NM_007294.3(BRCA1):c.5332+7G>T AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: Aug 21, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000590625.4

Allele description [Variation Report for NM_007294.3(BRCA1):c.5332+7G>T]

NM_007294.3(BRCA1):c.5332+7G>T

Gene:
BRCA1:BRCA1 DNA repair associated [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q21.31
Genomic location:
Preferred name:
NM_007294.3(BRCA1):c.5332+7G>T
HGVS:
  • NC_000017.11:g.43051056C>A
  • NG_005905.2:g.166928G>T
  • NM_007294.3:c.5332+7G>T
  • NM_007297.4:c.5191+7G>T
  • NM_007298.3:c.2020+7G>T
  • NM_007299.4:c.2020+7G>T
  • NM_007300.4:c.5395+7G>T
  • LRG_292t1:c.5332+7G>T
  • LRG_292:g.166928G>T
  • NC_000017.10:g.41203073C>A
Links:
dbSNP: rs773655919
NCBI 1000 Genomes Browser:
rs773655919
Molecular consequence:
  • NM_007294.3:c.5332+7G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_007297.4:c.5191+7G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_007298.3:c.2020+7G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_007299.4:c.2020+7G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_007300.4:c.5395+7G>T - intron variant - [Sequence Ontology: SO:0001627]
Functional consequence:
functionally_normal [Sequence Ontology: SO:0002219] - Comment(s)

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000699238Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Uncertain significance
(Feb 8, 2016)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001470397Quest Diagnostics Nichols Institute San Juan Capistranocriteria provided, single submitter
Likely benign
(Aug 21, 2020)
unknownclinical testing

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

Summary from all submissions

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

Citations

PubMed

Accurate classification of BRCA1 variants with saturation genome editing.

Findlay GM, Daza RM, Martin B, Zhang MD, Leith AP, Gasperini M, Janizek JD, Huang X, Starita LM, Shendure J.

Nature. 2018 Oct;562(7726):217-222. doi: 10.1038/s41586-018-0461-z. Epub 2018 Sep 12.

PubMed [citation]
PMID:
30209399
PMCID:
PMC6181777

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699238.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: This c.5332+7G>T variant affects a non-conserved nucleotide, resulting in intronic change. Although 5/5 splice-site tools via Alamut predict that this variant does not affect normal splicing, ESEfinder predicts activation of an ESE site. This variant was found in 3/120656 control chromosomes from the broad and large populations from ExAC at a frequency of 0.0000249, which does not exceed maximal expected frequency of a pathogenic allele (0.0010005) in this gene. The variant of interest has not been reported in affected individuals via publications and/or reputable databases/clinical laboratories, nor evaluated for functional impact by in vivo/vitro studies. Because of the absence of clinical information, the lack of functional studies and a very low frequency in general population, the variant has currently been classified as a variant of uncertain significance (VUS) until additional information becomes available.

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001470397.1

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

Last Updated: Jun 14, 2021

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