rs80359775

Positions:

• chr13-32398209-TTGTA-T

Variant summary

Our verdict is Likely pathogenic. Variant got 10 ACMG points: 18P and 8B. BS1 BP5_Strong PS3 PM5_Strong PVS1 PM3

This summary comes from the ClinGen Evidence Repository: The c.9699_9702del variant in BRCA2 is a deletion of four nucleotides, predicted to encode a frameshift with consequent premature termination of the protein at codon 15 of the frameshift, or amino acid 3247 (p.Cys3233TrpfsTer15). The highest non-cancer, non-founder population filter allele frequency in gnomAD v2.1 (exomes only, non-cancer subset, read depth ≥20) or gnomAD v3.1 (non-cancer subset, read depth ≥20) is 0.0002484 in the Latino/Admixed American population, which is above the ENIGMA BRCA1/2 VCEP threshold (>0.0001) for BS1, and below the BA1 threshold (>0.001) (BS1 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 7.08E-23 (based on Family History LR=7.08E-23), below the thresholds for Very strong benign evidence (LR <0.00285) (BP5_Very strong met; Ambry internal contributor). Additional published family history analysis also reflects that this variant does not behave like other high risk variants (PMID:25639900). Frameshift variant predicted to cause a premature stop codon that is predicted to escape nonsense mediated decay, however it is a truncation of a functionally important region (sequence upstream of BRCA2 p.Glu3309 is disrupted) (PVS1 met). The ENIGMA BRCA1/2 VCEP considered multiple lines of functional and clinical evidence to define exon-specific weights for PTC in BRCA2, and results indicate that strong evidence towards pathogenicity may be applied for a PTC variant in BRCA2 exon 27 (PTC occurs before p.T3310) (PM5_Strong (PTC)). Reported by one calibrated study to exhibit protein function similar to pathogenic control variants (PMID:33293522) (PS3 met). This variant has been detected in 1 individual with phenotype consistent with BRCA2-Fanconi Anemia (FA). At least one clinical feature of FA (physical features, pathology findings and cancer diagnosis ≤5yr) and confirmed chromosome breakage, is seen in this individual. The individual was compound heterozygous for the variant and a pathogenic or likely pathogenic variant confirmed to be in trans. BRCA2:c.9699_9702del has also been detected in multiple individuals with phenotypic features consistent with FA but who did not meet our criteria for applying PM3. Total points equated to 2 (PM3 met; Ambry and Invitae internal contributors, PMID:25639900). Due to the higher than expected frequency and results of family history analysis, this variant is considered likely pathogenic with suspected reduced penetrance.In summary, this variant meets the criteria to be classified as a Likely pathogenic variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (BS1, BP5_Very strong, PM5_Strong (PTC), PVS1, PS3, PM3). LINK:https://erepo.genome.network/evrepo/ui/classification/CA026270/MONDO:0012933/097

• Frequency:
  • Genomes: 𝑓 0.000026 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000023 (0 hom.)
• Consequence: BRCA2 NM_000059.4 frameshift
• Clinical Significance: Likely pathogenic reviewed by expert panel P:24 U:5
• Conservation: PhyloP100: 2.83

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_pathogenic. Variant got 10 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PM5: For more information check the summary or visit ClinGen Evidence Repository.
• BP5: For more information check the summary or visit ClinGen Evidence Repository.
• BS1: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.9699_9702del	p.Cys3233TrpfsTer15	frameshift_variant	27/27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.9699_9702del	p.Cys3233TrpfsTer15	frameshift_variant	27/27	5	NM_000059.4	ENSP00000369497	A2

Frequencies

GnomAD3 genomes AF: 0.0000263 AC: 4 AN: 152236 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

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: 0.0000441

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000639 AC: 16 AN: 250272 Hom.: 0 AF XY: 0.0000592 AC XY: 8 AN XY: 135234

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000407

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: 0.0000233 AC: 34 AN: 1460544 Hom.: 0 AF XY: 0.0000179 AC XY: 13 AN XY: 726554

Gnomad4 AFR exome AF: 0.0000300

Gnomad4 AMR exome AF: 0.000381

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: 0.0000126

Gnomad4 OTH exome AF: 0.0000331

GnomAD4 genome AF: 0.0000263 AC: 4 AN: 152236 Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2 AN XY: 74372

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.0000416

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:24 Uncertain:5

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:11

Likely pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Jul 30, 2012	- -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Jan 13, 2016	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Department of Medical Genetics, Oslo University Hospital	Jan 02, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -
Pathogenic, no assertion criteria provided	clinical testing	BRCAlab, Lund University	Mar 02, 2020	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Feb 05, 2024	- -
Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	May 29, 2002	- -
Likely pathogenic, criteria provided, single submitter	literature only	Counsyl	Jul 29, 2014	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Aug 19, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	St. Jude Molecular Pathology, St. Jude Children's Research Hospital	Mar 10, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	Jun 02, 2023	The observed stop gained variant c.228C>A(p.Tyr76Ter) in the MUTYH gene has been reported previously in individuals affected with colorectal cancer and MUTYH-associated polyposis syndrome (Win AK, et al., 2014; Vogt S, et al., 2009). This variant is reported with the allele frequency 0.01% in the gnomAD Exomes. It is submitted to ClinVar as Pathogenic/Likely Pathogenic. Computational evidence (MutationTaster - Disease causing) predicts damaging effect on protein structure and function for this variant. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:4 Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 28, 2022	The BRCA2 c.9699_c.9702delTATG; p.Cys3233TrpfsTer15 variant (rs80359775) has been described in individuals with breast cancer and individuals with a clinical diagnosis of hereditary breast and ovarian cancer (HBOC; Bunnell 2017, Rebbeck 2018, van der Hout 2006). Truncations occurring downstream of this position have been classified as pathogenic by our laboratory (c.96725dupA;p.Tyr3255fs, c.9924C>G; p.Tyr3308Ter) and identified in HBOC patients (Alsop 2012, Tea 2014, van der Hout 2006, Waddell 2008). However, the c.9699_9702delTATG; p.Cys3233TrpfsTer15 variant has also been described in individuals who also carry an additional BRCA2 variant, without Fanconi anemia symptoms (Alemar 2017, Rosenthal 2015). The variant is present in the ClinVar database with discrepant classifications, but is classified as pathogenic by an expert panel (Variation ID: 38260). The variant is found in the Latino/Admixed American population with an allele frequency of 0.04% (14/35,226 alleles) in the Genome Aggregation Database. This variant results in a premature termination codon in the last exon of the BRCA2 gene. While this may not lead to nonsense-mediated decay, it is expected to create a truncated BRCA2 protein. Due to conflicting information, the clinical significance of the c.9699_c.9702delTATG; p.Cys3233TrpfsTer15 variant is uncertain at this time. References: Alemar B et al. Probands From Southern Brazil: Are International Testing Criteria Appropriate for This Specific Population? BRCA1 and BRCA2 Mutational Profile and Prevalence in Hereditary Breast and Ovarian Cancer (HBOC). PLoS One. 2017 Nov 21;12(11):e0187630. Alsop K et al. BRCA mutation frequency and patterns of treatment response in BRCA mutation-positive women with ovarian cancer: a report from the Australian Ovarian Cancer Study Group. J Clin Oncol. 2012 30:2654-2663. Bunnell AE et al. The Clinical Utility of Next Generation Sequencing Results in a Community-Based Hereditary Cancer Risk Program. J Genet Couns. 2017 Feb;26(1):105-112. Rebbeck TR et al. Mutational Spectrum in a Worldwide Study of 29,700 Families With BRCA1 or BRCA2 Mutations. Hum Mutat. 2018 May;39(5):593-620. Rosenthal ET et al. Exceptions to the Rule: Case Studies in the Prediction of Pathogenicity for Genetic Variants in Hereditary Cancer Genes. Clin Genet. 2015 Dec;88(6):533-41. Tea MK et al. Central European BRCA2 mutation carriers: birth cohort status correlates with onset of breast cancer. Maturitas. 2014 Jan;77(1):68-72. van der Hout AH et al. A DGGE System for Comprehensive Mutation Screening of BRCA1 and BRCA2: Application in a Dutch Cancer Clinic Setting. Hum Mutat. 2006 Jul;27(7):654-66. Waddell N et al. BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression. PLoS Genet. 2008 4:e1000080. -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Feb 13, 2023	This variant alters the translational reading frame of the BRCA2 mRNA. However due to the location of the variant in the last exon of the gene, the premature termination of BRCA2 protein synthesis is possible but the effect on protein function is uncertain. In the published literature, this variant has been reported in individuals and families with breast and/or ovarian cancer (PMIDs: 35438911 (2022), 32939053 (2020), 31658756 (2019), 29997359 (2018), 29339979 (2018), 29084914 (2018), 29161300 (2017), 27276934 (2016), 16683254 (2006)), adenomatous polyposis (PMID: 33753322 (2021)), prostate cancer (PMIDs: 35260348 (2022), 32853339 (2021)), and in healthy individuals (PMIDs: 33804961 (2021), 32719484 (2020), 30720243 (2019), 29922827 (2018), 27276934 (2016)). Additionally, this variant is reported to occur in trans with known pathogenic BRCA variants in individuals with Fanconi Anemia (PMID: 25639900 (2015)). An experimental study's report regarding the impact of this variant on BRCA2 protein function was inconclusive (PMID: 33293522 (2020)). The frequency of this variant in the general population, 0.0004 (14/35226 chromosomes in Latino/Admixed American subpopulation (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is higher than would generally be expected for pathogenic variants in this gene. Based on the available information, we are unable to determine the clinical significance of this variant. -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	Sep 15, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2023	BRCA2: PM2, PS3:Moderate, PVS1:Moderate -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Mar 12, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Aug 09, 2020	DNA sequence analysis