TRIM63 p.Ala54=
c.162T>G · rs41284327 · VCV703828
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.249%, nfe)
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 -1.1 | GERP -4.5 |
| Overall | ||
| CADD | 5.471 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.249%
European (non-Finnish) · 2,885/1,158,604 alleles
Filtering AF
0.241%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.238%
Overall
0.194%
3,052/1,575,986 alleles · rare
exomes 2,885/1,423,684 · genomes 167/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.249% | 402 |
| Remaining individualsnot grpmax-eligible | 0.132% | 760 |
| South Asian | 0.0486% | 2,056 |
| African / African-American | 0.0256% | 3,906 |
| Finnishnot grpmax-eligible | 0.0248% | 4,036 |
| Admixed American | 0.0176% | 5,692 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00364% | 27,452 |
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
- TRIM63
- Protein
- p.Ala54=
- Coding
- c.162T>G
- MANE Select
- NM_032588
- dbSNP
- rs41284327
- Type
- single nucleotide variant
- Location
- chr1:26066438 (GRCh38)
- Gene constraint
- LOEUF 1.329 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.88 · 3 PDB
Similar variants
- TRIM63 p.Ala244Val Uncertain significance ★★ ⚠ same type
- TRIM63 p.Ala289Val Uncertain significance ★★ ⚠ same type
- TRIM63 p.Arg112Gln Uncertain significance ★★ ⚠ same type
- TRIM63 p.Arg183His Uncertain significance ★★ ⚠ same type
- TRIM63 p.Arg230Trp Uncertain significance ★★ ⚠ same type
- TRIM63 p.Arg62Gln Uncertain significance ★★ ⚠ same type
- TRIM63 p.Arg62Trp Uncertain significance ★★ ⚠ same type
- TRIM63 p.Arg74His 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/trim63-p-ala54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown