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NM_001165963.4(SCN1A):c.4945C>T (p.Leu1649=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Sep 30, 2021)
Last evaluated:
Nov 27, 2020
Accession:
VCV000195942.10
Variation ID:
195942
Description:
single nucleotide variant
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NM_001165963.4(SCN1A):c.4945C>T (p.Leu1649=)

Allele ID
193103
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 165992330 (GRCh38) GRCh38 UCSC
2: 166848840 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.166848840G>A
NC_000002.12:g.165992330G>A
NG_011906.1:g.86310C>T
... more HGVS
Protein change
-
Other names
p.L1649L:CTG>TTG
Canonical SPDI
NC_000002.12:165992329:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00045
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00046
The Genome Aggregation Database (gnomAD) 0.00047
Trans-Omics for Precision Medicine (TOPMed) 0.00056
1000 Genomes Project 0.00060
The Genome Aggregation Database (gnomAD), exomes 0.00144
The Genome Aggregation Database (gnomAD) 0.00038
Exome Aggregation Consortium (ExAC) 0.00148
Links
ClinGen: CA302866
dbSNP: rs148546224
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 4 criteria provided, multiple submitters, no conflicts Jan 19, 2017 RCV000176629.3
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000351229.2
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000390173.2
Likely benign 1 criteria provided, single submitter Apr 19, 2016 RCV000717437.1
Benign 1 criteria provided, single submitter Nov 27, 2020 RCV000553490.5
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV001136465.1
Likely benign 1 no assertion criteria provided - RCV001727617.1
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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
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Seizure Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000417770.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jan 22, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000228317.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Familial hemiplegic migraine type 3
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000417769.3
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
(Jun 11, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000242449.11
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
(Jan 19, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000615042.1
Submitted: (Aug 17, 2017)
Evidence details
Publications
PubMed (1)
Benign
(Nov 27, 2020)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV000633867.5
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Generalized epilepsy with febrile seizures plus, type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001296303.1
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)
Likely benign
(Apr 19, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000848287.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001951431.1
Submitted: (Sep 30, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001976000.1
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
Genotype-phenotype correlations in a group of 15 SCN1A-mutated Italian patients with GEFS+ spectrum (seizures plus, classical and borderline severe myoclonic epilepsy of infancy). Nicita F Journal of child neurology 2010 PMID: 20729507
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SCN1A - - - -

Text-mined citations for rs148546224...

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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