rs81002816

chr13-32346901-G-Achr13-32346901-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3 PP5

The NM_000059.4(BRCA2):c.7007+5G>A variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,449,698 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 splice_donor_5th_base, intron
• Scores: Splicing: ADA: 0.9997
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:8
• Conservation: PhyloP100: 2.93

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 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
• PP5: Variant 13-32346901-G-A is Pathogenic according to our data. Variant chr13-32346901-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 52239.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=4, Likely_pathogenic=2, Pathogenic=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.7007+5G>A		splice_donor_5th_base_variant, intron_variant		ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.7007+5G>A		splice_donor_5th_base_variant, intron_variant		5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.90e-7 AC: 1 AN: 1449698 Hom.: 0 Cov.: 29 AF XY: 0.00000139 AC XY: 1 AN XY: 721434

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: 9.05e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:8

Revision: criteria provided, conflicting classifications

Submissions by phenotype

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

Uncertain significance, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	May 01, 2012	- -
Pathogenic, no assertion criteria provided	research	University of Washington Department of Laboratory Medicine, University of Washington	Oct 28, 2019	Functional studies using RNA from a known carrier of this variant showed that this variant results in 70% of the BRCA2 transcript from the variant allele to have altered splicing. Cosegregation analysis of this patient's family shows a likelihood ratio of 5:1 that this variant is pathogenic (using the Thompson et al. cosegregation method [PMID 12900794] with AnalyzeMyVariant.org calculator). This analysis was performed in conjunction with the family studies project as part of the University of Washington Find My Variant study. Taken together with frequency and in-silico predictions this variant is considered likely pathogenic. -
Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	Feb 20, 2004	- -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Medical and Surgical Sciences, University of Bologna	Sep 01, 2023	PM2(Supporting)+PP4(Moderate) according to ACMG/AMP classification guidelines specified for BRCA1 & BRCA2 (Classification Criteria V1.0.0 2023-09-08 - https://cspec.genome.network/cspec/ui/svi/affiliation/50087) (PMID: 38160042) -

not provided Pathogenic:1 Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Feb 14, 2018	This variant is denoted BRCA2 c.7007+5G>A or IVS13+5G>A and consists of a G>A nucleotide substitution at the +5 position of intron 13 of the BRCA2 gene. Using alternate nomenclature, this variant would be defined as BRCA2 7235+5G>A. Multiple in silico models and a published computational prediction model (Mucaki 2011) predict this variant to damage or destroy the nearby natural donor site, and to possibly cause abnormal gene splicing; however, in the absence of RNA or functional studies, the actual effect of this variant is unknown. This variant has not, to our knowledge, been published in the literature as pathogenic or benign. BRCA2 c.7007+5G>A was not observed in large population cohorts (Lek 2016). The guanine (G) nucleotide that is altered is not conserved across species. Based on currently available information, it is unclear whether BRCA2 c.7007+5G>A is pathogenic or benign. We consider it to be a variant of uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Mar 15, 2022	BP4, PM2 -
Likely pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jun 14, 2023	The BRCA2 c.7007+5G>A variant (rs81002816) is reported in the literature in individuals affected with breast, ovarian, and pancreatic cancer (Puccini 2022, Santonocito 2020, Tsai 2019, Zuntini 2018). This variant has also been reported in three men who did not have colon or breast cancer (Tsai 2019). This variant is also reported in ClinVar (Variation ID: 52239), and is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. Additionally, another variant at this position (c.7007+5G>C) has been reported as likely pathogenic (Parsons 2019). Functional analyses using lymphoblast cell lines demonstrate that this change can result in exon 12-13 skipping and exon 13 skipping (Casadei 2019). This is an intronic variant in a moderately conserved nucleotide, and computational analyses (Alamut Visual Plus v.1.5.1) predict that this variant may impact splicing by weakening the nearby canonical donor splice site. Based on available information, this variant is considered to be likely pathogenic. References: Casadei S et al. Characterization of splice-altering mutations in inherited predisposition to cancer. Proc Natl Acad Sci U S A. 2019 Dec 26;116(52):26798-26807. PMID: 31843900. Parsons MT et al. Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification. Hum Mutat. 2019 Sep;40(9):1557-1578. PMID: 31131967. Puccini A et al. Clinical Significance of Germline Pathogenic Variants among 51 Cancer Predisposition Genes in an Unselected Cohort of Italian Pancreatic Cancer Patients. Cancers (Basel). 2022 Sep 13;14(18):4447. PMID: 36139606. Santonocito C et al. Spectrum of Germline BRCA1 and BRCA2 Variants Identified in 2351 Ovarian and Breast Cancer Patients Referring to a Reference Cancer Hospital of Rome. Cancers (Basel). 2020 May 19;12(5):1286. PMID: 32438681. Tsai GJ et al. Outcomes of 92 patient-driven family studies for reclassification of variants of uncertain significance. Genet Med. 2019 Jun;21(6):1435-1442. PMID: 30374176. Zuntini R et al. Dealing With BRCA1/2 Unclassified Variants in a Cancer Genetics Clinic: Does Cosegregation Analysis Help? Front Genet. 2018 Sep 11;9:378. PMID: 30254663. -

