CSF2RB p.Ser670=
c.2010C>T · rs372963427 · VCV2905311
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00945%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.7 | GERP -2.6 |
| Overall | ||
| CADD | 0.464 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00945%
European (non-Finnish) · 111/1,174,718 alleles
Filtering AF
0.00795%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00747%
Overall
0.00744%
119/1,600,186 alleles · very rare
exomes 117/1,448,250 · genomes 2/151,936 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00945% | 10,583 |
| East Asian | 0.00898% | 11,136 |
| South Asian | 0.00335% | 29,869 |
| African / African-American | 0.00134% | 74,760 |
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.Ser670=
- Coding
- c.2010C>T
- MANE Select
- NM_000395
- dbSNP
- rs372963427
- Type
- single nucleotide variant
- Location
- chr22:36937818 (GRCh38)
- Gene constraint
- LOEUF 0.511 · pLI 0.93 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.50 · 10 PDB
- Residue 670
- the 'disordered' region
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-ser670 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown