FGF3 p.Ala19=
c.57G>A · rs991290232 · VCV1204912
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0207%, afr)
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 0.053 | GERP -0.42, phastCons 0.1 |
| Overall | ||
| CADD | 8.831 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0207%
African / African-American · 14/67,708 alleles
Filtering AF
0.0125%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00994%
Overall
0.00116%
17/1,462,612 alleles · ultra-rare
exomes 5/1,310,806 · genomes 12/151,806 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0207% | 4,836 |
| Admixed American | 0.00498% | 20,064 |
| European (non-Finnish) | 8.98e-05% | 1,113,566 |
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
- FGF3
- Protein
- p.Ala19=
- Coding
- c.57G>A
- MANE Select
- NM_005247
- dbSNP
- rs991290232
- Type
- single nucleotide variant
- Location
- chr11:69818877 (GRCh38)
- Gene constraint
- LOEUF 1.815 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.32
Similar variants
- FGF3 p.Arg104Ter Pathogenic/Likely pathogenic ★★ same type
- FGF3 p.Arg209Ter Pathogenic/Likely pathogenic ★★ same type
- FGF3 p.Arg95Trp Pathogenic/Likely pathogenic ★★ same type
- FGF3 p.Tyr106Ter Pathogenic/Likely pathogenic ★★ same type
- FGF3 p.Arg132Trp Uncertain significance ★★ ⚠ same type
- FGF3 p.Arg145Gln Uncertain significance ★★ ⚠ same type
- FGF3 p.Arg171His Uncertain significance ★★ ⚠ same type
- FGF3 p.Asp184Val 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/fgf3-p-ala19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown