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NM_004369.3(COL6A3):c.1786G>T (p.Ala596Ser)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 23, 2020
Accession:
VCV000094912.6
Variation ID:
94912
Description:
single nucleotide variant
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NM_004369.3(COL6A3):c.1786G>T (p.Ala596Ser)

Allele ID
100812
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 237381026 (GRCh38) GRCh38 UCSC
2: 238289669 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_473:g.38182G>T
LRG_473t1:c.1786G>T LRG_473p1:p.Ala596Ser
NC_000002.11:g.238289669C>A
... more HGVS
Protein change
A189S, A390S
Other names
-
Canonical SPDI
NC_000002.12:237381025:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.01877 (A)

Allele frequency
1000 Genomes Project 0.01877
Trans-Omics for Precision Medicine (TOPMed) 0.01989
The Genome Aggregation Database (gnomAD) 0.01842
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.02245
Links
ClinGen: CA147922
dbSNP: rs34934127
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Sep 22, 2016 RCV000080917.10
Benign 2 criteria provided, multiple submitters, no conflicts Dec 15, 2017 RCV000224262.4
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000334755.2
Benign 1 criteria provided, single submitter Nov 23, 2020 RCV001082486.2
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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
1854 1934

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Sep 28, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000281108.1
Submitted: (May 19, 2016)
Evidence details
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000310148.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Sep 22, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000528493.4
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
(Dec 15, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000841212.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Nov 05, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000112824.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Collagen VI-related myopathy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000428855.3
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
(Nov 23, 2020)
criteria provided, single submitter
Method: clinical testing
Bethlem myopathy 1
Allele origin: germline
Invitae
Accession: SCV000657259.5
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: SCV000150826.2
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)

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=COL6A3 - - - -

Text-mined citations for rs34934127...

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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 16, 2021