Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.71%, mid)
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 -8.8 | GERP -4.7 |
| Overall | ||
| CADD | 1.305 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.71%
Middle Eastern · 164/6,060 alleles
Filtering AF
2.37%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.24%
Overall
0.408%
6,591/1,613,872 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 2.71% | 37 |
| Ashkenazi Jewishnot grpmax-eligible | 1.48% | 67 |
| Remaining individualsnot grpmax-eligible | 0.542% | 184 |
| European (non-Finnish) | 0.422% | 237 |
| Admixed American | 0.273% | 366 |
| Finnishnot grpmax-eligible | 0.259% | 386 |
| South Asian | 0.254% | 394 |
| African / African-American | 0.14% | 714 |
| East Asian | 0.00223% | 44,868 |
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
- FGR
- Protein
- p.Ser122=
- Coding
- c.366C>T
- MANE Select
- NM_005248
- dbSNP
- rs2231870
- Type
- single nucleotide variant
- Location
- chr1:27621621 (GRCh38)
- Gene constraint
- LOEUF 0.556 · pLI 0.50 (gnomAD)
- Structure
- AlphaFold pLDDT 83.00 · 7 PDB
- Residue 122
- the sh3 domain; a turn
Similar variants
- FGR c.533-8C>G Benign ★★ same type
- FGR p.Asp254= Benign ★★ same type
- FGR p.Ala30Thr Uncertain significance ★ ⚠ same type
- FGR p.Ala395Thr Uncertain significance ★ ⚠ same type
- FGR p.Ala60Thr Uncertain significance ★ ⚠ same type
- FGR p.Ala60Val Uncertain significance ★ ⚠ same type
- FGR p.Arg384Lys Uncertain significance ★ ⚠ same type
- FGR p.Arg465Trp 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/fgr-p-ser122 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown