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NM_001365536.1(SCN9A):c.965+13T>C

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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: Feb 20, 2020)
Last evaluated:
Jan 13, 2018
Accession:
VCV000331997.3
Variation ID:
331997
Description:
single nucleotide variant
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NM_001365536.1(SCN9A):c.965+13T>C

Allele ID
284867
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 166294586 (GRCh38) GRCh38 UCSC
2: 167151096 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_369:g.86402T>C
LRG_369t1:c.965+13T>C
NM_002977.3:c.965+13T>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:166294585:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00014
The Genome Aggregation Database (gnomAD) 0.00003
Exome Aggregation Consortium (ExAC) 0.00014
Trans-Omics for Precision Medicine (TOPMed) 0.00018
Links
ClinGen: CA1944626
dbSNP: rs772337722
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000280489.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000317791.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000349425.2
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000385347.2
Likely benign 1 criteria provided, single submitter Dec 2, 2016 RCV000436811.1
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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
Inherited Erythromelalgia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000418803.2
Submitted: (Oct 18, 2016)
Evidence details
Likely benign
(Dec 02, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000514578.4
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 13, 2018)
criteria provided, single submitter
Method: clinical testing
Paroxysmal extreme pain disorder
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000418799.3
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 13, 2018)
criteria provided, single submitter
Method: clinical testing
Indifference to pain, congenital, autosomal recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000418801.3
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
Primary erythromelalgia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000418802.3
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)

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 rs772337722...

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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 08, 2021