rs786201180

chr13-32362698-G-Achr13-32362698-G-Cchr13-32362698-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2 PP3_Moderate PP5

The NM_000059.4(BRCA2):c.7976+5G>A variant causes a splice donor 5th base, intron change. The variant allele was found at a frequency of 0.000000684 in 1,461,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 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: 6.8e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 splice_donor_5th_base, intron
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:3
• Conservation: PhyloP100: 4.50

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 5 ACMG points.

• 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 13-32362698-G-A is Pathogenic according to our data. Variant chr13-32362698-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 183947.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=3, Pathogenic=2, Uncertain_significance=2}. Variant chr13-32362698-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.7976+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.7976+5G>A		splice_donor_5th_base_variant, intron_variant		5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461696 Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1 AN XY: 727160

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: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Apr 25, 2023	The c.7976+5G>A intronic pathogenic mutation results from a G to A substitution 5 nucleotides after coding exon 16 in the BRCA2 gene. This alteration has been identified in several Asian cohorts being tested for BRCA1 and BRCA2 mutations (Bhaskaran SP et al. Int. J. Cancer, 2019 Aug;145:962-973; Wong MS et al. Mol. Cell, 2018 09;71:1012-1026.e3; Kwong A et al. J Mol Diagn, 2016 07;18:580-94; Kwong A et al. J. Med. Genet., 2016 Jan;53:15-23). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data; Wong MS et al. Mol. Cell, 2018 09;71:1012-1026.e3). A close match alteration at the same nucleotide position, BRCA2 c.7976+5G>T was shown to produce the same splice defect in multiple unrelated carriers tested at different Spanish institutions (Montalban G et al. Hum. Mutat., 2018 Sep;39:1155-1160). Based on the majority of evidence available to date, this alteration is considered a disease-causing mutation. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 26, 2020	This variant causes a G to A nucleotide substitution at the +5 position of intron 17 of the BRCA2 gene. This variant is also known as IVS17+5G>A in the literature. A minigene splicing assay found that this variant resulted in the skipping of exon 17 (PMID: 30174293). This variant has been observed in an individual at-risk for familial breast and/or ovarian cancer (PMID: 26187060). A different c.7976+5G>T variant has been shown by RNA studies to cause in-frame skipping of exon 17 (PMID: 29969168, 31191615), resulting in a non-functional protein (PMID: 15695382, 18451181). The c.7976+5G>T variant also has been observed in multiple individuals affected with breast and/or ovarian cancer (PMID: 29969168). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 14, 2022	Variant summary: BRCA2 c.7976+5G>A alters a conserved nucleotide in intron 17, located close to the splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. The 5' splice site of BRCA2 intron 17 has a non-canonical sequence, with a cytosine at the +2 position (CAG/GCAAGT), therefore computational tools were not able to predict the impact of the variant on normal splicing, however a publication reported experimental evidence demonstrating that the variant resulted in complete skipping of exon 17 in a minigene assay (Wong_2018). The skipping of exon 17 is predicted to result in the in-frame deletion of 57 amino acids, which was demonstrated to result in a protein product deficient in HDR activity (PMID: 18451181). The variant was absent in 251100 control chromosomes (gnomAD). The variant, c.7976+5G>A, has been reported in the literature in at least one Chinese individual affected with breast cancer (Kwong_2013, Rebbeck_2018, Bhaskaran_2019). Six other submitters have provided clinical-significance assessments for this variant in ClinVar after 2014, and classified the variant as pathogenic (n=2) / likely pathogenic (n=2) or VUS (n=2). Based on the evidence outlined above, the variant was classified as likely pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 07, 2023	This sequence change falls in intron 17 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 likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with breast cancer (PMID: 26187060). This variant is also known as IVS17+5G>A. ClinVar contains an entry for this variant (Variation ID: 183947). 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 skipping of exon 17, but is expected to preserve the integrity of the reading-frame (PMID: 30174293). This variant disrupts the c.7976+5G nucleotide in the BRCA2 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 29969168). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. 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. -

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

Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Apr 13, 2018	- -

not specified Uncertain:1

Uncertain significance, no assertion criteria provided

research

Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto

Jan 31, 2014

- -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Quest Diagnostics Nichols Institute San Juan Capistrano

Aug 24, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
Cadd	Benign	21
Dann	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.90		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.90		Position offset: -5

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

Publications

LitVar

Other links and lift over

dbSNP: rs786201180; hg19: chr13-32936835;