of the BRCA2 gene demonstrated a four base pair deletion in exon 27, c.9699_9702del. This sequence change results in an amino acid frameshift and creates a premature stop codon 15 amino acids downstream of the variant, p.Cys3233Trpfs*15. This sequence change is not anticipated to result in nonsense mediated decay, but does disrupt the c-terminal domain of the BRCA2 protein. This sequencing change has been described in the gnomAD database with a low population frequency of 0.006% (dbSNP rs1277986751). This variant has been reported in the heterozygous and the compound heterozygous states in individuals with breast cancer (PMIDs:25639900, 29875428, 29161300). However, family testing did not demonstrate consistent segregation of the this variant with breast or ovarian cancer (PMIDs:25639900). This variant in the compound heterozygous state with another pathogenic variant has been described in individuals with a mild form of Fanconi anemia (PMID: 25639900). Other truncating variants in this region and downstream of this variant have been determined to be pathogenic (PMID: 18607349, 18593900, 22711857, 17026620). Collectively these evidences indicate that, the c.9699_9702del sequence is pathogenic. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jan 09, 2019	This deletion of four nucleotides is denoted BRCA2 c.9699_9702delTATG at the cDNA level and p.Cys3233TrpfsX15 (C3233WfsX15) at the protein level. Using alternate nomenclature, this variant would be defined as 9927_9930delTATG or 9927del4. The normal sequence, with the bases that are deleted in brackets, is TTTG[delTATG]GCCA. The deletion causes a frameshift, which changes a Cysteine to a Tryptophan at codon 3233, and creates a premature stop codon at position 15 of the new reading frame. This variant has been observed in individuals with a personal and/or family history of breast and/or ovarian cancer, and in an individual with breast cancer who also carried a second BRCA2 frameshift variant (van der Hout 2006, Castera 2014, Kang 2015, Alemar 2017, Bunnell 2017, Grindedal 2017). BRCA2 c.9699_9702delTATG is predicted to result in a truncated protein that removes the nuclear localization signals, the Cyclin A binding domain, and part of the RAD51 binding domain (Esashi 2005, Borg 2010, Roy 2012). Although frameshift variants are typically considered pathogenic, this variant occurs just upstream of a well-known polymorphism that also results in a premature stop of translation (Lys3326Ter). In addition, this variant has been seen in trans with a known pathogenic BRCA2 variant in several individuals without classic features of Fanconi anemia and was not found to consistently segregate with cancer in other families harboring this variant (Rosenthal 2015). Despite the seemingly damaging nature of this variant and some evidence of pathogenicity, based on currently available and internal data, we consider this to be a variant of uncertain significance. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Nov 01, 2023	This variant deletes 4 nucleotides in exon 27 of the BRCA2 gene, creating a frameshift and premature translation stop signal in the last coding exon. This variant is also known as 9927del4 and c.9697_9700del. The mutant transcript is predicted to be expressed as a truncated protein lacking the C-terminal RAD51 interaction domain and nuclear localization signals. This variant has been reported to impact BRCA2 function in the rescue of cell viability and PARP-inhibitor sensitivity in BRCA2-deficient cells (PMID: 33293522). This variant has been reported in over ten individuals affected with breast, ovarian, and pancreatic cancer (PMID: 16683254, 25479140, 24549055, 25639900, 25863477, 28637432, 28888541, 29084914, 29161300, 29339979, 29875428; Color data). This variant, in trans with another pathogenic variant in the BRCA2 gene, has been reported in individuals showing clinical features of autosomal recessive Fanconi anemia (external communication, ClinVar SCV000073900.8). However, the variant has not shown consistent segregation with cancer in family studies and has also been observed biallelic with different BRCA2 pathogenic variants in several carriers without symptoms of Fanconi anemia (PMID: 25639900, 29161300; Color internal data). This variant has been identified in 17/281678 chromosomes in the general population by the Genome Aggregation Database (gnomAD). These findings suggest that this variant may show reduced penetrance compared to a traditional pathogenic BRCA2 variant. Based on available evidence this variant is classified as Likely Pathogenic with reduced penetrance. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Sep 12, 2023	The c.9699_9702delTATG (p.C3233Wfs*15) alteration, located in exon 27 (coding exon 26) of the BRCA2 gene, consists of a deletion of 4 nucleotides from position 9699 to 9702, causing a translational frameshift with a predicted alternate stop codon after 15 amino acids. This alteration occurs at the 3' terminus of the BRCA2 gene, is not expected to trigger nonsense-mediated mRNA decay, and impacts the last 5.4% of the protein. However, premature stop codons are typically deleterious in nature, the impacted region is critical for protein function, and a significant portion of the protein is affected (Ambry internal data)._x000D_ _x000D_ However, because this variant is identified in one or more patients with Fanconi Anemia it may be hypomorphic and 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. This alteration (also designated c.9699_9702del and 9927del4 in published literature) has been reported in hereditary breast and/or ovarian cancer families (van der Hout, 2006; Kang, 2015; Alemar, 2017). It has also been identified in multiple families with Fanconi Anemia in a compound heterozygous state with different pathogenic BRCA2 variants (Ambry internal data; external communication), including multiple families presenting with atypical (unusually mild) Fanconi Anemia (Rosenthal, 2015). This alteration occurs 5' to two nonsense mutations at Y3308* and E3309*, which have been shown to be deleterious in in vitro and in vivo functional assays utilizing mouse embryonic stem cells (Kuznetsov, 2008). Based on the available evidence, this alteration is classified as pathogenic. -

