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NM_000157.4(GBA1):c.762-18T>A AND not provided

Germline classification:
Benign (2 submissions)
Last evaluated:
Jul 13, 2023
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:
RCV000590360.15

Allele description [Variation Report for NM_000157.4(GBA1):c.762-18T>A]

NM_000157.4(GBA1):c.762-18T>A

Genes:
LOC106627981:GBA recombination region [Gene]
GBA1:glucosylceramidase beta 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q22
Genomic location:
Preferred name:
NM_000157.4(GBA1):c.762-18T>A
HGVS:
  • NC_000001.11:g.155237596A>T
  • NG_009783.1:g.12102T>A
  • NG_042867.1:g.4058A>T
  • NM_000157.4:c.762-18T>AMANE SELECT
  • NM_001005741.3:c.762-18T>A
  • NM_001005742.3:c.762-18T>A
  • NM_001171811.2:c.501-18T>A
  • NM_001171812.2:c.615-18T>A
  • NC_000001.10:g.155207387A>T
  • NM_001005741.2:c.762-18T>A
  • NM_001005741.3:c.762-18T>A
  • NM_001005742.2:c.762-18T>A
Links:
dbSNP: rs140335079
NCBI 1000 Genomes Browser:
rs140335079
Molecular consequence:
  • NM_000157.4:c.762-18T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001005741.3:c.762-18T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001005742.3:c.762-18T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001171811.2:c.501-18T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001171812.2:c.615-18T>A - intron variant - [Sequence Ontology: SO:0001627]

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
SCV000697595Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Aug 29, 2016) 		germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV002048975ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)		Benign
(Jul 13, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697595.1

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

Description

Variant summary: The GBA c.762-18T>A variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant. 3/5 splice prediction tools predict the creation of a non-canonical splice acceptor site. However, these predictions have yet to be confirmed by functional studies. This variant was found in 882/111976 control chromosomes (5 homozygotes) at a frequency of 0.0078767, which is approximately 2 times the estimated maximal expected allele frequency of a pathogenic GBA variant (0.005), suggesting this variant is likely a benign polymorphism. In addition, one clinical diagnostic laboratories/reputable databases classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.

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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002048975.2

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

Last Updated: Nov 10, 2024