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NM_004369.4(COL6A3):c.1389C>T (p.Ala463=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Sep 30, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000094906.8
Variation ID:
94906
Description:
single nucleotide variant
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NM_004369.4(COL6A3):c.1389C>T (p.Ala463=)

Allele ID
100806
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 237381423 (GRCh38) GRCh38 UCSC
2: 238290066 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.238290066G>A
NM_004369.3:c.1389C>T NP_004360.2:p.Ala463= synonymous
NC_000002.12:g.237381423G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:237381422:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00899 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.01019
1000 Genomes Project 0.00899
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01315
Trans-Omics for Precision Medicine (TOPMed) 0.01204
The Genome Aggregation Database (gnomAD), exomes 0.01124
Exome Aggregation Consortium (ExAC) 0.01148
Links
ClinGen: CA147910
dbSNP: rs112896869
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 5 criteria provided, multiple submitters, no conflicts May 3, 2016 RCV000080911.12
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000263383.2
Benign 1 criteria provided, single submitter Dec 8, 2020 RCV000556953.3
Benign 2 criteria provided, single submitter Nov 26, 2018 RCV000991645.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL6A3 - - GRCh38
GRCh37
1882 1962

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Nov 05, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000112818.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000310142.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(May 03, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000519818.4
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
(Nov 26, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143273.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (1)
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Collagen VI-related myopathy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000428868.3
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
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Bethlem myopathy 1
Allele origin: germline
Invitae
Accession: SCV000657248.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000150824.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001800379.1
Submitted: (Aug 19, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001952234.1
Submitted: (Sep 30, 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
Molecular consequences of dominant Bethlem myopathy collagen VI mutations. Baker NL Annals of neurology 2007 PMID: 17886299
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=COL6A3 - - - -

Text-mined citations for rs112896869...

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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