rs758732038

chr13-32316419-CAG-C

Variant summary

Our verdict is Pathogenic. Variant got 20 ACMG points: 20P and 0B. PVS1 PM2 PP3_Moderate PP5_Very_Strong

The NM_000059.4(BRCA2):c.-39-1_-39del variant causes a splice acceptor change. The variant allele was found at a frequency of 0.000000707 in 1,414,192 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 splice_acceptor
• Clinical Significance: Likely pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 4.97

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 20 ACMG points.

• PVS1: Splicing variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 13-32316419-CAG-C is Pathogenic according to our data. Variant chr13-32316419-CAG-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 421014.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-32316419-CAG-C is described in Lovd as [Likely_pathogenic]. Variant chr13-32316419-CAG-C is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.-39-1_-39del		splice_acceptor_variant		ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.-39-1_-39del		splice_acceptor_variant		5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000804 AC: 2 AN: 248884 Hom.: 0 AF XY: 0.00000743 AC XY: 1 AN XY: 134568

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000109

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 7.07e-7 AC: 1 AN: 1414192 Hom.: 0 AF XY: 0.00000142 AC XY: 1 AN XY: 706240

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000254

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial cancer of breast Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jan 01, 2019	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Aug 27, 2021	- -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Nov 16, 2017

This variant is denoted BRCA2 c.-39-1_-39delGA or IVS1-1delGA and consists of a deletion of two nucleotides at the intron 1/exon 2 boundary of the BRCA2 gene. Using alternate numbering, this variant would be defined as BRCA2 190-1_190delGA. The normal sequence with the bases that are deleted in brackets is tgca[delgA]CTTA, where the capital letters are exonic and lowercase are intronic. Of note, BRCA2 exon 1 is non-coding and the BRCA2 ATG translational start site is located in exon 2. This variant destroys a canonical splice acceptor site and is predicted to cause abnormal gene splicing resulting in the loss of exon 2, leading to either an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product. BRCA2 c.-39-1_-39delGA was not observed in large population cohorts (Lek 2016). This variant was observed in at least one individual with breast and/or ovarian cancer (Kwong 2016). Based on currently available information, we consider BRCA2 c.-39_-39delGA to be a likely pathogenic variant. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 15, 2021

The c.-39-1_-39delGA variant is located in the 5' untranslated region (5'UTR) of the BRCA2 gene and results from a deletion of two nucleotides (GA) spanning the intron/exon boundary of coding exon 1. This alteration has been identified in multiple breast cancer patients of Chinese descent (Kwong A et al. J. Med. Genet., 2016 Jan;53:15-23; Wen WX et al. J Med Genet, 2018 02;55:97-103; Bhaskaran SP et al. Int J Cancer, 2019 08;145:962-973). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and may result in the creation or strengthening of a novel splice donor site; however direct evidence is insufficient at this time (Ambry internal data). A close-match alteration, BRCA2 c.-39-1G>A, also impacts this canonical splice acceptor leads to skipping of coding exon 1 (also known as Exon 2 in the literature), removing the native translational start codon (Davy G et al. Eur. J. Hum. Genet., 2017 10;25:1147-1154). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Invitae

Oct 23, 2023

This sequence change affects a splice site in intron 1 of the BRCA2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BRCA2 are known to be pathogenic (PMID: 20104584). This variant is present in population databases (rs758732038, gnomAD 0.01%). Disruption of this splice site has been observed in individual(s) with with breast cancer (PMID: 26187060, 28993434, 31174498, 32091409), as well as an individual affected with medulloblastoma (PMID: 29753700). ClinVar contains an entry for this variant (Variation ID: 421014). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.97		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.97		Position offset: 3
DS_DG_spliceai		0.38		Position offset: -28

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

Publications

LitVar

Other links and lift over

dbSNP: rs758732038; hg19: chr13-32890556;