NM_000152.5(GAA):c.2571G>T (p.Leu857=) AND not provided

Clinical significance:Benign (Last evaluated: Jan 9, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000588826.3

Allele description [Variation Report for NM_000152.5(GAA):c.2571G>T (p.Leu857=)]

NM_000152.5(GAA):c.2571G>T (p.Leu857=)

Gene:
GAA:alpha glucosidase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q25.3
Genomic location:
Preferred name:
NM_000152.5(GAA):c.2571G>T (p.Leu857=)
HGVS:
  • NC_000017.11:g.80118282G>T
  • NG_009822.1:g.21727G>T
  • NM_000152.5:c.2571G>TMANE SELECT
  • NM_001079803.3:c.2571G>T
  • NM_001079804.3:c.2571G>T
  • NP_000143.2:p.Leu857=
  • NP_001073271.1:p.Leu857=
  • NP_001073272.1:p.Leu857=
  • LRG_673t1:c.2571G>T
  • LRG_673:g.21727G>T
  • NC_000017.10:g.78092081G>T
  • NM_000152.3:c.2571G>T
Links:
dbSNP: rs17853996
NCBI 1000 Genomes Browser:
rs17853996
Molecular consequence:
  • NM_000152.5:c.2571G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001079803.3:c.2571G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001079804.3:c.2571G>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000695656Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Jan 9, 2017)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

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, SCV000695656.1

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

Description

Variant summary: The GAA c.2571G>T (p.Leu857Leu) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 125/115766 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.0119071 (122/10246). This frequency is about 3 times the estimated maximal expected allele frequency of a pathogenic GAA variant (0.0042205), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; 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

Last Updated: Jun 14, 2021

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