Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.28%, 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 -0.62 | GERP -4.4 |
| Overall | ||
| CADD | 2.083 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.28%
African / African-American · 3,210/75,032 alleles
Filtering AF
4.15%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.1%
Overall
0.264%
4,261/1,613,088 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.28% | 23 |
| Ashkenazi Jewishnot grpmax-eligible | 1.48% | 68 |
| Remaining individualsnot grpmax-eligible | 0.382% | 262 |
| Admixed American | 0.333% | 300 |
| Middle Eastern | 0.182% | 549 |
| European (non-Finnish) | 0.0131% | 7,662 |
| South Asian | 0.00769% | 13,010 |
| East Asian | 0.00223% | 44,854 |
| Finnishnot grpmax-eligible | 0.00159% | 63,032 |
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
- CSF2
- Protein
- p.Ser22=
- Coding
- c.66G>A
- MANE Select
- NM_000758
- dbSNP
- rs2069621
- Type
- single nucleotide variant
- Location
- chr5:132073889 (GRCh38)
- Gene constraint
- LOEUF 0.619 · pLI 0.85 (gnomAD)
- Structure
- AlphaFold pLDDT 88.30 · 11 PDB
Similar variants
- CSF2 p.Ser22Leu Likely benign ★ same residue
- CSF2 p.Thr115Ile Likely benign ★★ same type
- CSF2 p.Ala13Thr Uncertain significance ★ ⚠ same type
- CSF2 p.Arg21Cys Uncertain significance ★ ⚠ same type
- CSF2 p.Arg41His Uncertain significance ★ ⚠ same type
- CSF2 p.Arg84Pro Uncertain significance ★ ⚠ same type
- CSF2 p.Glu52Asp Uncertain significance ★ ⚠ same type
- CSF2 p.Leu127Met 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/csf2-p-ser22 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown