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NM_000834.5(GRIN2B):c.15G>A (p.Ala5=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000098442.5
Variation ID:
98442
Description:
single nucleotide variant
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NM_000834.5(GRIN2B):c.15G>A (p.Ala5=)

Allele ID
104335
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12p13.1
Genomic location
12: 13866194 (GRCh38) GRCh38 UCSC
12: 14019128 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.14019128C>T
NC_000012.11:g.14019128C>T
NC_000012.12:g.13866194C>T
... more HGVS
Protein change
-
Other names
p.A5A:GCG>GCA
Canonical SPDI
NC_000012.12:13866193:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.05831 (T)

Allele frequency
1000 Genomes Project 0.05831
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.02445
Trans-Omics for Precision Medicine (TOPMed) 0.02938
The Genome Aggregation Database (gnomAD) 0.04207
The Genome Aggregation Database (gnomAD), exomes 0.04892
Exome Aggregation Consortium (ExAC) 0.05079
Links
ClinGen: CA225835
dbSNP: rs34315573
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, single submitter Sep 14, 2017 RCV000084733.4
Benign 2 criteria provided, single submitter Oct 25, 2013 RCV000117190.5
Benign 1 criteria provided, single submitter Mar 24, 2016 RCV000715377.1
Benign 1 criteria provided, single submitter Dec 5, 2020 RCV001517579.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GRIN2B Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
826 868

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Oct 25, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000168764.12
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
(Sep 14, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000842280.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Mar 24, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000846206.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA … (more)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Epileptic encephalopathy, early infantile, 27
Mental retardation, autosomal dominant 6
Allele origin: germline
Invitae
Accession: SCV001726104.1
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000151354.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
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 … (more)
not provided
(-)
no assertion provided
Method: not provided
not provided
Allele origin: not provided
Psychiatry Genetics Yale University
Accession: SCV000116869.1
Submitted: (Apr 18, 2013)
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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs34315573...

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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 Oct 24, 2021