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NM_001165963.4(SCN1A):c.4724G>A (p.Arg1575His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Oct 1, 2021)
Last evaluated:
Nov 15, 2020
Accession:
VCV000206845.5
Variation ID:
206845
Description:
single nucleotide variant
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NM_001165963.4(SCN1A):c.4724G>A (p.Arg1575His)

Allele ID
201471
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 166850784 (GRCh37) GRCh37 UCSC
2: 165994274 (GRCh38) GRCh38 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_8:g.84366G>A
NC_000002.11:g.166850784C>T
NC_000002.12:g.165994274C>T
... more HGVS
Protein change
R1564H, R1575H, R1546H, R761H, R1547H, R1563H
Other names
p.R1575H:CGC>CAC
Canonical SPDI
NC_000002.12:165994273:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00006
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00005
The Genome Aggregation Database (gnomAD) 0.00013
Exome Aggregation Consortium (ExAC) 0.00018
The Genome Aggregation Database (gnomAD), exomes 0.00023
Links
ClinGen: CA317525
dbSNP: rs368834365
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Jul 25, 2017 RCV000188972.4
Likely benign 1 criteria provided, single submitter Nov 15, 2020 RCV001393461.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Feb 14, 2019 RCV000731424.3
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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
1341 2698
LOC102724058 - - - GRCh38 - 1321

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jul 25, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000615038.1
Submitted: (Aug 17, 2017)
Evidence details
Uncertain significance
(Jan 29, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000859241.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Feb 14, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000559702.3
Submitted: (Mar 14, 2019)
Evidence details
Likely benign
(Nov 15, 2020)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV001595123.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jan 07, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000242603.11
Submitted: (Oct 01, 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=SCN1A - - - -

Text-mined citations for rs368834365...

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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