chr13-32362595-G-C

Variant names:

• chr13-32362595-G-C
• rs80359013
• NM_000059.4:c.7878G>C

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PS1 PM2 PP3_Strong PP5_Very_Strong

The NM_000059.4(BRCA2):​c.7878G>C​(p.Trp2626Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,850 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 the same amino acid substitution has been previously reported as Likely pathogenic in Lovd.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:33 U:1
• Conservation: PhyloP100: 9.89

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 18 ACMG points.

• PS1: Transcript NM_000059.4 (BRCA2) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in Lovd
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.987
• PP5: Variant 13-32362595-G-C is Pathogenic according to our data. Variant chr13-32362595-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 38125.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362595-G-C is described in Lovd as [Pathogenic]. Variant chr13-32362595-G-C is described in Lovd as [Pathogenic]. Variant chr13-32362595-G-C is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.7878G>C	p.Trp2626Cys	missense_variant	Exon 17 of 27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.7878G>C	p.Trp2626Cys	missense_variant	Exon 17 of 27	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.7509G>C	p.Trp2503Cys	missense_variant	Exon 17 of 27	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.7886G>C		non_coding_transcript_exon_variant	Exon 16 of 26	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000796 AC: 2 AN: 251276 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135794

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: 0.0000176

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461850 Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1 AN XY: 727226

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: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000277 Hom.: 0

Bravo AF: 0.00000378

ExAC AF: 0.0000165 AC: 2

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:33 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:10

Jul 02, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The BRCA2 c.7878G>C; p.Trp2626Cys variant (rs80359013, ClinVar Variation ID: 38125), is reported in the literature in multiple individuals with hereditary breast and ovarian cancer, Fanconi anemia D1, or triple-negative breast cancer (Barber 2005, Heramb 2018, Meyer 2012, Winter 2016). Functional analyses of the variant protein show this variant causes a decrease in BRCA2 protein function (Biswas 2011, Guidugli 2014, Ikegami 2020, Mesman 2019). Furthermore, this variant is reported to have an odds ratio favoring causality of 48:1 based on family history, co-occurrence, and co-segregation data (Easton 2007, Guidugli 2013). This variant is found in the non-Finnish European population with an allele frequency of 0.002% (2/113,590 alleles) in the Genome Aggregation Database (v2.1.1). Additionally, another variant at this codon (c.7876T>C; p.Trp2626Arg) has been reported in individuals with breast cancer and is considered pathogenic (Han 2006). Computational analyses predict that this variant is deleterious (REVEL: 0.908). Based on available information, this variant is considered to be pathogenic. References: Barber LM et al. Inherited FANCD1/BRCA2 exon 7 splice mutations associated with acute myeloid leukaemia in Fanconi anaemia D1 are not found in sporadic childhood leukaemia. Br J Haematol. 2005 Sep;130(5):796-7. PMID: 16115142. Biswas K et al. A comprehensive functional characterization of BRCA2 variants associated with Fanconi anemia using mouse ES cell-based assay. Blood. 2011 Sep 1;118(9):2430-42. PMID: 21719596. Easton DF et al. A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes. Am J Hum Genet. 2007 Nov;81(5):873-83. PMID: 17924331. Guidugli L et al. A classification model for BRCA2 DNA binding domain missense variants based on homology-directed repair activity. Cancer Res. 2013 Jan 1;73(1):265-75. PMID: 23108138. Guidugli L et al. Functional assays for analysis of variants of uncertain significance in BRCA2. Hum Mutat. 2014 Feb;35(2):151-64. PMID: 24323938. Han SH et al. Mutation analysis of BRCA1 and BRCA2 from 793 Korean patients with sporadic breast cancer. Clin Genet. 2006 Dec;70(6):496-501. PMID: 17100994. Heramb C et al. BRCA1 and BRCA2 mutation spectrum - an update on mutation distribution in a large cancer genetics clinic in Norway. Hered Cancer Clin Pract. 2018 Jan 10;16:3. PMID: 29339979. Ikegami M et al. High-throughput functional evaluation of BRCA2 variants of unknown significance. Nat Commun. 2020 May 22;11(1):2573. PMID: 32444794. Mesman RLS et al. The functional impact of variants of uncertain significance in BRCA2. Genet Med. 2019 Feb;21(2):293-302. PMID: 29988080. Meyer P et al. BRCA2 mutations and triple-negative breast cancer. PLoS One. 2012;7(5):e38361. PMID: 22666503. Winter C et al. Targeted sequencing of BRCA1 and BRCA2 across a large unselected breast cancer cohort suggests that one-third of mutations are somatic. Ann Oncol. 2016 Aug;27(8):1532-8. PMID: 27194814. -

