FGF3 p.Ser216=
c.648C>T · rs367789711 · VCV728881
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.319%, 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 0.39 | GERP -0.26, phastCons 0.009 |
| Overall | ||
| CADD | 2.722 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.319%
African / African-American · 235/73,710 alleles
Filtering AF
0.285%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.272%
Overall
0.016%
250/1,563,334 alleles · rare
exomes 113/1,411,010 · genomes 137/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.319% | 314 |
| Remaining individualsnot grpmax-eligible | 0.0116% | 8,590 |
| Admixed American | 0.00556% | 17,990 |
| European (non-Finnish) | 0.000435% | 230,146 |
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.Ser216=
- Coding
- c.648C>T
- MANE Select
- NM_005247
- dbSNP
- rs367789711
- Type
- single nucleotide variant
- Location
- chr11:69810377 (GRCh38)
- Gene constraint
- LOEUF 1.815 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.32
- Residue 216
- the 'disordered' region
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-ser216 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown