TRMT5 p.Ser77=
c.231T>C · rs114724212 · VCV787945
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.612%, 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 3 | GERP -0.56, phastCons 0.97 |
| Overall | ||
| CADD | 9.705 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.612%
African / African-American · 459/75,034 alleles
Filtering AF
0.565%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.547%
Overall
0.0335%
541/1,614,134 alleles · rare
exomes 277/1,461,878 · genomes 264/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.612% | 163 |
| Remaining individualsnot grpmax-eligible | 0.0688% | 1,454 |
| Admixed American | 0.0467% | 2,143 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0169% | 5,921 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.0022% | 45,539 |
| European (non-Finnish) | 0.000254% | 393,345 |
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.Ser77=
- Coding
- c.231T>C
- MANE Select
- NM_020810
- dbSNP
- rs114724212
- Type
- single nucleotide variant
- Location
- chr14:60979667 (GRCh38)
- Gene constraint
- LOEUF 0.969 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.50
Similar variants
- 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
- TRMT5 p.Arg291His 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-ser77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown