CSF2 p.Pro109=
c.327G>A · rs145753257 · VCV787041
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.207%, 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 1.3 | GERP -3.1, phastCons 0.87 |
| Overall | ||
| CADD | 12.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.207%
African / African-American · 155/75,046 alleles
Filtering AF
0.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.17%
Overall
0.0126%
203/1,613,462 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.207% | 484 |
| Admixed American | 0.0267% | 3,752 |
| Middle Eastern | 0.0167% | 5,974 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,414 |
| South Asian | 0.00878% | 11,385 |
| East Asian | 0.00223% | 44,882 |
| European (non-Finnish) | 0.00136% | 73,751 |
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.Pro109=
- Coding
- c.327G>A
- MANE Select
- NM_000758
- dbSNP
- rs145753257
- Type
- single nucleotide variant
- Location
- chr5:132074935 (GRCh38)
- Gene constraint
- LOEUF 0.619 · pLI 0.85 (gnomAD)
- Structure
- AlphaFold pLDDT 88.30 · 11 PDB
- Residue 109
- an α-helix; a disulfide bond
Similar variants
- CSF2 p.Pro109Leu 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-pro109 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown