13-32379747-C-G

Variant names:

• chr13-32379747-C-G
• rs81002844
• NM_000059.4:c.8954-3C>G

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.8954-3C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 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: 33)
• Consequence: BRCA2 NM_000059.4 splice_region, intron
• Scores: Splicing: ADA: 0.9998
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:2
• Conservation: PhyloP100: 0.722

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: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 13-32379747-C-G is Pathogenic according to our data. Variant chr13-32379747-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 52712.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=3, Uncertain_significance=2}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.8954-3C>G		splice_region_variant, intron_variant	Intron 22 of 26	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.8954-3C>G		splice_region_variant, intron_variant	Intron 22 of 26	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.8585-3C>G		splice_region_variant, intron_variant	Intron 22 of 26	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.*1012-3C>G		splice_region_variant, intron_variant	Intron 21 of 25	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

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

Dec 23, 2003

Breast Cancer Information Core (BIC) (BRCA2)

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jun 07, 2018

Counsyl

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 08, 2023

Biotechnology, Institute of Science, Nirma University

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The BRCA2c.8954-3C>G variant has been classified as likely pathogenic. The alteration takes place in the splice site of intron 22 which could be affecting the protein formation downstream. This particular variant has been validated by Trujillano D et al. J Mol Diagn, 2015 Mar;17:162-70, using the next generation sequencing panel for BRCA2 analysis. This mutation has been reported to play role in ovarian and breast cancers, which also corelates with the medical history of the proband. Validation of the mutation in the Mutation taster predicts the variant to be disease causing and having a pathogenic effect. The rs3819 has been classified well under BROVCA2. Given the evidences the variants has been classified as Likely Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1 Uncertain:1

Mar 13, 2018

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.8954-3C>G intronic variant (also known as IVS22-3C>G) results from a C to G substitution 3 nucleotides upstream from coding exon 23 of the BRCA2 gene. This alteration was identified once in a validation cohort for a BRCA1 and BRCA2 next-generation sequencing panel study (Trujillano D et al. J Mol Diagn, 2015 Mar;17:162-70). Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to create a new alternate splice acceptor site and in a functional splicing assay, this alteration resulted in the out-of-frame insertion of 2 nucleotides in exon 23 of BRCA2 (Acedo A et al. Breast Cancer Res., 2012 May;14:R87). Another nearby alteration, c.8954-5A>G, has been classified as likely pathogenic based on segregation with disease in one family and on RT-PCR analysis demonstrating that this alteration results in out-of-frame retention of 4 nucleotides of intron 22 and in a truncated mRNA transcript (Santos C et al. J Mol Diagn, 2014 May;16:324-34; Menéndez M et al. Breast Cancer Res. Treat., 2012 Apr;132:979-92; de Garibay GR et al. Hum. Mutat., 2014 Jan;35:53-7). This nucleotide position is poorly conserved in available vertebrate species. Alterations that cause aberrant splicing are expected to result in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic. -

Dec 13, 2021

Color Diagnostics, LLC DBA Color Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes a C to G nucleotide substitution at the -3 position of intron 22 of the BRCA2 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. This variant has been reported to cause the out-of-frame insertion of 2 nucleotides in a minigene splicing assay (PMID: 22632462). To our knowledge, this variant has not been reported in individuals affected with hereditary cancer in the literature. However, a similar variant c.8954-5A>G has been reported as disease-causing in ClinVar (variation ID 267712) and shown to cause out-of-framing splicing by RNA studies (PMID: 21735045, 24123850, 24607278, 29280214) and reported in individuals affected with breast cancer (PMID: 23479189, 24607278, 26187060) and in families suspected of being affected with hereditary breast and ovarian cancer (PMID: 21735045, 24123850, 30415210, 33875706). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion that this variant may be associated with disease, additional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

not provided Pathogenic:1

Jan 02, 2024

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Non-canonical splice site variant demonstrated to result in loss of function (PMID: 22632462); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; Also known as 9182-3C>G; This variant is associated with the following publications: (PMID: 28152038, 24123850, 25556971, 22632462) -

Hereditary breast ovarian cancer syndrome Pathogenic:1

May 22, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has been observed in individual(s) with BRCA2-related conditions (PMID: 25556971). 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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 22632462, 24123850; Invitae). ClinVar contains an entry for this variant (Variation ID: 52712). This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 22 of the BRCA2 gene. It does not directly change the encoded amino acid sequence of the BRCA2 protein. It affects a nucleotide within the consensus splice site. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	21
DANN	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.91
SpliceAI score (max)		0.90		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.31		Position offset: 1
DS_AL_spliceai		0.90		Position offset: 3

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

Publications

LitVar

Other links and lift over

dbSNP: rs81002844; hg19: chr13-32953884;