Familial cancer of breast Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 27, 2024	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jan 01, 2019	- -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Pathogenic, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Jan 31, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 03, 2024	This sequence change creates a premature translational stop signal (p.Cys3233Trpfs*15) in the BRCA2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 186 amino acid(s) of the BRCA2 protein. This variant is present in population databases (rs781465150, gnomAD 0.04%). This premature translational stop signal has been observed in individual(s) with clinical features of Fanconi anemia (Invitae). This finding is consistent with autosomal recessive inheritance and suggests that this variant contributes to disease. However, in two reported families, this variant occurred with a second pathogenic variant in individuals with early-onset breast cancer; both variants were also found in their healthy siblings, whose only features were abnormal cellular studies (PMID: 25639900). While this variant has been observed in individuals with breast, ovarian, pancreatic and brain cancer (PMID: 29161300, 29084914, 30716324, 29753700, Invitae), published data has shown inconsistent segregation with HBOC-associated cancers (PMID: 25639900). This suggests that this pathogenic variant may exhibit lower penetrance or an atypical clinical presentation (PMID: 25639900). ClinVar contains an entry for this variant (Variation ID: 38260). This variant disrupts a region of the BRCA2 protein in which other variant(s) (p.Gln3299Ilefs*29, p.Tyr3308*) have been determined to be pathogenic (PMID: 17026620, 18593900, 18607349, 22711857; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

