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NM_000334.4(SCN4A):c.1167T>C (p.Tyr389=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
11 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000130227.6
Variation ID:
130227
Description:
single nucleotide variant
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NM_000334.4(SCN4A):c.1167T>C (p.Tyr389=)

Allele ID
135674
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q23.3
Genomic location
17: 63966177 (GRCh38) GRCh38 UCSC
17: 62043537 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.62043537A>G
NC_000017.11:g.63966177A>G
NG_011699.1:g.11742T>C
NM_000334.4:c.1167T>C MANE Select NP_000325.4:p.Tyr389= synonymous
Protein change
-
Other names
-
Canonical SPDI
NC_000017.11:63966176:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.05351 (G)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.02196
Exome Aggregation Consortium (ExAC) 0.03956
1000 Genomes Project 0.05351
The Genome Aggregation Database (gnomAD) 0.03433
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.03596
Trans-Omics for Precision Medicine (TOPMed) 0.03982
Links
ClinGen: CA155065
dbSNP: rs16947296
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 Mar 11, 2016 RCV000118263.7
Benign 2 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000540577.5
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000264383.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000321996.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000318249.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000378890.2
Benign 1 criteria provided, single submitter Jun 9, 2017 RCV000576684.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SCN4A - - GRCh38
GRCh37
351 1078

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000303631.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Jun 09, 2017)
criteria provided, single submitter
Method: clinical testing
Paramyotonia congenita of von Eulenburg
Familial hyperkalemic periodic paralysis
Potassium-aggravated myotonia
Hypokalemic periodic paralysis, type 2
Congenital myasthenic syndrome, acetazolamide-responsive
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000677460.1
Submitted: (Jul 17, 2017)
Evidence details
Benign
(Mar 11, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000524410.4
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 04, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000338705.4
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
Hypokalemic periodic paralysis, type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405294.3
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 13, 2018)
criteria provided, single submitter
Method: clinical testing
Potassium-aggravated myotonia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405291.3
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 13, 2018)
criteria provided, single submitter
Method: clinical testing
Paramyotonia congenita of von Eulenburg
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405293.3
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 13, 2018)
criteria provided, single submitter
Method: clinical testing
Familial hyperkalemic periodic paralysis
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405292.3
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 13, 2018)
criteria provided, single submitter
Method: clinical testing
Congenital myasthenic syndrome, acetazolamide-responsive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000405295.3
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
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Familial hyperkalemic periodic paralysis
Allele origin: germline
Invitae
Accession: SCV000658512.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000152630.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (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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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SCN4A - - - -

Text-mined citations for rs16947296...

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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 Oct 30, 2021