FMN2 p.Ala973=
c.2919A>G · rs140720010 · VCV3037308
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.17%, afr)
Conditions
1
FMN2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Overall | ||
| CADD | 2.317 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.17%
African / African-American · 1,376/43,446 alleles
Filtering AF
3.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.97%
Overall
0.735%
8,220/1,118,162 alleles · low-frequency
exomes 7,368/1,039,692 · genomes 852/78,470 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.17% | 32 |
| Finnishnot grpmax-eligible | 1.54% | 65 |
| Remaining individualsnot grpmax-eligible | 0.957% | 104 |
| European (non-Finnish) | 0.632% | 158 |
| Admixed American | 0.584% | 171 |
| Middle Eastern | 0.438% | 228 |
| South Asian | 0.334% | 300 |
| Ashkenazi Jewishnot grpmax-eligible | 0.3% | 334 |
| East Asian | 0.141% | 711 |
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
- FMN2
- Protein
- p.Ala973=
- Coding
- c.2919A>G
- MANE Select
- NM_020066
- dbSNP
- rs140720010
- Type
- single nucleotide variant
- Location
- chr1:240207731 (GRCh38)
- Gene constraint
- LOEUF 0.51 · pLI 0.51 (gnomAD)
- Structure
- AlphaFold pLDDT 51.48 · 2 PDB
- Residue 973
- the fh1 domain; the 'disordered' region
Disease context
FMN2-related disorder
Similar variants
- FMN2 p.Ala973Thr Likely benign ★ same residue
- FMN2 p.Ala951= Likely benign ★★ same condition
- FMN2 p.Gly1005= Likely benign ★★ same condition
- FMN2 p.Gly1007= Likely benign ★★ same condition
- FMN2 p.Gly1062= Likely benign ★★ same condition
- FMN2 p.Gly941= Likely benign ★★ same condition
- FMN2 p.Leu1058= Likely benign ★★ same condition
- FMN2 p.Leu1069= Likely benign ★★ 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/fmn2-p-ala973 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown