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NM_001365536.1(SCN9A):c.3020G>A (p.Arg1007His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Sep 24, 2021)
Last evaluated:
Dec 1, 2020
Accession:
VCV000331974.7
Variation ID:
331974
Description:
single nucleotide variant
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NM_001365536.1(SCN9A):c.3020G>A (p.Arg1007His)

Allele ID
285361
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 166272730 (GRCh38) GRCh38 UCSC
2: 167129240 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_369:g.108258G>A
NC_000002.11:g.167129240C>T
NC_000002.12:g.166272730C>T
... more HGVS
Protein change
R996H, R1007H
Other names
-
Canonical SPDI
NC_000002.12:166272729:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00180 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00065
Trans-Omics for Precision Medicine (TOPMed) 0.00079
The Genome Aggregation Database (gnomAD) 0.00061
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00068
1000 Genomes Project 0.00180
The Genome Aggregation Database (gnomAD), exomes 0.00021
Exome Aggregation Consortium (ExAC) 0.00023
The Genome Aggregation Database (gnomAD) 0.00077
Links
ClinGen: CA1944153
dbSNP: rs188145203
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 Jan 12, 2018 RCV000308517.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000333798.2
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000330258.2
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000368610.2
Likely benign 1 criteria provided, single submitter Aug 8, 2017 RCV000478443.2
Likely benign 1 criteria provided, single submitter Dec 1, 2020 RCV000865153.3
Likely benign 1 criteria provided, single submitter Sep 28, 2020 RCV001705501.1
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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-AS1 - - - GRCh38 - 1176
SCN9A - - GRCh38
GRCh37
236 1439

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
Small Fiber Neuropathy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000418504.2
Submitted: (Oct 18, 2016)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Indifference to pain, congenital, autosomal recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000418507.3
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
Primary erythromelalgia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000418501.3
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
Paroxysmal extreme pain disorder
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000418505.3
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
(Aug 08, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000855945.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Dec 01, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary sensory and autonomic neuropathy type IIA
Generalized epilepsy with febrile seizures plus, type 7
Allele origin: germline
Invitae
Accession: SCV001006078.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Sep 28, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000565541.3
Submitted: (Sep 24, 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=SCN9A - - - -

Text-mined citations for rs188145203...

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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