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NM_198904.4(GABRG2):c.549-3T>G

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jul 4, 2021)
Last evaluated:
Mar 1, 2021
Accession:
VCV000205543.10
Variation ID:
205543
Description:
single nucleotide variant
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NM_198904.4(GABRG2):c.549-3T>G

Allele ID
201883
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q34
Genomic location
5: 162101232 (GRCh38) GRCh38 UCSC
5: 161528238 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.162101232T>G
NG_009290.1:g.38591T>G
NM_001375349.1:c.264-3T>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000005.10:162101231:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00003
The Genome Aggregation Database (gnomAD) 0.00005
The Genome Aggregation Database (gnomAD) 0.00006
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Exome Aggregation Consortium (ExAC) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00004
Links
ClinGen: CA314718
dbSNP: rs750459631
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Mar 1, 2021 RCV000187524.7
Uncertain significance 1 criteria provided, single submitter Oct 28, 2019 RCV001234167.2
Pathogenic 1 no assertion criteria provided Jan 1, 2017 RCV000655993.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GABRG2 Little evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
396 424

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Sep 09, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000241118.6
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.549-3 T>G variant in the GABRG2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. … (more)
Uncertain significance
(Oct 28, 2019)
criteria provided, single submitter
Method: clinical testing
Familial febrile seizures 8
Epilepsy, childhood absence 2
Allele origin: germline
Invitae
Accession: SCV001406798.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change falls in intron 4 of the GABRG2 gene. It does not directly change the encoded amino acid sequence of the GABRG2 protein, … (more)
Uncertain significance
(Mar 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000493387.13
Submitted: (Jul 04, 2021)
Evidence details
Pathogenic
(Jan 01, 2017)
no assertion criteria provided
Method: case-control
Rolandic epilepsy
Allele origin: germline
Bioinformatics Core,Luxembourg Center for Systems Biomedicine
Study: EUROEPINOMICS COGIE
Accession: SCV000588269.1
Submitted: (Aug 09, 2017)
Evidence details
Publications
PubMed (1)
Comment:
CAADphred>15

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
Exome-wide analysis of mutational burden in patients with typical and atypical Rolandic epilepsy. Bobbili DR European journal of human genetics : EJHG 2018 PMID: 29358611
Rare variants in γ-aminobutyric acid type A receptor genes in rolandic epilepsy and related syndromes. Reinthaler EM Annals of neurology 2015 PMID: 25726841
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098

Text-mined citations for rs750459631...

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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