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NM_000152.5(GAA):c.2332-12A>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 7, 2020
Accession:
VCV000092475.4
Variation ID:
92475
Description:
single nucleotide variant
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NM_000152.5(GAA):c.2332-12A>T

Allele ID
98384
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.3
Genomic location
17: 80117588 (GRCh38) GRCh38 UCSC
17: 78091387 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.78091387A>T
NC_000017.11:g.80117588A>T
NM_000152.5:c.2332-12A>T MANE Select
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000017.11:80117587:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00162
Trans-Omics for Precision Medicine (TOPMed) 0.00158
Exome Aggregation Consortium (ExAC) 0.00048
1000 Genomes Project 0.00080
The Genome Aggregation Database (gnomAD) 0.00163
The Genome Aggregation Database (gnomAD), exomes 0.00042
Links
ClinGen: CA220398
dbSNP: rs200965268
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 3 criteria provided, multiple submitters, no conflicts Apr 11, 2019 RCV000244544.6
Uncertain significance 1 criteria provided, single submitter Sep 10, 2012 RCV000723547.1
Benign 2 criteria provided, single submitter Oct 7, 2020 RCV001248964.2
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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
1499 1538

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: SCV000302677.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Aug 31, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000530270.4
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)
Uncertain significance
(Sep 10, 2012)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000110008.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Apr 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: SCV001361266.1
Submitted: (Mar 06, 2020)
Evidence details
Comment:
Variant summary: GAA c.2332-12A>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly … (more)
Benign
(Oct 07, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Invitae
Accession: SCV001731834.1
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 22, 2020)
no assertion criteria provided
Method: curation
Glycogen storage disease, type II
(Autosomal recessive inheritance)
Allele origin: germline
Broad Institute Rare Disease Group, Broad Institute
Accession: SCV001422770.1
Submitted: (Mar 09, 2020)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
The c.2332-12A>T variant in GAA has not been previously reported in individuals with Glycogen Storage Disease II but has been reported as a VUS by … (more)

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.

Text-mined citations for rs200965268...

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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