rs276174844

Positions:

• chr13-32326085-CTTTGT-C

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6

The NM_000059.4(BRCA2):​c.426-12_426-8del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,450,484 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000041 (0 hom.)
• Consequence: BRCA2 NM_000059.4 splice_polypyrimidine_tract, intron
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:11 B:2
• Conservation: PhyloP100: 1.38

Genes affected

BRCA2 (HGNC:1101): (BRCA2 DNA repair associated) Inherited mutations in BRCA1 and this gene, BRCA2, confer increased lifetime risk of developing breast or ovarian cancer. Both BRCA1 and BRCA2 are involved in maintenance of genome stability, specifically the homologous recombination pathway for double-strand DNA repair. The largest exon in both genes is exon 11, which harbors the most important and frequent mutations in breast cancer patients. The BRCA2 gene was found on chromosome 13q12.3 in human. The BRCA2 protein contains several copies of a 70 aa motif called the BRC motif, and these motifs mediate binding to the RAD51 recombinase which functions in DNA repair. BRCA2 is considered a tumor suppressor gene, as tumors with BRCA2 mutations generally exhibit loss of heterozygosity (LOH) of the wild-type allele. [provided by RefSeq, May 2020]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• BP6: Variant 13-32326085-CTTTGT-C is Benign according to our data. Variant chr13-32326085-CTTTGT-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 51619.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=8}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.426-12_426-8del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.426-12_426-8del		splice_polypyrimidine_tract_variant, intron_variant		5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000414 AC: 6 AN: 1450484 Hom.: 0 AF XY: 0.00000554 AC XY: 4 AN XY: 721796

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: 0.00000543

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:11 Benign:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

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

Uncertain significance, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Sep 21, 2015	- -
Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	Feb 20, 2004	- -

not provided Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jan 18, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Feb 15, 2024	Published functional studies demonstrate aberrant splicing leading to skipping of exon 5 resulting in a truncated BRCA2 protein, but also show the presence of wild-type transcript indicating an incomplete splice defect (PMID: 19070627, 20215541, 21394826, 30883759); Observed in individuals with a personal and/or family history of BRCA2-related cancers, some of whom also carried a pathogenic variant in BRCA1 or BRCA2, and reported to occur in trans with a pathogenic BRCA2 variant in individuals without known features of Fanconi anemia (PMID: 18446624, 19070627, 26681312, 30675319, 35050751); Not observed at significant frequency in large population cohorts (gnomAD); Also known as BRCA2 654-12_654-8delGTTTT and IVS4-12del5; This variant is associated with the following publications: (PMID: 27060066, 30675319, 31642931, 23893897, 16162645, 20215541, 21394826, 19070627, 32133419, 31131967, 18446624, 24212087, 31980526, 30883759, 10923033, 26681312, 21520333, 35050751) -

Hereditary cancer-predisposing syndrome Uncertain:3

Uncertain significance, criteria provided, single submitter	curation	Sema4, Sema4	Dec 07, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	May 27, 2020	This variant causes a deletion of 5 nucleotides in intron 4 of the BRCA2 gene. The variant is also known as IVS4-12del5, c.654-12_654-8delGTTTT, and c.426-12_8del5 in the literature. Experimental RNA studies of this variant have demonstrated a partial impact on splicing, increasing the skipping of exon 5 and producing a truncated protein in mutant cells (PMID: 19070627, 20215541, 21394826, 24212087, 30883759, 32133419). However, significant baseline expression of the exon 5 skipped transcript in normal cells may limit the variant's causal impact on disease (PMID: 27060066, 29774201, 32133419). This variant has been reported in individuals affected with breast cancer in the literature, but also in unaffected individuals (PMID: 10923033, 18446624, 19070627, 30675319, 16162645). This variant has also been observed to co-occur with pathogenic variants in BRCA1 (PMID: 18446624, Color Internal data). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion for a pathogenic role, the available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Aug 20, 2020	The c.426-12_426-8delGTTTT intronic variant, results from a deletion of 5 intronic nucleotides upstream of coding exon 4 in the BRCA2 gene. This alteration, designated as IVS4-12del5, was identified in a family with melanoma, breast and pancreatic cancer and segregated with disease in this family. Furthermore, a breast tumor from this family showed loss of heterozygosity for BRCA2 (Zhang L et al. Mutat. Res. 2009 Apr;663:84-9). This variant has been shown to cause incomplete exon skipping, leading to a frameshift and creation of a premature alternative stop codon (Zhang L et al. Mutat. Res. 2009 Apr;663:84-9; Sanz DJ et al. Clin. Cancer Res. 2010 Mar;16:1957-67; Whiley PJ et al. Hum. Mutat. 2011 Jun;32:678-87; Whiley PJ et al. Clin. Chem. 2014 Feb;60:341-52). In addition, internal, quantitative RNA studies have demonstrated this alteration results in a substantial amount of abnormal splicing. However, this alteration has also been reported in trans with other pathogenic BRCA2 variants in patients of unknown age and phenotype who do not have overt symptoms of Fanconi Anemia (Ambry internal data; Nix, P et al. JCO Prec. Onc. 2020 June;4:790-35). Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -

not specified Uncertain:2

Uncertain significance, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Jan 31, 2014	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 29, 2023	Variant summary: BRCA2 c.426-12_426-8delGTTTT alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Two computational tools predict the variant weakens a 3' acceptor site. In addition, a recent computational study predicted a high probability of splicing impact (Leman_2018). Several publications reported experimental evidence that this variant affects mRNA splicing, by increasing exon 5 skipping (predicted to result in a frameshift), and consequently decreasing the expression of the full-length transcript (e.g., Zhang_2009, Sanz_2010, Whiley_2011, Whiley_2014, Lattimore_2018, Fraile-Bethencourt_2019). However, a more recent study found that this aberrant splicing is inefficient and the percent splicing index (PSI) was determined to be ~20% in positive controls (vs. ~10% in healthy controls) (Landrith_2020); the amount of normal transcript needed for normal BRCA2 function is unknown (Nix_2020). The variant was absent in 249586 control chromosomes (gnomAD). c.426-12_426-8delGTTTT has been reported in the literature in individuals affected with breast cancer, as well as unaffected individuals (e.g., Zhang_2009, Whiley_2011, Susswein_2015). These reports do not allow any conclusion about variant significance. Multiple co-occurrences with other pathogenic variants have been reported (BRCA2 c.9257-1G>C [NHGRI BIC database, Nix_2020]; BRCA2 c.7248del, p.H2417TfsX50 [LOVD database]; BRCA1 c.5152+1G>T [Loughrey_2008]; BRCA2 c.7719dupA, p.W2574MfsX10 [Nix_2020]), providing supporting evidence for a benign role. Particularly, Nix et al (2020) report carriers of the variant did not have a personal or family history consistent with pathogenicity and they specify that the variant was found to co-occur in trans with two different pathogenic variants in BRCA2 in individuals with no known features of Fanconi anemia. The following publications have been ascertained in the context of this evaluation (PMID: 26992833, 27060066, 30675319, 30883759, 21702907, 31642931, 29774201, 29750258, 18446624, 20215541, 26681312, 24212087, 21394826, 19070627, 32133419, 35050751). Eight submitters have reported clinical-significance assessments for this variant to ClinVar after 2014; 7 submitters classified the variant as VUS, and 1 submitter classified it as likely benign. Based on the evidence outlined above, the variant was re-classified as VUS-possibly benign. -

Hereditary breast ovarian cancer syndrome Benign:2

Likely benign, criteria provided, single submitter	curation	German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne	Apr 09, 2024	According to the ClinGen ENIGMA BRCA2 v1.0.0 criteria we chose these criteria: PM2 (supporting pathogenic): absent from controls (gnomAD v2/3), PP3 (supporting pathogenic): SpliceAI ≥ 0.2, BP5 (medium benign): Combined LR (Parsons 2019): 0.1359 (cutoff 0.23:1<LR<0.05:1), BS2 (medium benign): Nix 2020 (PMID: 35050751): in 2 individuals with no known features of Fanconi anemia confirmed in trans with BRCA2 c.7719dupA or c.9257-1G>C -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 15, 2024	- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs276174844; hg19: chr13-32900222;