CSF2RB p.Ser491=
c.1473C>T · rs762834230 · VCV3016647
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00322%, nfe)
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 -4.1 | GERP -2.7 |
| Overall | ||
| CADD | 0.447 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00322%
European (non-Finnish) · 38/1,179,942 alleles
Filtering AF
0.00239%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0021%
Overall
0.0026%
42/1,612,614 alleles · very rare
exomes 40/1,460,444 · genomes 2/152,170 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00322% | 31,051 |
| East Asian | 0.00223% | 44,886 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,352 |
| African / African-American | 0.00134% | 74,872 |
| South Asian | 0.0011% | 91,020 |
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
- CSF2RB
- Protein
- p.Ser491=
- Coding
- c.1473C>T
- MANE Select
- NM_000395
- dbSNP
- rs762834230
- Type
- single nucleotide variant
- Location
- chr22:36936557 (GRCh38)
- Gene constraint
- LOEUF 0.511 · pLI 0.93 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.50 · 10 PDB
Similar variants
- CSF2RB p.Ala185Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala255Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala314Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala314Val Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala394Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala455Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala576Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala662Thr 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/csf2rb-p-ser491 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown