Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.84%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.72 | GERP -4.3, phastCons 0.03 |
| Overall | ||
| CADD | 2.265 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.84%
African / African-American · 1,373/74,500 alleles
Filtering AF
1.76%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.73%
Overall
0.105%
1,694/1,607,188 alleles · low-frequency
exomes 905/1,454,874 · genomes 789/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.84% | 54 |
| Middle Eastern | 0.332% | 301 |
| Remaining individualsnot grpmax-eligible | 0.19% | 527 |
| Admixed American | 0.133% | 754 |
| South Asian | 0.0133% | 7,491 |
| European (non-Finnish) | 0.00807% | 12,398 |
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
- TRMT5
- Protein
- p.Pro487=
- Coding
- c.1461A>G
- MANE Select
- NM_020810
- dbSNP
- rs1129311
- Type
- single nucleotide variant
- Location
- chr14:60975178 (GRCh38)
- Gene constraint
- LOEUF 0.969 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.50
- Residue 487
- the 'disordered' region
Similar variants
- TRMT5 p.Pro487Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
- TRMT5 p.Ala188Asp Uncertain significance ★★ ⚠ same type
- TRMT5 p.Ala45Thr Uncertain significance ★★ ⚠ same type
- TRMT5 p.Ala45Val Uncertain significance ★★ ⚠ same type
- TRMT5 p.Arg120Cys Uncertain significance ★★ ⚠ same type
- TRMT5 p.Arg125His Uncertain significance ★★ ⚠ same type
- TRMT5 p.Arg15Thr Uncertain significance ★★ ⚠ same type
- TRMT5 p.Arg266Gln 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/trmt5-p-pro487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown