TRPM2 p.Asp1282=
c.3846C>T · VCV3811011
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0847%, eas)
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 -2.3 | GERP -2.9 |
| Overall | ||
| CADD | 7.437 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0847%
East Asian · 38/44,876 alleles
Filtering AF
0.0634%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.056%
Overall
0.00898%
145/1,614,126 alleles · ultra-rare
exomes 127/1,461,804 · genomes 18/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0847% | 1,181 |
| South Asian | 0.0318% | 3,141 |
| African / African-American | 0.0213% | 4,691 |
| Middle Eastern | 0.0165% | 6,054 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,946 |
| European (non-Finnish) | 0.00432% | 23,138 |
| Admixed American | 0.00167% | 60,030 |
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
- TRPM2
- Protein
- p.Asp1282=
- Coding
- c.3846C>T
- MANE Select
- NM_003307
- Type
- single nucleotide variant
- Location
- chr21:44426710 (GRCh38)
- Gene constraint
- LOEUF 1.047 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.51 · 15 PDB
Similar variants
- TRPM2 c.1932+141G>A Benign ★★ same type
- TRPM2 c.1933-10T>C Benign ★★ same type
- TRPM2 c.2322-35T>C Benign ★★ same type
- TRPM2 c.2538+14C>T Benign ★★ same type
- TRPM2 c.2962+96A>G Benign ★★ same type
- TRPM2 c.3146+68T>C Benign ★★ same type
- TRPM2 c.3147-20T>C Benign ★★ same type
- TRPM2 c.3549+8C>T Likely benign ★★ 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/trpm2-p-asp1282 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown