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NM_007294.4(BRCA1):c.-19-3A>G AND Malignant tumor of breast

Germline classification:
Uncertain significance (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001353407.2

Allele description [Variation Report for NM_007294.4(BRCA1):c.-19-3A>G]

NM_007294.4(BRCA1):c.-19-3A>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.-19-3A>G
Other names:
IVS1-3A>G
HGVS:
  • NC_000017.11:g.43124118T>C
  • NG_005905.2:g.93866A>G
  • NM_007294.4:c.-19-3A>GMANE SELECT
  • NM_007297.4:c.-106-3A>G
  • NM_007299.4:c.-19-3A>G
  • NM_007300.4:c.-19-3A>G
  • LRG_292t1:c.-19-3A>G
  • LRG_292:g.93866A>G
  • NC_000017.10:g.41276135T>C
  • NM_007294.3:c.-19-3A>G
  • U14680.1:n.101-3A>G
Links:
Breast Cancer Information Core (BIC) (BRCA1): 101-3&base_change=A to G; dbSNP: rs273898669
NCBI 1000 Genomes Browser:
rs273898669
Molecular consequence:
  • NM_007294.4:c.-19-3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_007297.4:c.-106-3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_007299.4:c.-19-3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_007300.4:c.-19-3A>G - intron variant - [Sequence Ontology: SO:0001627]
Functional consequence:
functionally_normal [Sequence Ontology: SO:0002219] - Comment(s)
Observations:
1

Condition(s)

Name:
Malignant tumor of breast
Synonyms:
Malignant breast neoplasm; Cancer breast
Identifiers:
MONDO: MONDO:0007254; MedGen: C0006142

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000591228Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Uncertain significanceunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV000591228.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The BRCA1 c.-19-3A>G variant was not identified in the literature but was identified 2X in the BIC database as a variant of unknown clinical importance. This variant is located in the 3’ splice region of the BRCA1 5' untranslated region but does not affect the invariant -1 and -2 positions. However, positions -3 and -5 to -12 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In-silico or computational prediction software (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predicts a greater than 10% difference in splicing in 3 of 5 different programs, with the creation of a splice acceptor site 2 nucleotides upstream from the known splice acceptor site. The c.-19-3A>G variant is located in a region that may be involved in promoter or splicing activity, thus this variant may affect the binding of transcription factors and processing or expression of the BRCA1 mRNA transcript; however there is no supporting data for this claim. In summary, the clinical significance of this variant cannot be determined with certainty at this time. Therefore this variant is a variant of unknown significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Mar 30, 2024