Aug 05, 2024

Centre for Clinical Genetics and Genomic Diagnostics, Zealand University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 20, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Multifactorial studies suggest this variant is associated with breast and ovarian cancer, but may confer lower risks than typical BRCA2 pathogenic variants (Biswas et al., 2011; Lindor et al., 2012; Pruss et al., 2014; Li et al., 2020; Li et al., 2022); Published functional studies demonstrate a damaging effect: impaired homologous recombination and sensitivity to PARP inhibitors (Biswas et al., 2011; Stoepker et al., 2015; Guidugli et al., 2018; Ikegami et al., 2020; Lee et al., 2021; Iversen et al., 2022); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as 8106G>C; This variant is associated with the following publications: (PMID: 23108138, 17924331, 22666503, 20104584, 27194814, 29478780, 31409081, 29446198, 30291343, 12228710, 25146914, 25583207, 16115142, 21719596, 19043619, 24323938, 21520273, 25085752, 16825431, 18951461, 25782689, 27767231, 28315974, 21138478, 26566862, 28866612, 21203900, 21990165, 29339979, 28541631, 30257646, 30728895, 29988080, 30720243, 31853058, 30696104, 32444794, 29884841, 31263571, 30702160, 31825140, 32719484, 29625052, 32885271, 32853339, 30787465, 32295079, 34906479, 34680878, 29394989, 21990134, 15070707, 29922827, 31794323, 35665744, 33978741, 34308104) -

Jun 03, 2022

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The frequency of this variant in the general population, 0.000008 (2/251276 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, this variant is described as a pathogenic variant with reduced penetrance, carrying a lower breast cancer risk than other BRCA2 pathogenic variants (PMID: 34906479 (2022)). It has been reported in individuals or families with breast cancer (PMIDs: 34680878 (2021), 34906479 (2022), 30728895 (2019), 30257646 (2018), 29339979 (2018), 27194814 (2016), 26014432 (2015), 22666503 (2012), 21203900 (2011)) or prostate cancer (PMID: 32853339 (2021)). This variant has also been reported in trans with a second pathogenic BRCA2 variant in patients with Fanconi anemia (PMIDs: 21138478 (2011), 15070707 (2004)). Published functional studies indicate that this variant impairs BRCA2 protein activity (PMIDs: 33978741 (2021), 32444794 (2020), 30696104 (2019), 29884841 (2019), 29394989 (2018), 29988080 (2018), 25146914 (2014), 23108138 (2013), 21719596 (2011)). Based on the available information, this variant is classified as pathogenic with reduced penetrance. -

Oct 23, 2020

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 29, 2022

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BRCA2: PS3, PM1, PS4:Moderate, PM2:Supporting, PP3 -

Oct 06, 2022

Clinical Genetics Laboratory, Skane University Hospital Lund

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 16, 2024

Mayo Clinic Laboratories, Mayo Clinic

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PP4_strong, PM3_strong, PS3 -

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:9 Uncertain:1

Oct 02, 2015

Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 10, 2015

Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 5 based on posterior probability = 1 -

Dec 16, 2016

Department of Medical Genetics, Oslo University Hospital

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 29, 2002

Breast Cancer Information Core (BIC) (BRCA2)

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Feb 11, 2015

Institute of Human Genetics, Medical University Innsbruck

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Dec 19, 2012

Sharing Clinical Reports Project (SCRP)

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jan 15, 2016

Counsyl

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 27, 2024

Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PS3; PP3; PM1; Expert panel -

Mar 02, 2020

BRCAlab, Lund University

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 11, 2025

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PS3,PP4_STR,PM3,PM2_SUP,PP3 -

