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NM_006516.4(SLC2A1):c.679+4C>T

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Sep 23, 2021)
Last evaluated:
Nov 11, 2020
Accession:
VCV000139160.8
Variation ID:
139160
Description:
single nucleotide variant
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NM_006516.4(SLC2A1):c.679+4C>T

Allele ID
142863
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p34.2
Genomic location
1: 42929869 (GRCh38) GRCh38 UCSC
1: 43395540 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_1132:g.34308C>T
NC_000001.10:g.43395540G>A
NC_000001.11:g.42929869G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:42929868:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00073
Links
ClinGen: CA019252
dbSNP: rs139492241
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 Jul 24, 2013 RCV000186662.3
Benign 1 criteria provided, single submitter Mar 21, 2019 RCV000717984.1
Uncertain significance 3 criteria provided, single submitter Jan 26, 2015 RCV000723793.5
Likely benign 1 criteria provided, single submitter Nov 11, 2020 RCV001087312.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SLC2A1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
642 666

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jul 24, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000171698.12
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)
Uncertain significance
(Jan 26, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000203590.7
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Mar 21, 2019)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000848845.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Likely benign
(Nov 11, 2020)
criteria provided, single submitter
Method: clinical testing
GLUT1 deficiency syndrome 1, autosomal recessive
Allele origin: germline
Invitae
Accession: SCV000649808.4
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001930092.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001972383.1
Submitted: (Sep 21, 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=SLC2A1 - - - -

Text-mined citations for rs139492241...

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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