BRCA2-related cancer predisposition Pathogenic:1

Likely pathogenic, reviewed by expert panel

curation

ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen

Jun 11, 2024

The c.9699_9702del variant in BRCA2 is a deletion of four nucleotides, predicted to encode a frameshift with consequent premature termination of the protein at codon 15 of the frameshift, or amino acid 3247 (p.Cys3233TrpfsTer15). The highest non-cancer, non-founder population filter allele frequency in gnomAD v2.1 (exomes only, non-cancer subset, read depth >=20) or gnomAD v3.1 (non-cancer subset, read depth >=20) is 0.0002484 in the Latino/Admixed American population, which is above the ENIGMA BRCA1/2 VCEP threshold (>0.0001) for BS1, and below the BA1 threshold (>0.001) (BS1 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 7.08E-23 (based on Family History LR=7.08E-23), below the thresholds for Very strong benign evidence (LR <0.00285) (BP5_Very strong met; Ambry internal contributor). Additional published family history analysis also reflects that this variant does not behave like other high risk variants (PMID: 25639900). Frameshift variant predicted to cause a premature stop codon that is predicted to escape nonsense mediated decay, however it is a truncation of a functionally important region (sequence upstream of BRCA2 p.Glu3309 is disrupted) (PVS1 met). The ENIGMA BRCA1/2 VCEP considered multiple lines of functional and clinical evidence to define exon-specific weights for PTC in BRCA2, and results indicate that strong evidence towards pathogenicity may be applied for a PTC variant in BRCA2 exon 27 (PTC occurs before p.T3310) (PM5_Strong (PTC)). Reported by one calibrated study to exhibit protein function similar to pathogenic control variants (PMID: 33293522) (PS3 met). This variant has been detected in 1 individual with phenotype consistent with BRCA2-Fanconi Anemia (FA). At least one clinical feature of FA (physical features, pathology findings and cancer diagnosis <=5yr) and confirmed chromosome breakage, is seen in this individual. The individual was compound heterozygous for the variant and a pathogenic or likely pathogenic variant confirmed to be in trans. BRCA2:c.9699_9702del has also been detected in multiple individuals with phenotypic features consistent with FA but who did not meet our criteria for applying PM3. Total points equated to 2 (PM3 met; Ambry and Invitae internal contributors, PMID: 25639900). Due to the higher than expected frequency and results of family history analysis, this variant is considered likely pathogenic with suspected reduced penetrance. In summary, this variant meets the criteria to be classified as a Likely pathogenic variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (BS1, BP5_Very strong, PM5_Strong (PTC), PVS1, PS3, PM3). -

BRCA2-related disorder Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 18, 2024

