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NM_000059.4(BRCA2):c.9837A>G (p.Leu3279=) AND not provided

Germline classification:
Likely benign (2 submissions)
Last evaluated:
May 1, 2020
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:
RCV000586788.5

Allele description [Variation Report for NM_000059.4(BRCA2):c.9837A>G (p.Leu3279=)]

NM_000059.4(BRCA2):c.9837A>G (p.Leu3279=)

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.9837A>G (p.Leu3279=)
Other names:
p.L3279L:TTA>TTG
HGVS:
  • NC_000013.11:g.32398350A>G
  • NG_012772.3:g.87871A>G
  • NM_000059.4:c.9837A>GMANE SELECT
  • NP_000050.2:p.Leu3279=
  • NP_000050.3:p.Leu3279=
  • LRG_293t1:c.9837A>G
  • LRG_293:g.87871A>G
  • LRG_293p1:p.Leu3279=
  • NC_000013.10:g.32972487A>G
  • NM_000059.3:c.9837A>G
  • p.L3279L
  • p.Leu3279Leu
Links:
dbSNP: rs730881598
NCBI 1000 Genomes Browser:
rs730881598
Molecular consequence:
  • NM_000059.4:c.9837A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000600878Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)		Likely benign
(May 1, 2020) 		unknownclinical testing

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

SCV000695274Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely benign
(Feb 13, 2017) 		germlineclinical testing

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

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Genome annotation by shotgun inactivation of a native gene in hemizygous cells: application to BRCA2 with implication of hypomorphic variants.

Ghosh S, Bhunia AK, Paun BC, Gilbert SF, Dhru U, Patel K, Kern SE.

Hum Mutat. 2015 Feb;36(2):260-9. doi: 10.1002/humu.22736.

PubMed [citation]
PMID:
25451944
PMCID:
PMC4492117

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000600878.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695274.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: The BRCA2 c.9837A>G (p.Leu3279Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide, which 5/5 splice prediction tools predict no significant impact on normal splicing and ESE finder predicts that this variant may create an ESE binding site for SC35. However, these predictions have yet to be confirmed by functional studies. The variant of interest has not been observed in controls (ExAC, 1000 Gs, or ESP), nor has it been reported, to our knowledge, in affected individuals via publications. However, an internal LCA sample reports the variant to co-occur with a likely pathogenic BRCA1 variant, c.3964A>T (p.Lys1322X). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as "Likely Benign."

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024