rs81002840

chr13-32319330-G-Achr13-32319330-G-C

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PM2 PP5_Very_Strong BP4

The NM_000059.4(BRCA2):c.316+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 0.000000686 in 1,457,316 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 splice_donor_5th_base, intron
• Scores: Splicing: ADA: 0.7931
• Clinical Significance: Pathogenic reviewed by expert panel P:15 U:1
• Conservation: PhyloP100: 3.00

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 9 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 13-32319330-G-A is Pathogenic according to our data. Variant chr13-32319330-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 51409.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32319330-G-A is described in Lovd as [Pathogenic]. Variant chr13-32319330-G-A is described in Lovd as [Likely_pathogenic].
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.316+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.316+5G>A		splice_donor_5th_base_variant, intron_variant		5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1457316 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 725238

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: 9.02e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:15 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

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

Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jul 09, 2023	The c.316+5G>A variant in the BRCA2 gene is located at intron 3 and is predicted to result in abnormal splicing and disrupted protein product. The variant has been reported in individuals with breast and/or ovarian cancer (PMID: 29707112, 23192360, 26207792, 21769658). RNA analysis shows complete skipping of exon 3, which is deleterious to protein function (PMID: 21769658, 29707112, 35979650). The variant is reported in ClinVar as pathogenic (ID: 51409) and reviewed by the expert panel. The variant is absent in the general population database (gnomAD). Therefore, the c.316+5G>A variant of BRCA2 has been classified as pathogenic. -
Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	Dec 23, 2003	- -
Pathogenic, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Apr 01, 2018	Almost complete (94%) skipping of exon 3 (r.68_316del) in a minigene splicing assay. Molecular consequence is the same as other variants designated as pathogenic as determined by multifactorial likelihood analysis (PMID: 29707112). Specifically, pathogenic consequence of the in-frame transcript without exon 3 has been shown in another family with a deletion of this exon, by co-segregation analysis with LR >1300:1 in favour of pathogenicity (PMID: 29707112). -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Sep 17, 2012	- -

not provided Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 15, 2016	This variant is denoted BRCA2 c.316+5G>A or IVS3+5G>A and consists of a G>A nucleotide substitution at the +5 position of intron 3 of the BRCA2 gene. Using alternate nomenclature, this variant would be defined as BRCA2 544+5G>A. This variant was observed in several individuals with a personal and family history of breast and/or ovarian cancer (Thomassen 2012, Decker 2013). Multiple in silico models predict, and RT-PCR analysis confirm, that this variant causes and in-frame deletion of exon 3 (Thomassen 2012, Decker 2013). Although an alternate isoform of BRCA2 lacking exon 3 has been described in multiple tissues, the level of this transcript is significantly more abundant in those harboring BRCA2 544+5G>A, and other similar variants that also result in exon 3 skipping (Muller 2011, Thomassen 2012). BRCA2 c.316+5G>A was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. The guanine (G) nucleotide that is altered is conserved across species. Based on the currently available evidence, we consider BRCA2 c.316+5G>A to be a likely pathogenic variant. -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Feb 21, 2023	PP1, PP3, PP5, PM2, PS3, PVS1_strong -
Likely pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jun 02, 2017	- -

Hereditary cancer-predisposing syndrome Pathogenic:3

Likely pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	Sep 03, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Sep 25, 2023	This variant causes a G to A nucleotide substitution at the +5 position of intron 3 of the BRCA2 gene. RNA studies have shown that this variant causes in-frame skipping of exon 3, resulting in partial loss of the PALB2 binding site. This variant has been reported in individuals affected with breast or ovarian cancer, including 1 male individual and 1 individual affected with early-onset breast cancer (PMID: 21769658, 31512090). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Sep 11, 2023	The c.316+5G>A intronic pathogenic mutation results from a G to A substitution 5 nucleotides after coding exon 2 in the BRCA2 gene. This mutation has been identified in kindreds with hereditary breast and ovarian cancer (Muller D et al. BMC Med. Genet. 2011; 12:121) as well as in one family with members diagnosed with various types of cancers, including early onset breast cancer, prostate cancer, abdominal cancer, and basal cell carcinoma (Thomassen M et al. Breast Cancer Res. Treat. 2012 Apr;132(3):1009-23). Additionally, functional analysis has demonstrated that this alteration leads to a skipping of coding exon 2, a region with a high degree of evolutionary conservation and importance for protein function (Thomassen M et al. Breast Cancer Res.Treat. 2012 Apr; 132(3):1009-23). Of note, this alteration is also designated as IVS3+5G>A in published literature. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Familial cancer of breast Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	This variant has been observed in several individuals affected with breast and ovarian cancer (Thomassen M et al). In addition, this variant segregates with breast and prostate cancer in one family (Caputo SM et al). This variant has been reported to the ClinVar database as pathogenic. The variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This sequence change falls in intron 3 of the BRCA2 gene. It does not directly change the encoded amino acid sequence of the BRCA2 protein, but it affects a nucleotide within the consensus splice site of the intron. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (Buratti E et al). Experimental studies have shown that this sequence change causes skipping of exon 3 of the BRCA2 mRNA (Thomassen M et al). Skipping of exon 3 results in in-frame deletion of 83 amino acid residues from the BRCA2 protein partially including the PALB2 binding domain, which is important for DNA repair activity of the BRCA2 protein (Oliver AW et al). For these reasons, this variant has been classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Aug 02, 2021	- -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Oct 17, 2022	For these reasons, this variant has been classified as Pathogenic. This variant disrupts the c.316+5G nucleotide in the BRCA2 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 18424508, 21120943, 21939546, 22505045, 24549055, 29707112). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. 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 3, but is expected to preserve the integrity of the reading-frame (PMID: 21769658, 29707112; Invitae). ClinVar contains an entry for this variant (Variation ID: 51409). This variant has been observed in individual(s) with breast and ovarian cancer (PMID: 21120943, 21769658, 26207792, 29470806). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 3 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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mendelics	Jul 02, 2018	- -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research

Apr 04, 2013

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Malignant tumor of urinary bladder Pathogenic:1

Pathogenic, no assertion criteria provided

research

Laboratory of Urology, Hospital Clinic de Barcelona

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
Cadd	Benign	18
Dann	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.79
dbscSNV1_RF	Benign	0.62
SpliceAI score (max)		0.89		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.89		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: rs81002840; hg19: chr13-32893467;