NM_000059.4(BRCA2):c.3479G>A (p.Arg1160Lys) AND Breast-ovarian cancer, familial, susceptibility to, 2

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Nov 2, 2023
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:: RCV000082913.5

Allele description [Variation Report for NM_000059.4(BRCA2):c.3479G>A (p.Arg1160Lys)]

NM_000059.4(BRCA2):c.3479G>A (p.Arg1160Lys)

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.3479G>A (p.Arg1160Lys)

HGVS:

NC_000013.11:g.32337834G>A
NG_012772.3:g.27355G>A
NM_000059.4:c.3479G>AMANE SELECT
NP_000050.2:p.Arg1160Lys
NP_000050.3:p.Arg1160Lys
LRG_293t1:c.3479G>A
LRG_293:g.27355G>A
LRG_293p1:p.Arg1160Lys
NC_000013.10:g.32911971G>A
NM_000059.3:c.3479G>A

Nucleotide change:

3707G>A

Protein change:

R1160K

Links:

dbSNP: rs183920365

NCBI 1000 Genomes Browser:

rs183920365

Molecular consequence:

NM_000059.4:c.3479G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Breast-ovarian cancer, familial, susceptibility to, 2 (BROVCA2)
Synonyms:: Breast-ovarian cancer, familial 2
Identifiers:: MONDO: MONDO:0012933; MedGen: C2675520; Orphanet: 145; OMIM: 612555

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000114987	Sharing Clinical Reports Project (SCRP)	no assertion criteria provided	Uncertain significance (Nov 15, 2011)	germline	clinical testing
SCV000785773	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Uncertain significance (Nov 27, 2017)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Counsyl_Autosomal_Dominant_Disease_Classification_criteria_(2015)_v1.pdf, Citation Link,
SCV004845167	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Nov 2, 2023)	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

SCV000114987

Sharing Clinical Reports Project (SCRP)

no assertion criteria provided

Uncertain significance
(Nov 15, 2011)

germline

clinical testing

SCV000785773

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Uncertain significance
(Nov 27, 2017)

unknown

clinical testing

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

Counsyl_Autosomal_Dominant_Disease_Classification_criteria_(2015)_v1.pdf,

Citation Link,

SCV004845167

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely Benign
(Nov 2, 2023)

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	1	not provided	not provided	1	not provided	clinical testing
not provided	germline	unknown	7	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software.

Poulet A, Privat M, Ponelle F, Viala S, Decousus S, Perin A, Lafarge L, Ollier M, El Saghir NS, Uhrhammer N, Bignon YJ, Bidet Y.

Biomed Res Int. 2016;2016:5623089. Epub 2016 Aug 30.

PubMed [citation]

PMID:: 27656653
PMCID:: PMC5021467

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 Sharing Clinical Reports Project (SCRP), SCV000114987.3

#	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	not provided	1	not provided	not provided		not provided	not provided	not provided	not provided

From Counsyl, SCV000785773.2

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From All of Us Research Program, National Institutes of Health, SCV004845167.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	7	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	108544	not provided	not provided		7	not provided	not provided	not provided

Last Updated: Sep 1, 2024

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