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NM_000089.3(COL1A2):c.1350+11A>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Feb 20, 2020)
Last evaluated:
Mar 1, 2018
Accession:
VCV000035935.2
Variation ID:
35935
Description:
single nucleotide variant
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NM_000089.3(COL1A2):c.1350+11A>T

Allele ID
44599
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q21.3
Genomic location
7: 94411165 (GRCh38) GRCh38 UCSC
7: 94040477 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.94040477A>T
NC_000007.14:g.94411165A>T
LRG_2t1:c.1350+11A>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:94411164:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00180 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00079
Trans-Omics for Precision Medicine (TOPMed) 0.00143
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00208
The Genome Aggregation Database (gnomAD) 0.00141
1000 Genomes Project 0.00180
Exome Aggregation Consortium (ExAC) 0.00150
Links
ClinGen: CA260340
dbSNP: rs193922160
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Mar 1, 2018 RCV000616881.1
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV001160979.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Apr 27, 2017 RCV000029591.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL1A2 No evidence available No evidence available GRCh38
GRCh37
960 982

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
uncertain
(Aug 18, 2011)
criteria provided, single submitter
Method: curation, clinical testing
Osteogenesis Imperfecta
(autosomal unknown)
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000052243.1
Submitted: (Aug 18, 2011)
Evidence details
Comment:
Converted during submission to Uncertain significance.
Likely benign
(Mar 01, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000714134.1
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)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Ehlers-danlos syndrome, arthrochalasia type, 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001322820.1
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)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Osteogenesis imperfecta
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001322821.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
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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Title Author Journal Year Link
A novel DHPLC-based procedure for the analysis of COL1A1 and COL1A2 mutations in osteogenesis imperfecta. Fuccio A The Journal of molecular diagnostics : JMD 2011 PMID: 21884818

Text-mined citations for rs193922160...

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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