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NM_000393.5(COL5A2):c.2103C>T (p.Pro701=)

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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: Jan 7, 2021)
Last evaluated:
Mar 11, 2020
Accession:
VCV000501572.3
Variation ID:
501572
Description:
single nucleotide variant
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NM_000393.5(COL5A2):c.2103C>T (p.Pro701=)

Allele ID
492996
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q32.2
Genomic location
2: 189058876 (GRCh38) GRCh38 UCSC
2: 189923602 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.189923602G>A
NC_000002.12:g.189058876G>A
NM_000393.5:c.2103C>T MANE Select NP_000384.2:p.Pro701= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:189058875:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00017
The Genome Aggregation Database (gnomAD) 0.00023
The Genome Aggregation Database (gnomAD), exomes 0.00006
Exome Aggregation Consortium (ExAC) 0.00007
Links
ClinGen: CA2022445
dbSNP: rs376612765
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 Jan 10, 2018 RCV000598281.3
Likely benign 1 criteria provided, single submitter Mar 11, 2020 RCV001421042.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Oct 16, 2018 RCV000727375.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL5A2 - - GRCh38
GRCh37
940 984

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 10, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000726589.1
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
(Apr 24, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000707985.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Oct 16, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001002514.1
Submitted: (Mar 14, 2019)
Evidence details
Likely benign
(Mar 11, 2020)
criteria provided, single submitter
Method: clinical testing
Ehlers-Danlos syndrome, classic type
Allele origin: germline
Invitae
Accession: SCV001623556.1
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=COL5A2 - - - -

Text-mined citations for rs376612765...

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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 May 26, 2021