The BRCA2 c.9699_9702delTATG variant is predicted to result in a frameshift and premature protein termination (p.Cys3233Trpfs*15). This variant has been reported in an individual with medulloblastoma (Waszak et al. 2018. PubMed ID: 29753700, Table S2, Donor ID MD-054), an individual with pancreatic cancer (Grant et al. 2015. PubMed ID: 25479140, Table S1), and in individuals with a personal and/or family history of breast and/or ovarian cancer (van der Hout et al. 2006. PubMed ID: 16683254, Table 5; Castéra et al. 2014. PubMed ID: 24549055, Table 1; Kang et al. 2015. PubMed ID: 25863477, Table 5; Bunnell et al. 2017. PubMed ID: 27276934, Table 3; Lilyquist et al. 2017. PubMed ID: 28888541. Table S7; Labidi-Galy et al. PubMed ID: 29084914, Table S2; Turner et al. 2019. PubMed ID: 29875428, Table 2; Delgado-Balderas et al. 2018. PubMed ID: 29997359, Table 1; Le Page et al. 2020. PubMed ID: 31753525, Table 1; Olafsdottir et al. 2020. PubMed ID: 32939053, Table S1). This variant has been reported along with a second truncating BRCA2 variant (c.9699_9702del, which was suspected to occur in trans) in an individual with early onset breast cancer and their unaffected sibling (Rosenthal et al. 2015. PubMed ID: 25639900, Table 1). Interestingly, both siblings had abnormal mitomycin C stress testing. This variant has also been observed in trans with a pathogenic BRCA2 missense variant in an individual with atypical Fanconi anemia (FA) and their unaffected sibling (Rosenthal et al. 2015. PubMed ID: 25639900, Table 1). It has also been reported to co-occur with a BRCA2 truncating variant in an additional individual with breast cancer at age 39, but no indication of FA (Alemar et al. 2017. PubMed ID: 29161300, Table S2). It has been reported in many unaffected relatives of individuals with breast and ovarian cancer and has been reported to co-occur with pathogenic BRCA1 variants in two unrelated individuals (Rosenthal et al. 2015. PubMed ID: 25639900). It has also been reported in individuals and families without histories of hereditary cancer and/or FA (Rudolf et al. 2016. PubMed ID: 27352968; Grzymski et al. 2020. PubMed ID: 32719484, Table S3). In vitro experimental studies and in silico models suggest this variant leads to the production of a truncated protein that may be partially defective in IR-induced RAD51 foci formation and in protecting replication fork stability (Biswas et al. 2020. PubMed ID: 33293522). This variant is reported in 0.040% of alleles in individuals of Latino descent in gnomAD and has also been reported in 0.08% of alleles in individuals from the Mexican population (Fernández-Lopez et al. 2019. PubMed ID: 30630528, Table S3). This variant has been reported as likely pathogenic for susceptibility to familial breast-ovarian cancer with suspected reduced penetrance by the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel (https://www.ncbi.nlm.nih.gov/clinvar/variation/38260/). Taken together, this variant is interpreted as likely pathogenic for hereditary cancer, however due to the higher than expected frequency and results of family history analysis, reduced penetrance is suspected. This variant is interpreted as likely pathogenic for autosomal recessive Fanconi anemia. -

Genetic non-acquired premature ovarian failure Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University

Oct 01, 2018

- -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

May 30, 2024

Variant summary: BRCA2 c.9699_9702delTATG (p.Cys3233TrpfsX15) results in a premature termination codon located in the BRCA2 C-terminal domain encoded by exon 27 that contains a nuclear localization signal, interacts with RAD51 in a CDK-dependent manner, and is required for maintaining genomic stability after DNA damage. Truncations downstream of this position have been classified as pathogenic by our laboratory and cited in HBOC patients. 2/4 splicing prediction tools predict that this variant may strengthen a cryptic 3' splicing acceptor site, which may lead to alternative start of exon 27 and frameshift. However, no alternatively spliced transcripts were detected for this variant (Biswas_2020). This variant was predicted not to result in Nonsense-Mediated Decay and associated with stable mutant proteins (Rebbeck_2018). The variant allele was found at a frequency of 6.4e-05 in 250272 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in BRCA2 causing Hereditary Breast and Ovarian Cancer (6.4e-05 vs 0.00075), allowing no conclusion about variant significance. The variant, c.9699_9702delTATG, has been reported in the literature in individuals affected with Breast and Ovarian Cancer (example, Castera_2014, Rosenthal_2015, Kan_2015, Alemar_2017, Bunnell_2017, Rebbeck_2018, Palmero_2018, Delgado-Balderas_2018, Heramb_2018, Le Page_2019, Turner_2019, Olafsdottir_2020, Chavarri-Guerra_2022), medulloblastoma (Waszak_2018) and intraductal papillary mucinous neoplasms (Skaro_2019). At-least one patient carried this variant along with a second BRCA2 variant (c.8878C>T, p.Gln2960X) and no associated phenotype of Fanconi Anemia (Alemar_2017). In our evaluation of this supporting literature, we conservatively ascertained at-least 11 transmissions of the variant allele and 4 transmissions of the reference allele to affected individuals in families with this variant. The ascertained penetrance of Hereditary Breast and Ovarian Cancer (0.44) due to this variant appears to be lower than expected allowing no firm conclusions from these data. Rosenthal_2015 evaluated the variant of interest and observed the variant in at least 1 Family with a suggested mild form of Fanconi Anemia. This family was ascertained because a female was diagnosed with breast cancer at 22 y/o and carried the variant of interest and another BRCA2 variant, c.145G>T (p.Glu49X) believed to be in trans, although not confirmed. Her brother (15 y/o) who carried the same two variants (identical genotype) was indicated to have no symptoms at the time of publication. However, both siblings were reported to have had abnormal chromosome mitomycin C stress testing. The authors went on to state that they "detected this variant in 67 apparently unrelated individuals undergoing comprehensive analysis of BRCA1 and BRCA2, it has been seen in two individuals who also carry a pathogenic variant in BRCA1." The authors further evaluated the variant of interest in the Myriad database and found multiple relatives of probands that carried the variant of interest that were either affected or unaffected, along with affected individuals that did not carry the variant of interest. Therefore, the authors concluded that the variant of interest needs to be reported as a "special interpretation variant" and conclude "there is as yet no compelling hypothetical mechanism as to why BRCA2 c.9699_9702del is not causative of HBOC." "It is important to note that the variant of interest described here is yet proven to have absolutely no impact on cancer risk, although the available data in each case suggest that the risk falls far short of what is considered to be diagnostic of the associated clinical syndrome." Multiple co-occurrences with other pathogenic variants have been reported from databases and publications (Rosenthal_2015, Alemar_2017), providing supporting evidence for a benign role (UMD-BRCA1 c.3979C>T, p.Gln1327X; BIC-BRCA1 c.3759_3760del -