Hereditary breast ovarian cancer syndrome Pathogenic:4

Nov 15, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces tryptophan, which is neutral and slightly polar, with cysteine, which is neutral and slightly polar, at codon 2626 of the BRCA2 protein (p.Trp2626Cys). This variant is present in population databases (rs80359013, gnomAD 0.0009%). This missense change has been observed in individual(s) with breast and/or ovarian cancer and Fanconi anemia (PMID: 11802209, 15070707, 16115142, 20104584, 21138478, 21203900, 22666503, 25085752). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 38125). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a high probability of being pathogenic (PMID: 17924331, 21990134). Experimental studies have shown that this missense change affects BRCA2 function (PMID: 17924331, 21719596, 21990134, 23108138, 25146914). For these reasons, this variant has been classified as Pathogenic. -

Nov 11, 2024

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

According to the ClinGen ENIGMA BRCA2 v1.1.0 criteria we chose these criteria: PS3 (strong pathogenic): Reported by three calibrated studies to exhibit protein function similar to pathogenic control variants (PMIDs:29988080, 29884841, 32444794), PM3 (medium pathogenic): Kopic et al. 2011, PMID: 21138478 & Wagner et al. 2004, PMID: 15070707 (3pt), PP3 (supporting pathogenic): BayesDel no AF: 0,48, PP4 (strong pathogenic): Combined LR Score (USCS): 48.97788, BS4 (strong benign): Reduced Penetrance??? -

Jul 20, 2017

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Trp2626Cys variant in BRCA2 has been reported in >16 individuals with BRCA 2-associated cancers (Han 2006, Petersen 2016, Breast Cancer Information Core). This variant has been identified in 2/66726 of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs80359013) . However, this frequency is low enough to be consistent with the frequency of h ereditary breast and ovarian cancer (HBOC) in the general population. In vitro f unctional studies provide some evidence that the p.Trp2626Cys may impact protein function (Hendriks 2014). Computational prediction tools and conservation analy sis suggest that the p.Trp2626Cys variant may impact the protein, though this in formation is not predictive enough to determine pathogenicity. In addition, this variant was classified as Pathogenic on Aug 10, 2016 by the ClinGen-approved EN IGMA expert panel (ClinVar SCV000244475.1). In summary, although additional stud ies are required to fully establish its clinical significance, the p.Trp2626Cys variant is likely pathogenic. -

Oct 28, 2019

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BRCA2 c.7878G>C (p.Trp2626Cys) results in a non-conservative amino acid change in the helical domain (IPR015252). Five in-silico tools predict a damaging effect. Observed at a frequency of 7.9e-06 in 251676 control chromosomes. Reported in individuals with Hereditary Breast and Ovarian Cancer (PMID's listed) and in trans with another BRCA2 variant (2041insA) in individuals with Fanconi Anemia (PMID's listed and BIC database). Several publications report experimental evidence demonstrating an inability to complement the cell lethal phenotype induced by loss of endogenous mouse BRCA2 (PMID's listed). One expert panel (ENIGMA) and ten clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic (n=6)/likely pathogenic (n=5). Based on the evidence outlined above, the variant was re-classified as pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Mar 20, 2023

