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NM_002047.4(GARS1):c.882-15T>G

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Feb 20, 2020)
Last evaluated:
Jan 13, 2018
Accession:
VCV000360008.3
Variation ID:
360008
Description:
single nucleotide variant
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NM_002047.4(GARS1):c.882-15T>G

Allele ID
311085
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p14.3
Genomic location
7: 30612081 (GRCh38) GRCh38 UCSC
7: 30651697 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.30651697T>G
NC_000007.14:g.30612081T>G
NG_007942.1:g.22517T>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:30612080:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (G)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00022
Exome Aggregation Consortium (ExAC) 0.00024
1000 Genomes Project 0.00040
Trans-Omics for Precision Medicine (TOPMed) 0.00006
The Genome Aggregation Database (gnomAD) 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00008
Links
ClinGen: CA4205851
dbSNP: rs199741850
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 13, 2018 RCV000285735.2
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV000324356.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000372565.2
Uncertain significance 1 criteria provided, single submitter Jan 16, 2017 RCV000443897.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GARS1 - - GRCh38
GRCh37
450 478

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 16, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000535770.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.882-15 T>G variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Distal Spinal Muscular Atrophy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000468664.3
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
Distal hereditary motor neuronopathy type 5
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000468662.3
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 13, 2018)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease type 2D
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000468663.3
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 rs199741850...

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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