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NM_001165963.4(SCN1A):c.5286A>G (p.Gly1762=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Sep 21, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000195943.8
Variation ID:
195943
Description:
single nucleotide variant
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NM_001165963.4(SCN1A):c.5286A>G (p.Gly1762=)

Allele ID
193104
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 165991989 (GRCh38) GRCh38 UCSC
2: 166848499 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.166848499T>C
NC_000002.12:g.165991989T>C
NG_011906.1:g.86651A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:165991988:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00140 (C)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00040
1000 Genomes Project 0.00140
Exome Aggregation Consortium (ExAC) 0.00063
The Genome Aggregation Database (gnomAD), exomes 0.00076
The Genome Aggregation Database (gnomAD) 0.00016
Trans-Omics for Precision Medicine (TOPMed) 0.00041
Trans-Omics for Precision Medicine (TOPMed) 0.00090
Links
ClinGen: CA202037
dbSNP: rs150570058
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 2 criteria provided, multiple submitters, no conflicts Sep 29, 2016 RCV000176632.2
Benign 1 criteria provided, single submitter Dec 4, 2020 RCV000228454.7
Likely benign 1 criteria provided, single submitter Sep 30, 2016 RCV000717501.1
Benign 1 criteria provided, single submitter Mar 3, 2015 RCV001689714.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SCN1A Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1348 2705
LOC102724058 - - - GRCh38 - 1321

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV000286284.7
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 30, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000228320.5
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (1)
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Sep 29, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000615044.1
Submitted: (Aug 17, 2017)
Evidence details
Likely benign
(Sep 30, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000848354.4
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Synonymous alterations with insufficient evidence to classify as benign
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001908687.1
Submitted: (Sep 21, 2021)
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
Generalized epilepsy with febrile seizures plus (GEFS+) spectrum: clinical manifestations and SCN1A mutations in Indonesian patients. Herini ES Epilepsy research 2010 PMID: 20452746
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SCN1A - - - -

Text-mined citations for rs150570058...

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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