Genetic Information
Gene & Transcript Details
Gene
TERT
Transcript
NM_198253.2
MANE Select
Total Exons
—
Reference Sequence
NC_000005.9
Alternative Transcripts
| ID | Status | Details |
|---|---|---|
| NM_198253.3 | MANE Select | 4039 nt | 80–3478 |
| NM_198253.1 | Alternative | 3644 nt | 56–2479 |
| NM_198253.2 | RefSeq Select | 4018 nt | 59–3457 |
Variant Details
HGVS Notation
NM_198253.2:c.835G>A
Protein Change
A279T
Location
Exon 2
(Exon 2 of )
2
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—
Clinical & Population Data
Population Frequency
gnomAD Global Frequency
2.31 in 100,000
Extremely Rare
ACMG Criteria Applied
BA1
ClinVar
OpenClassification
Benign
1 publications
Publications List
Clinical Statement
"This variant has been reported in ClinVar as Benign (18 clinical laboratories)."
COSMIC Somatic Evidence
OpenCOSMIC ID
COSM3760906
Recurrence
11 occurrences
PM1 Criteria
Not Applied
COSMIC Database Preview
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Functional Impact & Domains
Functional Domain
Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain.
Related Variants in This Domain
No evidence of other pathogenic variants at this position in gene TERT.
Functional Summary
Error in OpenAI Consolidation. OncoKB: TERTA279TTERTA279TSomaticNCBI Gene:7015|Show additional gene information Variant OverviewTERT is an enzyme that functions to maintain telomere length and genomic stability. The TERT promoter is frequently mutated in various cancer types.The TERT A279T mutation has not specifically been reviewed by the OncoKB team, and therefore its biological significance is unknown. JAX-CKB: No results found
Database Previews
OncoKB
JAX-CKB
Click on previews to view full database entries. External databases may require institutional access.
Computational Analysis
Pathogenicity Predictions
SpliceAIPredictor Consensus
Mixed/VUS
PP3 Applied
No
REVEL Score
0.0
Threshold: ≥0.75 = PP3 applied
SpliceAI Scores
Window: ±500bp| Effect Type | Score | Position |
|---|---|---|
| Acceptor Loss (AL) | 0.0 | -172 bp |
| Donor Loss (DL) | 0.0 | 328 bp |
| Acceptor Gain (AG) | 0.0 | -7 bp |
| Donor Gain (DG) | 0.0 | -24 bp |
High impact (≥0.5)
Medium impact (0.2-0.49)
Low impact (<0.2)
VCEP Guidelines
Applied ACMG/AMP Criteria (VCEP Specific)
Filter Criteria:
BP4
BP4 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
BP6
BP6 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)