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NM_080680.3(COL11A2):c.4863+7G>A

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000178924.3
Variation ID:
178924
Description:
single nucleotide variant
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NM_080680.3(COL11A2):c.4863+7G>A

Allele ID
174498
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6p21.32
Genomic location
6: 33164845 (GRCh38) GRCh38 UCSC
6: 33132622 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.11:g.33132622C>T
NC_000006.12:g.33164845C>T
NM_080680.3:c.4863+7G>A MANE Select
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000006.12:33164844:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00161
1000 Genomes Project 0.00040
Exome Aggregation Consortium (ExAC) 0.00028
Trans-Omics for Precision Medicine (TOPMed) 0.00051
The Genome Aggregation Database (gnomAD) 0.00026
Links
ClinGen: CA183322
dbSNP: rs200947059
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 Jan 8, 2018 RCV000155699.4
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Dec 4, 2020 RCV000724273.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL11A2 - - GRCh38
GRCh38
GRCh38
GRCh38
GRCh38
GRCh38
GRCh38
GRCh37
610 620

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 08, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000716238.1
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)
Uncertain significance
(Dec 10, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000231926.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jul 27, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000205409.4
Submitted: (Mar 21, 2019)
Evidence details
Comment:
c.4863+7G>A in intron 64 of COL11A2: This variant is not expected to have clinic al significance because it is not located within the conserved splice … (more)
Likely benign
(Nov 09, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143585.1
Submitted: (Sep 25, 2019)
Evidence details
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001724548.1
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=COL11A2 - - - -

Text-mined citations for rs200947059...

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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 Jul 07, 2021