TRAP1 p.Arg658=
c.1974C>T · rs369893908 · VCV1633410
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0822%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not looked up on this page · why |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -3.4 |
| Overall | ||
| CADD | 2.512 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0822%
Middle Eastern · 5/6,084 alleles
Filtering AF
0.0654%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0599%
Overall
0.00942%
152/1,613,862 alleles · ultra-rare
exomes 144/1,461,648 · genomes 8/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0822% | 1,217 |
| South Asian | 0.0802% | 1,248 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0372% | 2,692 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,463 |
| East Asian | 0.00446% | 22,446 |
| European (non-Finnish) | 0.00373% | 26,818 |
| African / African-American | 0.00267% | 37,472 |
| Admixed American | 0.00167% | 60,000 |
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
- TRAP1
- Protein
- p.Arg658=
- Coding
- c.1974C>T
- MANE Select
- NM_016292
- dbSNP
- rs369893908
- Type
- single nucleotide variant
- Location
- chr16:3658832 (GRCh38)
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/trap1-p-arg658 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown