NM_000059.4(BRCA2):c.8755-1G>A AND not provided

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Jan 30, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001529355.14

Allele description [Variation Report for NM_000059.4(BRCA2):c.8755-1G>A]

NM_000059.4(BRCA2):c.8755-1G>A

Gene:

BRCA2:BRCA2 DNA repair associated [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q13.1

Genomic location:

Preferred name:

NM_000059.4(BRCA2):c.8755-1G>A

HGVS:

NC_000013.11:g.32379316G>A
NG_012772.3:g.68837G>A
NM_000059.4:c.8755-1G>AMANE SELECT
NM_001406719.1:c.8659-1G>A
NM_001406720.1:c.8755-1G>A
NM_001406721.1:c.3823-1G>A
NM_001406722.1:c.2338-1G>A
LRG_293t1:c.8755-1G>A
LRG_293:g.68837G>A
NC_000013.10:g.32953453G>A
NM_000059.3:c.8755-1G>A
U43746.1:n.8983-1G>A

Nucleotide change:

IVS21-1G>A

Links:

Breast Cancer Information Core (BIC) (BRCA2): 8983-1&base_change=G to A; dbSNP: rs81002812

NCBI 1000 Genomes Browser:

rs81002812

Molecular consequence:

NM_000059.4:c.8755-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406719.1:c.8659-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406720.1:c.8755-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406721.1:c.3823-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406722.1:c.2338-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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amplicon.MF03.CALR
amplicon.MF03.CALR

biosample
SAMN11533753 (1)
SRA
10x.ET05
10x.ET05

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001742648	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001959477	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV002820677	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jan 12, 2023)	germline	clinical testing	Citation Link,
SCV004226699	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 30, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 23451180, 25382762, 29446198, 31131967, 25741868

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Comparative in vitro and in silico analyses of variants in splicing regions of BRCA1 and BRCA2 genes and characterization of novel pathogenic mutations.

Colombo M, De Vecchi G, Caleca L, Foglia C, Ripamonti CB, Ficarazzi F, Barile M, Varesco L, Peissel B, Manoukian S, Radice P.

PLoS One. 2013;8(2):e57173. doi: 10.1371/journal.pone.0057173. Epub 2013 Feb 22.

PubMed [citation]

PMID:: 23451180
PMCID:: PMC3579815

Functional classification of BRCA2 DNA variants by splicing assays in a large minigene with 9 exons.

Acedo A, Hernández-Moro C, Curiel-García Á, Díez-Gómez B, Velasco EA.

Hum Mutat. 2015 Feb;36(2):210-21. doi: 10.1002/humu.22725.

PubMed [citation]

PMID:: 25382762
PMCID:: PMC4371643

See all PubMed Citations (5)

Details of each submission

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001742648.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001959477.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV002820677.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Observed in individuals with a personal or family history consistent with pathogenic variants in this gene (Wagner et al., 1999; Tea et al., 2014; Lerner-Ellis et al., 2021; Solao et al., 2021); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Not observed at significant frequency in large population cohorts (gnomAD); Also known as 8983-1G>A; This variant is associated with the following publications: (PMID: 23199084, 31131967, 29785153, 23451180, 9971877, 18489799, 25382762, 24156927, 23772696, 27060066, 20104584, 28726806, 29360161, 30257646, 29387975, 29446198, 29922827, 28918466, 32206145, 32885271, 32438681, 35264596, 24312913, 34072659, Eniu2017[Abstract])

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV004226699.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (5)

Description

PP5, PM2, PVS1

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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