NM_000059.4(BRCA2):c.7617+1G>A AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jul 31, 2024
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:: RCV000486153.19

Allele description [Variation Report for NM_000059.4(BRCA2):c.7617+1G>A]

NM_000059.4(BRCA2):c.7617+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.7617+1G>A

HGVS:

NC_000013.11:g.32356610G>A
NG_012772.3:g.46131G>A
NM_000059.4:c.7617+1G>AMANE SELECT
NM_001406719.1:c.7521+1G>A
NM_001406720.1:c.7617+1G>A
NM_001406721.1:c.2685+1G>A
NM_001406722.1:c.1200+1G>A
LRG_293t1:c.7617+1G>A
LRG_293:g.46131G>A
NC_000013.10:g.32930747G>A
NM_000059.3:c.7617+1G>A

Nucleotide change:

IVS15+1G>A

Links:

dbSNP: rs397507922

NCBI 1000 Genomes Browser:

rs397507922

Molecular consequence:

NM_000059.4:c.7617+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406719.1:c.7521+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406720.1:c.7617+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406721.1:c.2685+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406722.1:c.1200+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000568483	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 8, 2024)	germline	clinical testing	Citation Link,
SCV002551568	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000568483

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Apr 8, 2024)

germline

clinical testing

Citation Link,

SCV002551568

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 31, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

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	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000568483.5

#	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 demonstrated to result in skipping of exon 15 leading to a null allele in a gene for which loss of function is a known mechanism of disease (PMID: 11389159, 21184276, 24123850); 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 7845+1G>A; This variant is associated with the following publications: (PMID: 26360800, 17301269, 31589614, 33754277, 25525159, 11389159, 23479189, 18712473, 21184276, 21324516, 29093764, 26833046, 29339979, 30720863, 29446198, 30702160, 31191615, 24123850, 35264596)

#	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 Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, SCV002551568.7

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

#	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		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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