13-32362573-G-A

Variant names:

• chr13-32362573-G-A
• rs397507941
• NM_000059.4:c.7856G>A

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000059.4(BRCA2):​c.7856G>A​(p.Trp2619*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BRCA2 NM_000059.4 stop_gained
• Clinical Significance: Pathogenic reviewed by expert panel P:6
• Conservation: PhyloP100: 9.89
• Publications: 8 publications found

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]

BRCA2 Gene-Disease associations (from GenCC):

• breast-ovarian cancer, familial, susceptibility to, 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), ClinGen
• Fanconi anemia complementation group D1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen, G2P
• pancreatic cancer, susceptibility to, 2

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• sarcoma

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• hereditary breast ovarian cancer syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Fanconi anemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• medulloblastoma

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Pathogenic. The variant received 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 13-32362573-G-A is Pathogenic according to our data. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362573-G-A is described in CliVar as Pathogenic. Clinvar id is 52427.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.7856G>A	p.Trp2619*	stop_gained	Exon 17 of 27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.7856G>A	p.Trp2619*	stop_gained	Exon 17 of 27	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.7487G>A	p.Trp2496*	stop_gained	Exon 17 of 27	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.7864G>A		non_coding_transcript_exon_variant	Exon 16 of 26	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00000570 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6

Revision: reviewed by expert panel

Submissions by phenotype

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

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

- -

Sep 08, 2016

Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

Variant allele predicted to encode a truncated non-functional protein. -

not provided Pathogenic:2

-

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Malignant tumor of breast Pathogenic:1

-

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The BRCA2 p.Trp2619X variant was identified in 2 of 2972 proband chromosomes (frequency: 0.001) from individuals with breast or ovarian cancer (Hansen 2011, Nanda 2005). The variant was also identified in HGMD and the BIC database (1X with clinical importance). The p.Trp2619X variant leads to a premature stop codon at position 2619, which is predicted to lead to a truncated or absent protein and loss of function. Loss of function variants of the BRCA2 gene are an established mechanism of disease in hereditary breast and ovarian cancer and is the type of variant expected to cause the disorder. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:1

Dec 18, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal at codon 2619 (p.Trp2619*). It is expected to result in an absent or disrupted protein product. Truncating sequence changes in BRCA2 are known to be pathogenic. This particular truncation has been reported previously in an individual with breast cancer (PMID: 21318380). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.58	D
BayesDel_noAF	Pathogenic	0.60
CADD	Pathogenic	45
DANN	Uncertain	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.96
FATHMM_MKL	Pathogenic	0.97	D
PhyloP100		9.9
Vest4		0.90
GERP RS		5.7
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs397507941; hg19: chr13-32936710;