TOM1 p.Asp38=
c.114C>T · rs57755951 · VCV778918
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.9%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.124 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 2.3, phastCons 1 |
| Overall | ||
| CADD | 13.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.9%
African / African-American · 3,676/75,024 alleles
Filtering AF
4.77%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.71%
Overall
0.261%
4,217/1,614,132 alleles · low-frequency
exomes 2,058/1,461,854 · genomes 2,159/152,278 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.9% | 20 |
| Remaining individualsnot grpmax-eligible | 0.365% | 274 |
| Admixed American | 0.303% | 330 |
| Middle Eastern | 0.181% | 551 |
| European (non-Finnish) | 0.00958% | 10,442 |
| South Asian | 0.00769% | 13,012 |
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
- TOM1
- Protein
- p.Asp38=
- Coding
- c.114C>T
- MANE Select
- NM_005488
- dbSNP
- rs57755951
- Type
- single nucleotide variant
- Location
- chr22:35317938 (GRCh38)
- Gene constraint
- LOEUF 0.866 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.67 · 6 PDB
- Residue 38
- the vhs domain; an α-helix
Similar variants
- TOM1 p.Ala401Pro Uncertain significance ★★ ⚠ same type
- TOM1 p.Arg450Gln Uncertain significance ★★ ⚠ same type
- TOM1 p.Asp324Asn Uncertain significance ★★ ⚠ same type
- TOM1 p.Ile40Val Uncertain significance ★★ ⚠ same type
- TOM1 p.Ser461Phe Uncertain significance ★★ ⚠ same type
- TOM1 p.Ser235= Benign ★★ same type
- TOM1 c.1028-8C>T Uncertain significance ★ same type
- TOM1 c.138-6C>T 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/tom1-p-asp38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown