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NM_000152.5(GAA):c.2400C>T (p.Ser800=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000167115.6
Variation ID:
167115
Description:
single nucleotide variant
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NM_000152.5(GAA):c.2400C>T (p.Ser800=)

Allele ID
177735
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.3
Genomic location
17: 80117668 (GRCh38) GRCh38 UCSC
17: 78091467 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.78091467C>T
NC_000017.11:g.80117668C>T
NM_000152.5:c.2400C>T MANE Select NP_000143.2:p.Ser800= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000017.11:80117667:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00919 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00179
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00777
Exome Aggregation Consortium (ExAC) 0.00229
1000 Genomes Project 0.00919
The Genome Aggregation Database (gnomAD) 0.00692
Trans-Omics for Precision Medicine (TOPMed) 0.00794
Links
ClinGen: CA180077
dbSNP: rs115705591
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Mar 11, 2019 RCV000153291.7
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV001079574.3
Benign 1 no assertion criteria provided Sep 27, 2017 RCV000675245.3
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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
1519 1559

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000302679.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(May 20, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000526400.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
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 … (more)
Benign
(Dec 13, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000202768.7
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001282687.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Mar 11, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001361267.1
Submitted: (Mar 06, 2020)
Evidence details
Comment:
Variant summary: GAA c.2400C>T alters a non-conserved nucleotide resulting in a synonymous change. Several computational tools predict a significant impact on normal splicing: Four predict … (more)
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Invitae
Accession: SCV000626566.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Sep 27, 2017)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000800892.1
Submitted: (May 23, 2018)
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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GAA - - - -

Text-mined citations for rs115705591...

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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 Jun 23, 2021