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NM_000334.4(SCN4A):c.483-9C>A

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Jan 7, 2021)
Last evaluated:
Jul 24, 2020
Accession:
VCV000255857.7
Variation ID:
255857
Description:
single nucleotide variant
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NM_000334.4(SCN4A):c.483-9C>A

Allele ID
256333
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q23.3
Genomic location
17: 63971859 (GRCh38) GRCh38 UCSC
17: 62049219 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.62049219G>T
NC_000017.11:g.63971859G>T
NG_011699.1:g.6060C>A
NM_000334.4:c.483-9C>A MANE Select
Protein change
-
Other names
-
Canonical SPDI
NC_000017.11:63971858:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00012
Links
ClinGen: CA8710143
dbSNP: rs201552497
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter - RCV000250421.1
Likely benign 1 criteria provided, single submitter Jan 12, 2018 RCV000286461.2
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000290044.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000326290.2
Likely benign 1 criteria provided, single submitter Jan 12, 2018 RCV000380892.2
Benign 1 criteria provided, single submitter May 23, 2018 RCV000713117.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jul 24, 2020 RCV000823932.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SCN4A - - GRCh38
GRCh37
354 1081

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000303660.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Hypokalemic periodic paralysis, type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405358.3
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
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Potassium-aggravated myotonia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405356.3
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
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Paramyotonia congenita of von Eulenburg
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405359.3
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
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Familial hyperkalemic periodic paralysis
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405360.3
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)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Congenital myasthenic syndrome, acetazolamide-responsive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405357.3
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
(May 23, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000843688.1
Submitted: (Aug 31, 2018)
Evidence details
Uncertain significance
(Jul 24, 2020)
criteria provided, single submitter
Method: clinical testing
Familial hyperkalemic periodic paralysis
Allele origin: germline
Invitae
Accession: SCV000964807.3
Submitted: (Jan 07, 2021)
Evidence details
Comment:
This sequence change falls in intron 3 of the SCN4A gene. It does not directly change the encoded amino acid sequence of the SCN4A protein. … (more)

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs201552497...

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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