Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 25.3%, amr) — too common for a highly-penetrant pathogenic allele
Conditions
1
trimethylaminuria
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 -6.5 | GERP -4 |
| Overall | ||
| CADD | 7.873 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
25.3%
Admixed American · 15,178/59,976 alleles
Filtering AF
25%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 24.8%
Overall
7.53%
121,494/1,613,590 alleles · common
exomes 108,657/1,461,478 · genomes 12,837/152,112 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 25.3% | 4 |
| East Asian | 20.1% | 5 |
| South Asian | 17.6% | 6 |
| Amishnot grpmax-eligible | 11.5% | 9 |
| Middle Eastern | 9.52% | 11 |
| Remaining individualsnot grpmax-eligible | 8.4% | 12 |
| African / African-American | 8.02% | 12 |
| Ashkenazi Jewishnot grpmax-eligible | 7.99% | 13 |
| European (non-Finnish) | 5.44% | 18 |
| Finnishnot grpmax-eligible | 4.45% | 22 |
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
- FMO3
- Protein
- p.Ser147=
- Coding
- c.441C>T
- MANE Select
- NM_001002294
- dbSNP
- rs1800822
- Type
- single nucleotide variant
- Location
- chr1:171107794 (GRCh38)
- Gene constraint
- LOEUF 1.314 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.50
Similar variants
- FMO3 c.484+2T>G Likely pathogenic ★★ same condition
- FMO3 c.828-2A>G Likely pathogenic ★★ same condition
- FMO3 p.Arg223Gln Likely pathogenic ★★ same condition
- FMO3 p.Arg223Trp Likely pathogenic ★★ same condition
- FMO3 p.Arg238Gln Pathogenic/Likely pathogenic ★★ same condition
- FMO3 p.Arg238Ter Pathogenic/Likely pathogenic ★★ same condition
- FMO3 p.Arg492Trp Pathogenic/Likely pathogenic ★★ same condition
- FMO3 p.Arg500Ter Pathogenic/Likely pathogenic ★★ same condition
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/fmo3-p-ser147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown