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NM_001040142.2(SCN2A):c.5229A>G (p.Lys1743=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000139018.8
Variation ID:
139018
Description:
single nucleotide variant
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NM_001040142.2(SCN2A):c.5229A>G (p.Lys1743=)

Allele ID
142721
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 165389035 (GRCh38) GRCh38 UCSC
2: 166245545 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.166245545A>G
NC_000002.12:g.165389035A>G
NG_008143.1:g.154634A>G
... more HGVS
Protein change
-
Other names
p.K1743K:AAA>AAG
Canonical SPDI
NC_000002.12:165389034:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00160 (G)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00123
The Genome Aggregation Database (gnomAD), exomes 0.00041
Exome Aggregation Consortium (ExAC) 0.00049
Trans-Omics for Precision Medicine (TOPMed) 0.00135
The Genome Aggregation Database (gnomAD) 0.00112
1000 Genomes Project 0.00160
Links
ClinGen: CA302875
dbSNP: rs2227898
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 May 21, 2015 RCV000176761.3
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000311626.2
Benign 1 criteria provided, single submitter Sep 7, 2017 RCV000713075.4
Likely benign 1 criteria provided, single submitter Oct 8, 2016 RCV000720413.1
Benign 1 criteria provided, single submitter Dec 4, 2020 RCV001080072.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SCN2A Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1412 1470

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(May 16, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000171515.12
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)
Likely benign
(May 21, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000228473.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Sep 07, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000843643.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Seizures, benign familial infantile, 3
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000417459.3
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)
Likely benign
(Oct 08, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000851290.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Seizures, benign familial infantile, 3
Early infantile epileptic encephalopathy 11
Allele origin: germline
Invitae
Accession: SCV000639634.5
Submitted: (Jan 07, 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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SCN2A - - - -

Text-mined citations for rs2227898...

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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 20, 2021