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NM_198253.3(TERT):c.887A>C (p.His296Pro)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 30, 2020
Accession:
VCV000268080.6
Variation ID:
268080
Description:
single nucleotide variant
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NM_198253.3(TERT):c.887A>C (p.His296Pro)

Allele ID
263518
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5p15.33
Genomic location
5: 1293999 (GRCh38) GRCh38 UCSC
5: 1294114 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.9:g.1294114T>G
NC_000005.10:g.1293999T>G
NG_009265.1:g.6049A>C
... more HGVS
Protein change
H296P
Other names
-
Canonical SPDI
NC_000005.10:1293998:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00005
Exome Aggregation Consortium (ExAC) 0.00010
The Genome Aggregation Database (gnomAD) 0.00013
Trans-Omics for Precision Medicine (TOPMed) 0.00010
Links
ClinGen: CA3184895
dbSNP: rs778187343
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 Jan 13, 2018 RCV000283392.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000322037.2
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000378796.2
Uncertain significance 1 criteria provided, single submitter Oct 30, 2020 RCV000471556.6
Uncertain significance 1 criteria provided, single submitter Oct 31, 2018 RCV000765804.1
Uncertain significance 1 no assertion criteria provided Jun 1, 2016 RCV000503276.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TERT Little evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1358 1608

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Dyskeratosis congenita, autosomal dominant 1
Idiopathic Pulmonary Fibrosis
Acute myeloid leukemia
Aplastic anemia
Dyskeratosis congenita, autosomal dominant, 2
Pulmonary fibrosis and/or bone marrow failure, telomere-related, 1
Cutaneous malignant melanoma 9
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000897194.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Aplastic anemia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000452701.3
Submitted: (Feb 20, 2020)
Evidence details
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)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Pulmonary fibrosis and/or bone marrow failure, telomere-related, 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000452702.3
Submitted: (Feb 20, 2020)
Evidence details
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)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Dyskeratosis congenita, autosomal dominant, 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000452700.3
Submitted: (Feb 20, 2020)
Evidence details
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)
Uncertain significance
(Oct 30, 2020)
criteria provided, single submitter
Method: clinical testing
Dyskeratosis congenita, autosomal dominant, 2
Idiopathic Pulmonary Fibrosis
Allele origin: germline
Invitae
Accession: SCV000551510.6
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces histidine with proline at codon 296 of the TERT protein (p.His296Pro). The histidine residue is weakly conserved and there is a … (more)
Uncertain significance
(Jun 01, 2016)
no assertion criteria provided
Method: case-control
Hepatocellular carcinoma
Allele origin: germline
Metabolic Liver Diseases Lab,Fondazione IRCCS Ca Granda Policlinico, University of Milan
Accession: SCV000328547.1
Submitted: (Oct 28, 2016)
Evidence details
Publications
PubMed (1)

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
Telomerase reverse transcriptase germline mutations and hepatocellular carcinoma in patients with nonalcoholic fatty liver disease. Donati B Cancer medicine 2017 PMID: 28677271
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868

Text-mined citations for rs778187343...

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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 Nov 20, 2021