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NM_000152.5(GAA):c.2417C>T (p.Thr806Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Aug 30, 2021)
Last evaluated:
Jul 22, 2021
Accession:
VCV000252467.11
Variation ID:
252467
Description:
single nucleotide variant
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NM_000152.5(GAA):c.2417C>T (p.Thr806Met)

Allele ID
247145
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.3
Genomic location
17: 80117685 (GRCh38) GRCh38 UCSC
17: 78091484 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_673t1:c.2417C>T
LRG_673:g.21130C>T
NC_000017.10:g.78091484C>T
... more HGVS
Protein change
T806M
Other names
-
Canonical SPDI
NC_000017.11:80117684:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00041
The Genome Aggregation Database (gnomAD), exomes 0.00044
Exome Aggregation Consortium (ExAC) 0.00037
Trans-Omics for Precision Medicine (TOPMed) 0.00069
The Genome Aggregation Database (gnomAD) 0.00026
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00038
The Genome Aggregation Database (gnomAD) 0.00056
Links
ClinGen: CA8815734
dbSNP: rs139850074
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Oct 16, 2015 RCV000238987.3
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Jul 22, 2021 RCV000542072.8
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Oct 1, 2020 RCV000725668.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GAA - - GRCh38
GRCh37
1547 1587

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 16, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia
Accession: SCV000296876.2
Submitted: (Jan 06, 2016)
Evidence details
Uncertain significance
(Jan 23, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000338490.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Invitae
Accession: SCV000626569.6
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Aug 11, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001767605.1
Submitted: (Aug 03, 2021)
Evidence details
Comment:
Reported previously as part of a thesis project of genetic variation identified among healthy Armenian individuals through exome sequencing (Akopyan, 2019); In silico analysis, which … (more)
Uncertain significance
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001810193.1
Submitted: (Aug 30, 2021)
Evidence details
Likely benign
(Oct 01, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001502250.3
Submitted: (Jul 04, 2021)
Evidence details
Uncertain significance
(Jan 17, 2020)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease type II
Allele origin: germline
Natera, Inc.
Accession: SCV001455441.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GAA - - - -

Text-mined citations for rs139850074...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021