RNMT p.Glu155=
c.465A>G · rs563526257 · VCV758114
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.213%, sas)
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 1.2 | GERP -4.7, phastCons 1 |
| Overall | ||
| CADD | 7.042 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.213%
South Asian · 194/90,966 alleles
Filtering AF
0.189%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.179%
Overall
0.0125%
201/1,613,718 alleles · rare
exomes 193/1,461,378 · genomes 8/152,340 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.213% | 469 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,499 |
| East Asian | 0.00223% | 44,854 |
| European (non-Finnish) | 8.48e-05% | 1,179,798 |
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
- RNMT
- Protein
- p.Glu155=
- Coding
- c.465A>G
- MANE Select
- NM_003799
- dbSNP
- rs563526257
- Type
- single nucleotide variant
- Location
- chr18:13734511 (GRCh38)
- Gene constraint
- LOEUF 0.92 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.27 · 8 PDB
Similar variants
- RNMT p.Tyr399= Benign ★★ same type
- RNMT p.Ala151Val Uncertain significance ★ ⚠ same type
- RNMT p.Ala2Thr Uncertain significance ★ ⚠ same type
- RNMT p.Ala56Thr Uncertain significance ★ ⚠ same type
- RNMT p.Arg107Gly Uncertain significance ★ ⚠ same type
- RNMT p.Arg239Trp Uncertain significance ★ ⚠ same type
- RNMT p.Arg247Cys Uncertain significance ★ ⚠ same type
- RNMT p.Asn31Thr 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/rnmt-p-glu155 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown