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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
ClinVar Genomic variation as it relates to human health
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- Interpretation:
-
Conflicting interpretations of pathogenicity
Uncertain significance(1); Likely benign(1)
- Review status:
- criteria provided, conflicting interpretations
- Submissions:
- 2
- First in ClinVar:
- May 31, 2020
- Most recent Submission:
- Feb 7, 2023
- Last evaluated:
- Aug 16, 2022
- Accession:
- VCV000891224.8
- Variation ID:
- 891224
- Description:
- single nucleotide variant
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NM_018714.3(COG1):c.1722C>T (p.Ser574=)
- Allele ID
- 878346
- Variant type
- single nucleotide variant
- Variant length
- 1 bp
- Cytogenetic location
- 17q25.1
- Genomic location
- 17: 73201549 (GRCh38) GRCh38 UCSC
- 17: 71197688 (GRCh37) GRCh37 UCSC
- HGVS
-
Nucleotide Protein Molecular
consequenceNM_018714.3:c.1722C>T MANE Select NP_061184.1:p.Ser574= synonymous NC_000017.11:g.73201549C>T NC_000017.10:g.71197688C>T NG_008971.1:g.13516C>T - Protein change
- -
- Other names
- -
- Canonical SPDI
- NC_000017.11:73201548:C:T
- Functional consequence
- -
- Global minor allele frequency (GMAF)
- 0.00040 (T)
- Allele frequency
- Exome Aggregation Consortium (ExAC) 0.00006
- Trans-Omics for Precision Medicine (TOPMed) 0.00013
- The Genome Aggregation Database (gnomAD), exomes 0.00004
- The Genome Aggregation Database (gnomAD) 0.00009
- 1000 Genomes Project 0.00040
- Links
- dbSNP: rs149888309
- VarSome
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Aggregate interpretations per condition
| Interpreted condition | Interpretation | Number of submissions | Review status | Last evaluated | Variation/condition record |
|---|---|---|---|---|---|
| Conflicting interpretations of pathogenicity | 2 | criteria provided, conflicting interpretations | Aug 16, 2022 | RCV001126375.8 |
Submitted interpretations and evidence
Help| Interpretation (Last evaluated) |
Review status (Assertion criteria) |
Condition (Inheritance) |
Submitter | More information | |
|---|---|---|---|---|---|
|
Uncertain significance
(Jan 13, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
COG1 congenital disorder of glycosylation
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services,Illumina
Accession: SCV001285559.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
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)
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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. (less)
|
|
|
Likely benign
(Aug 16, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
COG1 congenital disorder of glycosylation
Affected status: unknown
Allele origin:
germline
|
Invitae
Accession: SCV002435492.2
First in ClinVar: Apr 08, 2022 Last updated: Feb 07, 2023 |
|
Functional evidence
Help| 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
Help| 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 rs149888309...
HelpThese 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 Apr 09, 2023