13-32326151-G-T

Position:

• chr13-32326151-G-T

Variant summary

Our verdict is Pathogenic. Variant got 22 ACMG points: 22P and 0B. PVS1 PM2 PP3_Strong PP5_Very_Strong

The NM_000059.4(BRCA2):​c.475+1G>T variant causes a splice donor change. The variant allele was found at a frequency of 0.000000686 in 1,456,716 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 splice_donor
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Pathogenic reviewed by expert panel P:12
• Conservation: PhyloP100: 4.85

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 22 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: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 13-32326151-G-T is Pathogenic according to our data. Variant chr13-32326151-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 51709.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32326151-G-T is described in Lovd as [Pathogenic]. Variant chr13-32326151-G-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.475+1G>T		splice_donor_variant		ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.475+1G>T		splice_donor_variant		5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1456716 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 724970

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:12

Revision: reviewed by expert panel

Submissions by phenotype

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

Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	Feb 20, 2004	- -
Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -
Pathogenic, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Jun 18, 2019	IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 5 based on posterior probability = 0.998544 -

Hereditary breast ovarian cancer syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	Aug 01, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 22, 2016	Variant summary: The c.475+1G>T in a BRCA2 gene is a splice-site variant that alters a conserved nucleotide. 5/5 in silico tools via Alamut predict this variant to disrupt a canonical acceptor sequence, but functional studies are yet to be conducted to confirm those predictions. The variant has been reported in several affected individuals from HBOC families. The variant is absent from ExAC. Lastly, it has been classified as pathogenic via publications and/or reputable databases/clinical laboratories. Taken together, the variant was classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Sep 21, 2023	This sequence change affects a donor splice site in intron 5 of the BRCA2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. For these reasons, this variant has been classified as Pathogenic. Studies have shown that disruption of this splice site alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 30883759; Invitae). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a high probability of being pathogenic (PMID: 31131967). ClinVar contains an entry for this variant (Variation ID: 51709). This variant is also known as IVS5+1G>T. Disruption of this splice site has been observed in individual(s) with a personal and/or family history of breast or ovarian cancer (PMID: 18703817, 24156927, 28724667, 29446198). This variant is not present in population databases (gnomAD no frequency). -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 01, 2023	Canonical splice site variant demonstrated to result in out-of-frame exon skipping in a gene for which loss of function is a known mechanism of disease (Colombo et al., 2013; Fraile-Bethencourt et al., 2019); Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Also known as 703+1G>T; This variant is associated with the following publications: (PMID: 24156927, 32772980, 25525159, 18703817, 28724667, 29446198, 23451180, 21523855, 30883759, 29673794, 31131967, 30702160, 31825140, 30787465, 34645131, 35957765) -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Feb 28, 2017	- -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Sep 01, 2021	This variant causes a G to T nucleotide substitution at the +1 position of intron 5 of the BRCA2 gene. RNA studies have detected the out-of-frame skipping of exon 5 in carrier-derived RNA and in a minigene splicing assay (PMID: 23451180, 30883759). This aberrant mRNA transcript is expected to result in an absent or non-functional protein product. This variant has been reported in three individuals affected with breast cancer (PMID: 28724667, 32963034) and in additional suspected hereditary breast and ovarian cancer families (PMID: 18703817, 24156927). A multifactorial analysis has reported a family history likelihood ratio for pathogenicity of 9.1893 from three pedigrees (PMID: 31131967). 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	Feb 08, 2022	The c.475+1G>T intronic pathogenic mutation results from a G to T substitution one nucleotide after coding exon 4 of the BRCA2 gene. This alteration has been identified in multiple breast and/or ovarian cancer families to date (Palma MD et al. Cancer Res. 2008 Sep;68:7006-14; Tea MK et al. Maturitas. 2014 Jan;77:68-72; Rebbeck TR et al. Hum Mutat, 2018 05;39:593-620; Bhaskaran SP et al. Int J Cancer, 2019 08;145:962-973). This alteration as well as several close-match alterations at this same donor site results in skipping of coding exon 4 (Fraile-Bethencourt E et al. J Pathol, 2019 08;248:409-420; Colombo M et al. PLoS One. 2013 Feb;8:e57173). Of note, this alteration is also designated as IVS5+1G>T in published literature. This alteration segregated with disease as reported in a multifactorial analysis model (Parsons MT et al. Hum Mutat, 2019 09;40:1557-1578). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -

BRCA2-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 09, 2023

The BRCA2 c.475+1G>T variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant, also known as IVS5+1G>T , has been reported in multiple individuals with personal and/or family history of breast or ovarian cancer (Palma MD et al 2008. PubMed ID: 18703817; Tea MK et al 2013. PubMed ID: 24156927; Sun J et al 2017. PubMed ID: 28724667; Bang YJ et al 2021. PubMed ID: 34645131). In vitro functional studies show this variant results in exon skipping (Colombo M et al 2013. PubMed ID: 23451180; Fraile-Bethencourt E et al 2019. PubMed ID: 30883759). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Variants that disrupt the consensus splice donor site in BRCA2 are expected to be pathogenic. This variant is interpreted as pathogenic. -

Familial cancer of breast Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Jul 07, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.27	D
BayesDel_noAF	Pathogenic	0.15
CADD	Pathogenic	32
DANN	Uncertain	0.99
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.82
FATHMM_MKL	Pathogenic	0.97	D
MutationTaster	Benign	1.0	D;D
GERP RS		4.9

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.98		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.98		Position offset: -1

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

Publications

LitVar

Other links and lift over

dbSNP: rs81002797; hg19: chr13-32900288; COSMIC: COSV101204544;