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.W2626C pathogenic mutation (also known as c.7878G>C), located in coding exon 16 of the BRCA2 gene, results from a G to C substitution at nucleotide position 7878. The tryptophan at codon 2626 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been described in families with phenotypes consistent with hereditary breast and ovarian cancer (HBOC) syndrome (Meindl A et al. Int. J. Cancer 2002 Feb;97:472-80; Borg A et al. Hum. Mutat. 2010 Mar;31:E1200-40; Konecny M et al. Breast Cancer Res. Treat. 2011 Feb;126:119-30; Meyer P et al. PLoS ONE 2012;7:e38361; Winter C et al. Ann. Oncol. 2016 Aug;27:1532-8; Polsler L et al. Eur. J. Hum. Genet. 2016 Feb;24:258-62). This variant has also been identified in two unrelated patients with Fanconi Anemia (Wagner JE et al. Blood. 2004 Apr;103:3226-9; Kopic S et al. Acta Paediatr. 2011 May;100:780-3). In one of these patients, this alteration was confirmed to be in trans with a frameshift mutation (Wagner JE et al. Blood. 2004 Apr;103:3226-9). Functional assays evaluating homology-directed DNA break repair (HDR), embryonic stem cell rescue viability, susceptibility to DNA damaging agents, chromosomal aberration, and RAD51 foci have all indicated deficient function in BRCA2 p.W2626C mutants (Biswas K et al. Blood. 2011 Sep;118:2430-42; Guidugli L et al. Cancer Res. 2013 Jan;73:265-75; Hendriks G et al. Hum. Mutat. 2014 Nov;35:1382-91; Guidugli L et al. Am. J. Hum. Genet. 2018 Jan; Mesman RLS et al. Genet. Med., 2018 Jul;). However, one paper describes this as a hypomorphic variant based on a history weighting algorithm (Pruss D et al. Breast Cancer Res. Treat., 2014 Aug;147:119-32). 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 alteration is interpreted as a disease-causing mutation. However, because this variant is identified in one or more patients with Fanconi Anemia it may 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. -

Mar 04, 2025

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces tryptophan with cysteine at codon 2626 in the DNA binding of the BRCA2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function. Functional studies have shown that this variant showed loss of function in homology-directed repair and DNA damage response assays, a haploid cell proliferation assay and the complementation of Brca2-deficient mouse embryonic stem cells, and it impaired nuclear localization of BRCA2 protein (PMID: 21719596, 23108138, 25146914, 29884841, 29988080, 33978741, 39779857). This variant has been reported in individuals affected with breast or ovarian cancer (PMID: 11802209, 20104584, 21203900, 22666503, 26014432, 27194814) and this variant also has been detected in a breast cancer case-control meta-analysis in 7/60466 cases and 5/53461 unaffected individuals (PMID: 33471991; Leiden Open Variation Database DB-ID BRCA2_000238). In a study of 34 families, this variant has shown reduced penetrance and lower risk of breast cancer compared with other pathogenic variants in the BRCA1 and BRCA2 genes (PMID: 34906479). This variant has also been observed in two unrelated, biallelic individuals affected with Fanconi anemia, who were compound heterozygous with pathogenic variant in the same gene (PMID: 15070707; 16115142, 21138478), indicating that this variant contribute to disease. This variant has been identified in 2/251276 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic with reduced penetrance. -

Familial cancer of breast Pathogenic:2

Apr 20, 2022

MGZ Medical Genetics Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 22, 2024

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Medulloblastoma;C0346153:Familial cancer of breast;C0376358:Malignant tumor of prostate;C1838457:Fanconi anemia complementation group D1;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2;C2751641:Glioma susceptibility 3;C3150546:Pancreatic cancer, susceptibility to, 2;CN033288:Wilms tumor 1 Pathogenic:1

Feb 08, 2022

Fulgent Genetics, Fulgent Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breast and/or ovarian cancer Pathogenic:1

Jun 11, 2019

CZECANCA consortium

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

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

Oct 16, 2024

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PS3, PM3_SUP, PP1_STR, PM2_SUP, PP3 -

BRCA2-related cancer predisposition Pathogenic:1

Sep 27, 2024

All of Us Research Program, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces tryptophan with cysteine at codon 2626 in the DNA binding 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). Functional studies have shown that this variant showed loss of function in homology-directed repair and DNA damage response assays and the complementation of Brca2-deficient mouse embryonic stem cells, and it impaired nuclear localization of BRCA2 protein (PMID: 21719596, 23108138, 25146914, 29884841, 29988080, 33978741). This variant has been reported in individuals affected with breast or ovarian cancer (PMID: 11802209, 20104584, 21203900, 22666503, 26014432, 27194814) and this variant also has been detected in a breast cancer case-control meta-analysis in 7/60466 cases and 5/53461 unaffected individuals (PMID: 33471991; Leiden Open Variation Database DB-ID BRCA2_000238). In a study of 34 families, this variant has shown reduced penetrance and lower risk of breast cancer compared with other pathogenic variants in the BRCA1 and BRCA2 genes (PMID: 34906479). This variant has also been observed in two unrelated, biallelic individuals affected with Fanconi anemia, who were compound heterozygous with pathogenic variant in the same gene (PMID: 15070707; 16115142, 21138478), indicating that this variant contribute to disease. This variant has been identified in 2/251276 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic with reduced penetrance. -

