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NM_004369.4(COL6A3):c.4169C>T (p.Ser1390Leu)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Sep 30, 2021)
Last evaluated:
Nov 6, 2020
Accession:
VCV000259300.6
Variation ID:
259300
Description:
single nucleotide variant
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NM_004369.4(COL6A3):c.4169C>T (p.Ser1390Leu)

Allele ID
250688
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 237371848 (GRCh38) GRCh38 UCSC
2: 238280491 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.238280491G>A
LRG_473:g.47360C>T
LRG_473t1:c.4169C>T LRG_473p1:p.Ser1390Leu
... more HGVS
Protein change
S1390L, S783L, S983L, S1184L
Other names
-
Canonical SPDI
NC_000002.12:237371847:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00200 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00033
The Genome Aggregation Database (gnomAD) 0.00088
1000 Genomes Project 0.00200
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00085
The Genome Aggregation Database (gnomAD), exomes 0.00026
Trans-Omics for Precision Medicine (TOPMed) 0.00081
The Genome Aggregation Database (gnomAD) 0.00095
Trans-Omics for Precision Medicine (TOPMed) 0.00110
Links
ClinGen: CA2188982
dbSNP: rs115548605
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 2 criteria provided, multiple submitters, no conflicts May 26, 2016 RCV000251265.6
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000268008.2
Likely benign 1 criteria provided, single submitter Nov 6, 2020 RCV000532892.4
Likely benign 1 criteria provided, single submitter Aug 22, 2018 RCV001722319.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL6A3 - - GRCh38
GRCh37
1865 1968

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000310172.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(May 26, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000333688.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Collagen VI-related myopathy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000428802.3
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
(Nov 06, 2020)
criteria provided, single submitter
Method: clinical testing
Bethlem myopathy 1
Allele origin: germline
Invitae
Accession: SCV000657309.4
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Aug 22, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000524627.5
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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=COL6A3 - - - -

Text-mined citations for rs115548605...

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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 Dec 04, 2021