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NM_001848.3(COL6A1):c.2809A>G (p.Lys937Glu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 30, 2021)
Last evaluated:
Feb 25, 2021
Accession:
VCV000196954.10
Variation ID:
196954
Description:
single nucleotide variant
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NM_001848.3(COL6A1):c.2809A>G (p.Lys937Glu)

Allele ID
194115
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
21q22.3
Genomic location
21: 46003735 (GRCh38) GRCh38 UCSC
21: 47423649 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_475:g.26987A>G
LRG_475t1:c.2809A>G LRG_475p1:p.Lys937Glu
NC_000021.8:g.47423649A>G
... more HGVS
Protein change
K937E
Other names
-
Canonical SPDI
NC_000021.9:46003734:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00082
1000 Genomes Project 0.00040
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00115
The Genome Aggregation Database (gnomAD) 0.00061
Links
ClinGen: CA244794
dbSNP: rs117583120
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 RCV000279845.2
Likely benign 1 criteria provided, single submitter Sep 17, 2020 RCV001087752.2
Conflicting interpretations of pathogenicity 6 criteria provided, conflicting interpretations Feb 25, 2021 RCV000431648.9
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL6A1 - - GRCh38
GRCh37
1123 1217

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Collagen VI-related myopathy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000436577.3
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
(Jul 19, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000229789.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain Significance
(Nov 08, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000510585.1
Submitted: (Feb 17, 2017)
Evidence details
Comment:
Converted during submission to Uncertain significance.
Likely benign
(Sep 17, 2020)
criteria provided, single submitter
Method: clinical testing
Bethlem myopathy 1
Allele origin: germline
Invitae
Accession: SCV000657051.5
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Feb 25, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000567531.3
Submitted: (Sep 24, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 24036952, 30564623)
Likely benign
(Nov 26, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143270.1
Submitted: (Sep 25, 2019)
Evidence details
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001954370.1
Submitted: (Sep 30, 2021)
Evidence details
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001809516.1
Submitted: (Aug 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=COL6A1 - - - -

Text-mined citations for rs117583120...

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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