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NM_001849.4(COL6A2):c.2980G>A (p.Ala994Thr)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 6, 2020
Accession:
VCV000128815.5
Variation ID:
128815
Description:
single nucleotide variant
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NM_001849.4(COL6A2):c.2980G>A (p.Ala994Thr)

Allele ID
134264
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
21q22.3
Genomic location
21: 46132472 (GRCh38) GRCh38 UCSC
21: 47552386 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000021.9:g.46132472G>A
NG_008675.1:g.39354G>A
NM_001849.4:c.2980G>A MANE Select NP_001840.3:p.Ala994Thr missense
... more HGVS
Protein change
A994T
Other names
-
Canonical SPDI
NC_000021.9:46132471:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.02656 (A)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00108
1000 Genomes Project 0.02656
The Genome Aggregation Database (gnomAD), exomes 0.01191
The Genome Aggregation Database (gnomAD) 0.00915
Exome Aggregation Consortium (ExAC) 0.01238
Links
ClinGen: CA152462
dbSNP: rs117931394
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 5 criteria provided, multiple submitters, no conflicts Dec 9, 2016 RCV000116794.7
Benign 1 criteria provided, single submitter Jun 14, 2016 RCV000281717.2
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000290682.2
Benign 1 criteria provided, single submitter Jun 14, 2016 RCV000339033.2
Benign 1 criteria provided, single submitter Dec 6, 2020 RCV000557640.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL6A2 - - GRCh38
GRCh37
1248 1362
FTCD - - GRCh38
GRCh38
GRCh37
103 235

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Mar 31, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000228613.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000308308.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Myosclerosis
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000436827.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Collagen Type VI-Related Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000436826.2
Submitted: (Oct 18, 2016)
Evidence details
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Formiminotransferase Deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000483965.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Dec 09, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000613013.1
Submitted: (Aug 17, 2017)
Evidence details
Publications
PubMed (1)
Benign
(Jun 10, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000519953.4
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 06, 2020)
criteria provided, single submitter
Method: clinical testing
Bethlem myopathy 1
Allele origin: germline
Invitae
Accession: SCV000657191.3
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: SCV000150818.2
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
Novel collagen VI mutations identified in Chinese patients with Ullrich congenital muscular dystrophy. Zhang YZ World journal of pediatrics : WJP 2014 PMID: 24801232
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=COL6A2 - - - -

Text-mined citations for rs117931394...

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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