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NM_007294.4(BRCA1):c.671-8A>G AND not provided

Clinical significance:Benign (Last evaluated: Mar 26, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000588347.5

Allele description [Variation Report for NM_007294.4(BRCA1):c.671-8A>G]

NM_007294.4(BRCA1):c.671-8A>G

Gene:
BRCA1:BRCA1 DNA repair associated [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q21.31
Genomic location:
Preferred name:
NM_007294.4(BRCA1):c.671-8A>G
Other names:
IVS10-8A>G
HGVS:
  • NC_000017.11:g.43094868T>C
  • NG_005905.2:g.123116A>G
  • NM_007294.4:c.671-8A>GMANE SELECT
  • NM_007297.4:c.530-8A>G
  • NM_007298.3:c.671-8A>G
  • NM_007299.4:c.671-8A>G
  • NM_007300.4:c.671-8A>G
  • LRG_292t1:c.671-8A>G
  • LRG_292:g.123116A>G
  • NC_000017.10:g.41246885T>C
  • NM_007294.3:c.671-8A>G
  • U14680.1:n.790-8A>G
Links:
Breast Cancer Information Core (BIC) (BRCA1): 790-8&base_change=A to G; dbSNP: rs80358144
NCBI 1000 Genomes Browser:
rs80358144
Molecular consequence:
  • NM_007294.4:c.671-8A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_007297.4:c.530-8A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_007298.3:c.671-8A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_007299.4:c.671-8A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_007300.4:c.671-8A>G - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000699288Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Mar 26, 2016)
germlineclinical testing

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

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001552352Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Application of embryonic lethal or other obvious phenotypes to characterize the clinical significance of genetic variants found in trans with known deleterious mutations.

Judkins T, Hendrickson BC, Deffenbaugh AM, Eliason K, Leclair B, Norton MJ, Ward BE, Pruss D, Scholl T.

Cancer Res. 2005 Nov 1;65(21):10096-103.

PubMed [citation]
PMID:
16267036

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699288.1

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

Description

Variant Summary: The c.671-8A>G variant involves the alteration of a non-conserved nucleotide resulting in an intronic change. This variant is located at a position that is not widely known to affect splicing, 3/5 splicing prediction programs via Alamut predict no significant effect on splicing, and mutation taster predicts the variant to be a polymorphism. The variant was observed in the large and broad cohorts of the ExAC project at an allele frequency of 0.012%, predominantly observed in the East Asian subpopulation at a frequency of 0.18%. This frequency exceeds the maximal expected allele frequency for a pathogenic variant in BRCA1 (0.10%), suggesting this is a benign polymorphism found primarily in population(s) of East Asian origin. The variant has been reported in multiple databases to co-occur in individuals with pathogenic BRCA1 variants including two patients with c.2296_2297delAG, p.Ser766X (UMD), one patient with c.68_69delAG, p.Glu23ValfsX17 (UMD), and one patient with c.188T>A, p.Leu63Ter (BIC). Taken together, the multiple co-occurrences with pathogenic variants along with the intronic nature of the variant and the relatively high frequency in the East Asian population, this variant was classified as Benign.

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

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001552352.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jan 21, 2023

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