13-32356426-A-T

Variant names:

• chr13-32356426-A-T
• rs397507917
• NM_000059.4:c.7436-2A>T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000059.4(BRCA2):​c.7436-2A>T variant causes a splice acceptor, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: BRCA2 NM_000059.4 splice_acceptor, intron
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 4.68

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 18 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) 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
• PP5: Variant 13-32356426-A-T is Pathogenic according to our data. Variant chr13-32356426-A-T is described in ClinVar as [Pathogenic]. Clinvar id is 52330.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-32356426-A-T is described in Lovd as [Pathogenic]. Variant chr13-32356426-A-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.7436-2A>T		splice_acceptor_variant, intron_variant	Intron 14 of 26	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.7436-2A>T		splice_acceptor_variant, intron_variant	Intron 14 of 26	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.7067-2A>T		splice_acceptor_variant, intron_variant	Intron 14 of 26	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.7436-2A>T		splice_acceptor_variant, intron_variant	Intron 13 of 25	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

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

Sep 05, 2022

MGZ Medical Genetics Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 02, 2015

Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Jul 20, 2017

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.7436-2A>T variant in BRCA2 has been reported in 2 individuals with BRCA2-a ssociated cancer (Castera 2014) and was absent from large population studies. It has also been reported by other clinical laboratories in ClinVar (Variation ID 52330). This variant occurs in the invariant region (+/- 1,2) of the splice cons ensus sequence and is predicted to cause altered splicing leading to an abnormal or absent protein. Heterozygous loss of function of the BRCA2 gene is an establ ished disease mechanism in individuals with hereditary breast and ovarian cancer (HBOC). In summary, this variant meets criteria to be classified as pathogenic for HBOC in an autosomal dominant manner based upon presence in affected individ uals, absence in the general population and predicted impact to the protein. -

Apr 08, 2016

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: The c.7436-2A>T variant involves the alteration of a conserved nucleotide resulting in an intronic change. This variant is located at a position that is widely known to affect splicing and 5/5 splicing prediction programs via Alamut predict the loss of a splice acceptor site. These predictions have been confirmed by functional studies of patient mRNA which shows the variant to have a severe impact on splicing (Houdayer_2012). The variant is absent from the large, broad ExAC control population and has been reported in multiple affected individuals in the literature. Reputable clinical databases have classified the variant as "pathogenic". One publications cites the variant in an individual who also carries a potentially pathogenic BRCA1 variant (De Brakeleer_2015), which does not rule out the pathogenicity of the variant of interest. Taken together, this variant has been reported in affected individuals and has been shown to result in splicing defects, therefore it has been classified as a Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

May 21, 2020

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes an A to T nucleotide substitution at the -2 position of intron 14 of the BRCA2 gene. Splice site prediction tools suggest that this variant may have a significant impact on RNA splicing. Functional RNA studies have shown that this variant causes the use of an alternative splice acceptor site 13-nucleotide downstream of the reference splice site, creating a frameshift and premature translation stop signal in the RNA transcript (PMID: 22505045, 31191615). This aberrant transcript is expected to result in an absent or non-functional protein product. This variant has been reported in individuals with personal and/or family history of breast and/or ovarian cancer (PMID: 20858050, 22505045, 24549055, 26010302, Color internal data). 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.20	D
BayesDel_noAF	Uncertain	0.060
CADD	Pathogenic	34
DANN	Uncertain	0.99
Eigen	Pathogenic	0.95
Eigen_PC	Pathogenic	0.76
FATHMM_MKL	Pathogenic	0.99	D
GERP RS		5.5

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.95		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.91		Position offset: 15
DS_AL_spliceai		0.95		Position offset: 2

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

Publications

LitVar

Other links and lift over

dbSNP: rs397507917; hg19: chr13-32930563;