing (PMID: 24123850). Experimental functional studies have demonstrated partial or intermediate effects on homology directed repair (HDR; PMID: 23108138, 24323938, 29884841, 29394989, 29988080, 32354836, 32482800) and intermediate sensitivity to mitomicin C (MMC) or PARP inhibitors (PMID: 32354836), but normal sensitivity to cisplatin and normal complementation of a BRCA2-null cell lethal phenotype (PMID: 29988080). It has also been shown to be defective in replication fork protection of stalled replication forks during interstrand crosslink (ICL) repair, but without an increase in chromosomal breakage (PMID: 32354836). This variant has been reported in compound heterozygous state in 2 siblings diagnosed with atypical Fanconi anemia, and in compound heterozygous state in 1 unrelated individual diagnosed with Fanconi anemia; all 3 individuals with no evidence of bone marrow failure or malignancy at time of reporting despite family history of cancer (PMID: 32354836, ClinVar: SCV000897864.1). The variant was also reported in homozygous state in an individual with primary ovarian insufficiency without any personal or family history of BRCA2-associated cancer (PMID: 32482800). Cells homozygous for this variant showed intermediate defects compared with cells from non-carriers and cells from individuals with Fanconi anemia, in terms of MMC-induced chromosomal breaks, cell proliferation rate and radiation-induced RAD51 foci formation (PMID: 32482800). This variant has been detected in two breast cancer case-control studies in 0/2575 cases and 1/2809 unaffected individuals (PMID: 28993434) and in 3/60466 cases and 2/53461 unaffected individuals (PMID: 33471991; Leiden Open Variation Database DB-ID BRCA2_000340). This variant has also been reported in an individual considered at-risk for hereditary breast cancer (PMID: 31851867) and in two individuals affected with BRCA2-associated cancers and/or relevant family history (Color internal data). Lastly, it was also found to co-occur with a BRCA1 pathogenic variant in an individual in the BIC database (PMID: 10923033). This variant has been identified in 3/282388 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Although there is evidence of a hypomorphic role for this variant in an autosomal recessive, atypical Fanconi Anemia phenotype, the available evidence is insufficient to conclusively determine the role in autosomal dominant hereditary cancer. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Hereditary breast ovarian cancer syndrome Pathogenic:1 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Dec 28, 2023	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 2842 of the BRCA2 protein (p.Arg2842Cys). This variant is present in population databases (rs80359104, gnomAD 0.008%). This missense change has been observed in individual(s) with clinical features of BRCA2-related conditions (PMID: 32354836, 32482800; external communication). This variant is also known as c.8752C>T. ClinVar contains an entry for this variant (Variation ID: 52610). 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 not expected to disrupt BRCA2 protein function with a negative predictive value of 95%. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on BRCA2 function (PMID: 23108138, 29988080, 32354836, 32482800). 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. -
Pathogenic, criteria provided, single submitter	clinical testing	Cancer Variant Interpretation Group UK, Institute of Cancer Research, London	Oct 31, 2018	Data used in classification: This variant has been seen in trans with an established pathogenic variant in BRCA2 in a UK case of Fanconi D1 (chromosome breakage studies abnormal, BRCA2 ubiquitination function intermediate). Reduced level of BRCA2 protein on Western blot giving gene-phenotype specificity (PP4). BRCA2 was fully screened in this case (PM3). The variant is deleterious on the HR assay described by Guidugli et al (Couch laboratory), p=0.99 in 2013 and p=0.987 (2018) (PS3). Delirious on AlignGVGD, SIFT, Polyphen (PP3). Located in DNA binding domain (PM1_sup). In the GNOMAD NFE population of 63,369 individuals, the frequency of this variant is 1 (PM2-sup). Additional Information (not included in classification): There are additional reports of this variant in [ClinVar (5) , BIC (1), UMD (5) and BRCA2 LOVD (1)]. Reported several times in ENIGMA in HBOC families (verbal report). Comment: We have classified this as pathogenic but of intermediate penetrance based on (i) lack of cancer in index Fanconi case at age 10 (ii) Couch assay of 0.987 (all positive controls were p>0.99) (iii) BRCA2 ubiquitination function intermediate (iii) lack of family history in large pedigree for UK Fanconi case. -

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 27, 2022	Variant summary: BRCA2 c.8524C>T (p.Arg2842Cys) results in a non-conservative amino acid change located in the Tower domain (IPR015205) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 256724 control chromosomes. c.8524C>T has been reported in the literature as a VUS in individuals with breast cancer (example, Wen_2017, Chan_2018). Additionally, two recent studies have reported this as a hypomorphic BRCA2 variant in a homozygous individual with primary ovarian insufficiency without cancer or Fanconi anaemia traits (Caburet_2020) and as a compound heterozygous genotype with a BRCA2 frameshift variant (c.2330dupA) in two female siblings from the International Fanconi Anemia Registry (IFAR) reported as having an atypical presentation of Fanconi anemia with a multitude of congenital abnormalities and mildly elevated levels of chromosomal breakage at birth (Rickman_2020). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. At-least one co-occurrence with another pathogenic variant(s) have been reported in the BIC database (BRCA1 c.135-1G>T), providing supporting evidence for a benign role. Multiple publications report experimental evidence evaluating an impact on protein function (example, Mesman_2018, Guidugli_2018, Hart_2019, Caburet_2020, Rickman_2020). The most pronounced variant effect results in intermediate levels of homology directed repair (HDR) activity. Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (VUS, n=7; Pathogenic/Likely pathogenic with a risk factor verbiage (n=3). Some submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -
Uncertain significance, criteria provided, single submitter	clinical testing	Department of Pathology and Molecular Medicine, Queen's University	Apr 20, 2017	- -

Familial cancer of breast Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Baylor Genetics

Oct 26, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.51
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.37
Cadd	Pathogenic	28
Dann	Pathogenic	1.0
Eigen	Pathogenic	0.70
Eigen_PC	Pathogenic	0.67
FATHMM_MKL	Uncertain	0.95	D
M_CAP	Pathogenic	0.50	D
MetaRNN	Pathogenic	0.89	D;D
MetaSVM	Uncertain	0.66	D
MutationTaster	Benign	1.0	D;D
PrimateAI	Benign	0.47	T
PROVEAN	Uncertain	-2.4	N;N
REVEL	Pathogenic	0.84
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Vest4		0.74
MVP		0.95
MPC		0.18
ClinPred		0.99	D
GERP RS		5.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
gMVP		0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs80359104; hg19: chr13-32945129; COSMIC: COSV66450665;