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NM_001844.5(COL2A1):c.3003+9G>A

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 18, 2020
Accession:
VCV000283607.5
Variation ID:
283607
Description:
single nucleotide variant
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NM_001844.5(COL2A1):c.3003+9G>A

Allele ID
267844
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q13.11
Genomic location
12: 47978282 (GRCh38) GRCh38 UCSC
12: 48372065 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.48372065C>T
NC_000012.12:g.47978282C>T
NM_001844.5:c.3003+9G>A MANE Select
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000012.12:47978281:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00120 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00048
The Genome Aggregation Database (gnomAD) 0.00150
1000 Genomes Project 0.00120
Trans-Omics for Precision Medicine (TOPMed) 0.00142
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00161
Exome Aggregation Consortium (ExAC) 0.00058
Links
ClinGen: CA6534930
dbSNP: rs200403247
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 Nov 18, 2020 RCV000841352.4
Benign 1 criteria provided, single submitter Oct 8, 2015 RCV000329102.1
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV001112708.1
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV001114063.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL2A1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1101 1112

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Oct 08, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000335806.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Apr 09, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000983314.1
Submitted: (Apr 12, 2019)
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)
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Stickler syndrome type 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001270399.1
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
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Type II Collagenopathies
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001271894.1
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 18, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001052224.3
Submitted: (Jan 07, 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=COL2A1 - - - -

Text-mined citations for rs200403247...

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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 Jun 14, 2021