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NM_014363.6(SACS):c.2926C>A (p.Arg976Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Sep 13, 2021)
Last evaluated:
Feb 26, 2021
Accession:
VCV000448199.8
Variation ID:
448199
Description:
single nucleotide variant
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NM_014363.6(SACS):c.2926C>A (p.Arg976Ser)

Allele ID
441622
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q12.12
Genomic location
13: 23340950 (GRCh38) GRCh38 UCSC
13: 23915089 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.10:g.23915089G>T
NC_000013.11:g.23340950G>T
NG_012342.1:g.97753C>A
... more HGVS
Protein change
R976S, R829S
Other names
-
Canonical SPDI
NC_000013.11:23340949:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00160 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00208
1000 Genomes Project 0.00160
Trans-Omics for Precision Medicine (TOPMed) 0.00138
Links
ClinGen: CA6911590
dbSNP: rs139993038
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 Dec 5, 2020 RCV001081341.2
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV001109615.1
Benign 1 criteria provided, single submitter Feb 26, 2021 RCV001644611.1
Uncertain significance 1 no assertion criteria provided - RCV000516574.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SACS - - GRCh38
GRCh37
1808 1900

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Feb 26, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV000614947.3
Submitted: (Sep 13, 2021)
Evidence details
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Charlevoix-Saguenay spastic ataxia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001266969.1
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
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Spastic paraplegia
Allele origin: germline
Invitae
Accession: SCV001004581.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001549454.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The SACS p.Arg976Ser variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP … (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 rs139993038...

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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