Malignant tumor of breast Pathogenic:1

-

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The BRCA2 p.Trp2626Cys variant was identified in 4 of 7208 proband chromosomes (frequency: 0.0006) from individuals or families with contralateral and unilateral breast cancers, and was not identified in 2996 control chromosomes from healthy individuals (Borg 2010 PMID:20104584, Pruss 2014 PMID:25085752, Capanu 2011 PMID:21520273, Petersen 2016 PMID:26733283). The variant has also been identified in at least one patient with Fanconi anemia who also harboured a BRCA2 frameshift pathogenic variant (Stoepker 2015 PMID:25583207). In a study done to classify unknown variants, the variant was submitted to web-based algorithms using Align-GVGD, Grantham Variation and Grantham Deviation scores and found to be class (C65) of substitutions, which is most likely to interfere with function and was scored as possibly deleterious (Borg 2010 PMID:20104584). Furthermore studies classified the variant as deleterious based on a loss of DNA repair function identified through function studies (Biswas 2011 PMID:21719596, Guidugli 2013 PMID: 23108138, Hendriks 2014 PMID:25146914). The variant was shown to be sensitive to PARP inhibitors when present in a cell line derived from a patient with Fanconi anemia (Stoepker 2015). In addition Lindor et al. 2011 (PMID:21990134) determined the variant to be pathogenic (48.14 possibility of causality) when they weighted together segregation data, co-occurrence with pathogenic variants, personal and family history, and tumor pathology. However the above study by Biswas et al. 2011 demonstrated that the variant may be hypomorphic as it was able to recuse lethality in embryonic stem cells (notably in a similar experiment in the Hendrick et al. study the variant did not rescue lethality), and Pruss et al. 2014 also classified the variant as hypomorphic based on clinic history weighting algorithm. The variant was identified in dbSNP (ID: rs80359013 “With Pathogenic Allele”, in 1000 Genomes Project in 2 of 100000 chromosomes (frequency: 0.00002). The variant was also identified in the Exome Aggregation Consortium database (released Mar 14, 2016) in 2 of 121350 chromosomes (frequency: 0.00002) from a population of 2 of 66726 (0.00003) of European (Non-Finnish) alleles, although this low number of observations and low frequency is not substantive enough to determine the prevalence of the variant in the general population and its relationship to disease. The variant was also identified in GeneInsight-COGR by Trillum Health Partners 1x as Class 5, in Clinvar (pathogenic by ENIGMA, Quest, CIMBA, Counsyl, LMM, and Invitae, AND as likely pathogenic by LabCorp, GeneDx, Oslo University, Ambry, SCRP, and Medical University Innsbruck as well as Uncertain Significance by BIC). The variant is further identified in the BIC database 14X with unknown clinical importance, in the ARUP Laboratories BRCA Mutations Database 1x as definitely pathogenic, in the Fanconi Anemia Mutation Database (LOVD) 2x as predicted deleterious and 1x with reduced complementation. The variant was not listed in the COSMIC, MutDB, and UMD databases. The p.Trp2626 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The 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 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. -

Uterine corpus cancer Pathogenic:1

Feb 21, 2023

CZECANCA consortium

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.93
BayesDel_addAF	Pathogenic	0.50	D
BayesDel_noAF	Pathogenic	0.48
CADD	Pathogenic	29
DANN	Uncertain	0.99
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.99
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Pathogenic	0.54	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Pathogenic	0.99	D
PrimateAI	Uncertain	0.76	T
PROVEAN	Uncertain	-3.5	D;D
REVEL	Pathogenic	0.91
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Vest4		0.93
MutPred		0.94		Loss of MoRF binding (P = 0.0262);Loss of MoRF binding (P = 0.0262);
MVP		0.99
MPC		0.19
ClinPred		0.98	D
GERP RS		5.7
gMVP		0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs80359013; hg19: chr13-32936732;