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NM_001844.5(COL2A1):c.2949C>T (p.Val983=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(4);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Aug 13, 2021)
Last evaluated:
Nov 3, 2020
Accession:
VCV000258231.7
Variation ID:
258231
Description:
single nucleotide variant
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NM_001844.5(COL2A1):c.2949C>T (p.Val983=)

Allele ID
254534
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q13.11
Genomic location
12: 47978345 (GRCh38) GRCh38 UCSC
12: 48372128 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.48372128G>A
NC_000012.12:g.47978345G>A
NM_001844.5:c.2949C>T MANE Select NP_001835.3:p.Val983= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000012.12:47978344:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00006
Exome Aggregation Consortium (ExAC) 0.00009
The Genome Aggregation Database (gnomAD), exomes 0.00006
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
Trans-Omics for Precision Medicine (TOPMed) 0.00012
1000 Genomes Project 0.00020
Links
ClinGen: CA6534943
dbSNP: rs201719788
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 3 criteria provided, multiple submitters, no conflicts Nov 3, 2020 RCV000918676.5
Likely benign 1 criteria provided, single submitter - RCV000249904.1
Uncertain significance 1 criteria provided, single submitter Apr 28, 2017 RCV001114064.1
Uncertain significance 1 criteria provided, single submitter Apr 28, 2017 RCV001114065.1
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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
Likely benign
(Aug 06, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV001476974.1
Submitted: (Dec 30, 2020)
Evidence details
Likely benign
(Nov 03, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001063995.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jun 12, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001785915.1
Submitted: (Aug 13, 2021)
Evidence details
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000308092.1
Submitted: (Apr 28, 2016)
Evidence details
Uncertain significance
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Type II Collagenopathies
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001271895.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Uncertain significance
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Stickler syndrome type 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001271896.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs201719788...

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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 Aug 17, 2021