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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
ClinVar Genomic variation as it relates to human health
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- Interpretation:
-
Conflicting interpretations of pathogenicity
Uncertain significance(2); Likely benign(1)
- Review status:
- criteria provided, conflicting interpretations
- Submissions:
- 3 (Most recent: Feb 20, 2020)
- Last evaluated:
- Jan 13, 2018
- Accession:
- VCV000317313.4
- Variation ID:
- 317313
- Description:
- single nucleotide variant
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NM_002693.3(POLG):c.3644-72C>A
- Allele ID
- 333243
- Variant type
- single nucleotide variant
- Variant length
- 1 bp
- Cytogenetic location
- 15q26.1
- Genomic location
- 15: 89316899 (GRCh38) GRCh38 UCSC
- 15: 89860130 (GRCh37) GRCh37 UCSC
- HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001113378.2:c.*440G>T MANE Select 3 prime UTR NM_002693.3:c.3644-72C>A MANE Select NM_001126131.2:c.3644-72C>A NM_001376910.1:c.*440G>T 3 prime UTR NM_001376911.1:c.*440G>T 3 prime UTR NM_018193.3:c.*440G>T 3 prime UTR NC_000015.10:g.89316899G>T NC_000015.9:g.89860130G>T NG_008218.2:g.22897C>A NG_011736.1:g.77937G>T LRG_500:g.77937G>T LRG_500t1:c.*440G>T LRG_765:g.22897C>A LRG_765t1:c.3644-72C>A - Protein change
- -
- Other names
- -
- Canonical SPDI
- NC_000015.10:89316898:G:T
- Functional consequence
- -
- Global minor allele frequency (GMAF)
- 0.00419 (T)
- Allele frequency
- 1000 Genomes Project 0.00419
- The Genome Aggregation Database (gnomAD) 0.00312
- Trans-Omics for Precision Medicine (TOPMed) 0.00283
- The Genome Aggregation Database (gnomAD) 0.00299
- Links
- ClinGen: CA10642662
- dbSNP: rs1801377
- VarSome
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Aggregate interpretations per condition
| Interpreted condition | Interpretation | Number of submissions | Review status | Last evaluated | Variation/condition record |
|---|---|---|---|---|---|
| Uncertain significance | 1 | criteria provided, single submitter | Jun 14, 2016 | RCV000280138.3 | |
| Likely benign | 1 | criteria provided, single submitter | Jan 12, 2018 | RCV001116316.2 | |
| Uncertain significance | 1 | criteria provided, single submitter | Jan 13, 2018 | RCV001116317.2 |
Submitted interpretations and evidence
Help| Interpretation (Last evaluated) |
Review status (Assertion criteria) |
Condition (Inheritance) |
Submitter | More information | |
|---|---|---|---|---|---|
|
Uncertain significance
(Jun 14, 2016)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi Anemia
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services,Illumina
Accession: SCV000394250.2
Submitted: (Oct 18, 2016) |
|
|
|
Likely benign
(Jan 12, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Fanconi anemia complementation group I
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services,Illumina
Accession: SCV001274372.1
Submitted: (Feb 20, 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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. (less)
|
|
|
Uncertain significance
(Jan 13, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
POLG-Related Spectrum Disorders
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services,Illumina
Accession: SCV001274373.1
Submitted: (Feb 20, 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)
|
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 rs1801377...
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 24, 2022