Hereditary breast ovarian cancer syndrome;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:1

Pathogenic, no assertion criteria provided

research

King Laboratory, University of Washington

Sep 01, 2019

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 30, 2023

The c.7007+5G>A intronic variant results from a G to A substitution 5 nucleotides after coding exon 12 in the BRCA2 gene. This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive. This alteration has been identified in multiple individuals with a personal and/or family history of BRCA2-associated disease including one individual whose tumor had loss of heterozygosity of the wildtype allele (Spearman AD et al. J Clin Oncol, 2008 Nov;26:5393-400; Zuntini R et al. Front Genet, 2018 Sep;9:378; Tsai GJ et al. Genet Med, 2019 Jun;21:1435-1442; Santonocito C et al. Cancers (Basel), 2020 May;12). RNA studies have demonstrated this alteration results in abnormal splicing in the set of samples tested (Ambry internal data; Casadei S et al. Proc Natl Acad Sci U S A, 2019 Dec). Several close-match alterations that are expected to have a similar splicing profile, BRCA2 c.7007G>A and BRCA2 c.7007G>C, have been observed in multiple patients with Fanconi Anemia (Meng L et al. JAMA Pediatr. 2017 12;171(12):e173438; Barber LM et al. Br. J. Haematol. 2005 Sep;130:796-7). Based on the majority of available evidence to date, this variant is likely to be pathogenic. However, because several close-match variants are 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. -

Hereditary breast ovarian cancer syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Dec 22, 2023

This sequence change falls in intron 13 of the BRCA2 gene. It does not directly change the encoded amino acid sequence of the BRCA2 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with breast and/or ovarian cancer (PMID: 30254663). ClinVar contains an entry for this variant (Variation ID: 52239). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in exon 13 skipping and exon 12-13 skipping and introduces a premature termination codon (PMID: 31843900; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Oct 12, 2023

Variant summary: BRCA2 c.7007+5G>A alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: One predict the variant abolishes a canonical 5' splicing donor site. Two predict the variant weakens a canonical 5' donor site. A functional study using lymphoblast cell lines created from patients showed the variant to result in 66% full lenth transcript, with 33% transcript that skips exon 12-13 or skips exon 13 (Casadei_2019). Neither abbertant transcript was found in controls. Additionally, one clinical lab via ClinVar reports RNA studies showing this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). The variant was absent in 247222 control chromosomes (gnomAD). c.7007+5G>A has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome and pancreatic cancer (examples: Puccini_2022, Santonocito_2020, Tsai_2019, Zuntini_2018), without strong evidence for causality. In one report, three men carried the variant, all without breast or prostate cancer (Tsai_2019). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. The following publications have been ascertained in the context of this evaluation (PMID: 31843900, 32438681, 30374176, 30254663, 36139606). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Multiple submitters reported the variant with conflicting assessments: two classified as VUS while four classified as likely pathogenic/pathogenic. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

Breast and/or ovarian cancer Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research

Jun 05, 2015

- -

Familial cancer of breast Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Baylor Genetics

Jan 12, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
Cadd	Benign	22
Dann	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.74
SpliceAI score (max)		0.13		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: rs81002816; hg19: chr13-32921038;