Malignant tumor of breast Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

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BRCA2, Exon 27, c.9699_9702delTATG, p.Cys3233TrpfsX15, Heterozygous, Uncertain Significance The BRCA2 p.Cys3233TrpfsX15 variant was identified in 1 of 862 proband chromosomes (frequency: 0.001) from individuals or families with hereditary breast and ovarian cancer (HBOC), and this study classifies this variant as deleterious (van der Hout 2006). The variant was also identified in dbSNP (ID: rs80359775) “With pathogenic allele”, Clinvitae database, ARUP Laboratories BRCA Mutations Database (as definitely pathogenic), the ClinVar database with conflicting classifications (pathogenic by Ambry Genetics and BIC, likely pathogenic by Counsyl and SCRP, and uncertain significance by GeneDX), and the BIC database (3X with clinical importance). In UMD the variant was classified as a causal variant, but it was also identified with a co-occurring pathogenic BRCA1 variant (p.Gln1327X), increasing the likelihood that the p.Cys3233TrpfsX15 variant does not have clinical significance. This variant was also identified in the Exome Aggregation Consortium (ExAC) database (released Jan 13, 2015) in 9 of 11534 chromosomes (frequency: 0.00078) from a population of Latino individuals, as well as at a much lower frequency in European (Non-Finnish) individuals, 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. Myriad published a case study on the pathogenicity of this variant (Rosenthal 2015). Although this variant is near the 3′ end of the BRCA2 gene, there are known pathogenic variants downstream of this position, i.e. c.9924C>G (p.Tyr3308X), therefore this variant is expected to cause HBOC and would typically be classified as pathogenic. However, the Myriad study reports observations of the variant in trans with other deleterious BRCA2 variants in two sets of patients with no reported symptoms of Fanconi Anemia, and in two more individuals who also carry a pathogenic variant in BRCA2. The study further reports that they have detected this variant in 67 apparently unrelated individuals undergoing comprehensive analysis of BRCA1 and BRCA2. These observations currently meet the threshold for a benign designation. The study further states that family testing outcomes do not demonstrate consistent segregation of the variant with breast or ovarian cancer, although some contribution of the variant to the familial aggregation of cancer cannot be excluded. Therefore the Myriad study states that BRCA2 c.9699_9702del is currently reported as a ‘special interpretation variant’. The authors state that there is as yet no compelling hypothetical mechanism as to why BRCA2 c.9699_9702del is not causative of HBOC. They further conclude that it is important to note that the variant is not yet proven to have absolutely no impact on cancer risk, although the available data suggests that the risk falls far short of what is considered to be diagnostic of the associated clinical syndrome. 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. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs80359775; hg19: chr13-32972346;