NM_000059.4(BRCA2):c.517-11T>C AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Apr 18, 2016
Review status:: criteria provided, conflicting classifications

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:: RCV000589738.5

Allele description [Variation Report for NM_000059.4(BRCA2):c.517-11T>C]

NM_000059.4(BRCA2):c.517-11T>C

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.517-11T>C

HGVS:

NC_000013.11:g.32326488T>C
NG_012772.3:g.16009T>C
NM_000059.4:c.517-11T>CMANE SELECT
LRG_293t1:c.517-11T>C
LRG_293:g.16009T>C
NC_000013.10:g.32900625T>C
NM_000059.3:c.517-11T>C
U43746.1:n.745-11T>C

Nucleotide change:

IVS6-11T>C

Links:

Breast Cancer Information Core (BIC) (BRCA2): 745-11&base_change=T to C; dbSNP: rs81002828

NCBI 1000 Genomes Browser:

rs81002828

Molecular consequence:

NM_000059.4:c.517-11T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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C-C motif chemokine 14 isoform 1 precursor [Homo sapiens]
C-C motif chemokine 14 isoform 1 precursor [Homo sapiens]
gi|14589961|ref|NP_116739.1|

Protein
Atrioventricular septal defect 4
Atrioventricular septal defect 4

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000694835	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Apr 18, 2016)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 17262179, 21523855 LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV004219673	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely benign (Apr 7, 2016)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 21523855, 17262179, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000694835

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Apr 18, 2016)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV004219673

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely benign
(Apr 7, 2016)

unknown

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Comprehensive prediction of mRNA splicing effects of BRCA1 and BRCA2 variants.

Mucaki EJ, Ainsworth P, Rogan PK.

Hum Mutat. 2011 Jul;32(7):735-42. doi: 10.1002/humu.21513. Epub 2011 May 5.

PubMed [citation]

PMID:: 21523855

Differences in the frequency and distribution of BRCA1 and BRCA2 mutations in breast/ovarian cancer cases from the Basque country with respect to the Spanish population: implications for genetic counselling.

Beristain E, Martínez-Bouzas C, Guerra I, Viguera N, Moreno J, Ibañez E, Díez J, Rodríguez F, Mallabiabarrena G, Luján S, Gorostiaga J, De Pablo JL, Mendizabal JL, Tejada MI.

Breast Cancer Res Treat. 2007 Dec;106(2):255-62. Epub 2007 Jan 30.

PubMed [citation]

PMID:: 17262179

See all PubMed Citations (3)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000694835.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: The c.517-11T>C variant affects a non-conserved intronic nucleotide. Mutation taster predicts benign outcome for this variant. 4/5 programs in Alamut predict no significant effect on RNA splicing sites. However, these predictions are not confirmed by experimental studies. This variant is found in 4/119782 control chromosomes in ExAC at a frequency of 0.0000334, which does not exceed maximal expected frequency of a pathogenic allele (0.0007503). This variant has been reported in one BC/OC patient without strong evidence for causality. Because of the absence of clinical information and the lack of functional studies, the variant was classified as a variant of uncertain significance (VUS) until additional information becomes available.

#	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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004219673.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

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

Last Updated: Sep 29, 2024

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