Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.17%, 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 -0.93 | GERP -5.2 |
| Overall | ||
| CADD | 3.273 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.17%
African / African-American · 2,382/75,030 alleles
Filtering AF
3.07%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.03%
Overall
0.167%
2,694/1,613,206 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.17% | 31 |
| Remaining individualsnot grpmax-eligible | 0.205% | 488 |
| Admixed American | 0.178% | 561 |
| Middle Eastern | 0.099% | 1,010 |
| South Asian | 0.00659% | 15,181 |
| European (non-Finnish) | 0.00542% | 18,438 |
| East Asian | 0.00223% | 44,872 |
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.Thr27=
- Coding
- c.81G>A
- MANE Select
- NM_000758
- dbSNP
- rs2069622
- Type
- single nucleotide variant
- Location
- chr5:132073904 (GRCh38)
- Gene constraint
- LOEUF 0.619 · pLI 0.85 (gnomAD)
- Structure
- AlphaFold pLDDT 88.30 · 11 PDB
- Residue 27
- a turn
Similar variants
- 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
- CSF2 p.Met53Thr 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-thr27 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown