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NM_000152.5(GAA):c.2780C>T (p.Thr927Ile) AND not specified

Germline classification:
Benign (5 submissions)
Last evaluated:
Dec 10, 2015
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:
RCV000078178.29

Allele description [Variation Report for NM_000152.5(GAA):c.2780C>T (p.Thr927Ile)]

NM_000152.5(GAA):c.2780C>T (p.Thr927Ile)

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.2780C>T (p.Thr927Ile)
HGVS:
  • NC_000017.11:g.80118786C>T
  • NG_009822.1:g.22231C>T
  • NM_000152.4(GAA):c.2780C>T
  • NM_000152.5:c.2780C>TMANE SELECT
  • NM_001079803.3:c.2780C>T
  • NM_001079804.3:c.2780C>T
  • NP_000143.2:p.Thr927Ile
  • NP_000143.2:p.Thr927Ile
  • NP_001073271.1:p.Thr927Ile
  • NP_001073272.1:p.Thr927Ile
  • LRG_673t1:c.2780C>T
  • LRG_673:g.22231C>T
  • LRG_673p1:p.Thr927Ile
  • NC_000017.10:g.78092585C>T
  • NM_000152.3:c.2780C>T
  • NM_000152.4(GAA):c.2780C>T
  • NM_000152.4:c.2780C>T
  • P10253:p.Thr927Ile
Protein change:
T927I
Links:
UniProtKB: P10253#VAR_004317; dbSNP: rs1800315
NCBI 1000 Genomes Browser:
rs1800315
Molecular consequence:
  • NM_000152.5:c.2780C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001079803.3:c.2780C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001079804.3:c.2780C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
8

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000110016Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Benign
(Aug 13, 2013)
germlineclinical testing

Citation Link,

SCV000151259Genetic Services Laboratory, University of Chicago
no assertion criteria provided
Likely benigngermlineclinical testing

SCV000302685PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benigngermlineclinical testing

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

SCV000517803GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Benign
(Dec 10, 2015)
germlineclinical testing

Citation Link,

SCV001929227Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown8not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Eurofins Ntd Llc (ga), SCV000110016.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided8not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided8not providednot providednot provided

From Genetic Services Laboratory, University of Chicago, SCV000151259.2

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

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.

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

From PreventionGenetics, part of Exact Sciences, SCV000302685.1

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

From GeneDx, SCV000517803.4

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001929227.1

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

Last Updated: Oct 8, 2024