FGFR2 p.Arg84=
c.252G>A · rs779848635 · VCV788701
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0033%, nfe)
Conditions
1
FGFR2-related craniosynostosis
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 4.9 | GERP 0.96, phastCons 1 |
| Overall | ||
| CADD | 13.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0033%
European (non-Finnish) · 39/1,180,056 alleles
Filtering AF
0.00247%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00217%
Overall
0.00254%
41/1,614,086 alleles · very rare
exomes 40/1,461,894 · genomes 1/152,192 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0033% | 30,258 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
| African / African-American | 0.00133% | 74,924 |
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
- FGFR2
- Protein
- p.Arg84=
- Coding
- c.252G>A
- MANE Select
- NM_000141
- dbSNP
- rs779848635
- Type
- single nucleotide variant
- Location
- chr10:121565562 (GRCh38)
- Gene constraint
- LOEUF 0.278 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.33 · 65 PDB
- Residue 84
- the ig-like c2-type 1 domain
Similar variants
- FGFR2 c.1084+1G>A Pathogenic ★★ same condition
- FGFR2 c.1084+2T>C Pathogenic ★★ same condition
- FGFR2 c.1084+3A>G Pathogenic ★★ same condition
- FGFR2 c.940-1G>T Pathogenic ★★ same condition
- FGFR2 p.Ala648Thr Pathogenic ★★ same condition
- FGFR2 p.Asp321Ala Pathogenic ★★ same condition
- FGFR2 p.Cys342Phe Pathogenic ★★ same condition
- FGFR2 p.Cys342Ser 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/fgfr2-p-arg84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown