TRMT5 p.Ser74=
c.222A>G · rs372936436 · VCV1879280
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.752%, sas)
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 0.83 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 9.658 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.752%
South Asian · 685/91,076 alleles
Filtering AF
0.705%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.687%
Overall
0.0466%
753/1,614,188 alleles · rare
exomes 722/1,461,876 · genomes 31/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.752% | 133 |
| Remaining individualsnot grpmax-eligible | 0.064% | 1,563 |
| Middle Eastern | 0.0495% | 2,021 |
| East Asian | 0.00891% | 11,220 |
| Admixed American | 0.00167% | 60,022 |
| European (non-Finnish) | 0.00161% | 62,107 |
| Finnishnot grpmax-eligible | 0.00156% | 64,038 |
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.Ser74=
- Coding
- c.222A>G
- MANE Select
- NM_020810
- dbSNP
- rs372936436
- Type
- single nucleotide variant
- Location
- chr14:60979676 (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-ser74 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown