TELO2 p.Ala483=
c.1449G>A · rs9938945 · VCV2065985
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.128%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.4 | GERP -3.1, phastCons 0.97 |
| Overall | ||
| CADD | 6.815 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.128%
African / African-American · 96/75,048 alleles
Filtering AF
0.107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0995%
Overall
0.00813%
131/1,610,488 alleles · rare
exomes 62/1,458,144 · genomes 69/152,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.128% | 782 |
| Admixed American | 0.0233% | 4,286 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,805 |
| East Asian | 0.00891% | 11,221 |
| South Asian | 0.0011% | 91,044 |
| European (non-Finnish) | 0.000678% | 147,479 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- TELO2
- Protein
- p.Ala483=
- Coding
- c.1449G>A
- MANE Select
- NM_016111
- dbSNP
- rs9938945
- Type
- single nucleotide variant
- Location
- chr16:1501750 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.74 · 4 PDB
Similar variants
- TELO2 p.Ala483Glu Likely benign ★ same residue
- TELO2 p.Ala483Val Likely benign ★ same residue
- TELO2 c.2034+2T>C Likely pathogenic ★★ same type
- TELO2 c.2291+1G>C Likely pathogenic ★★ same type
- TELO2 p.Arg403Ter Pathogenic/Likely pathogenic ★★ same type
- TELO2 p.Arg609His Pathogenic/Likely pathogenic ★★ same type
- TELO2 p.Cys367Phe Pathogenic/Likely pathogenic ★★ same type
- TELO2 c.830+5G>T Uncertain significance ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/telo2-p-ala483 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown