CYBC1 p.Ile153=
c.459C>T · rs375281920 · VCV1682693
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0588%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.017 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.8 | GERP -3.4 |
| Overall | ||
| CADD | 0.606 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0588%
African / African-American · 44/74,886 alleles
Filtering AF
0.0449%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0401%
Overall
0.00558%
90/1,611,974 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0588% | 1,702 |
| Admixed American | 0.00667% | 14,993 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,803 |
| European (non-Finnish) | 0.00305% | 32,743 |
| East Asian | 0.00223% | 44,846 |
| Finnishnot grpmax-eligible | 0.00157% | 63,564 |
| South Asian | 0.0011% | 91,056 |
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
- CYBC1
- Protein
- p.Ile153=
- Coding
- c.459C>T
- MANE Select
- NM_001033046
- dbSNP
- rs375281920
- Type
- single nucleotide variant
- Location
- chr17:82444109 (GRCh38)
- Gene constraint
- LOEUF 1.556 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.65 · 1 PDB
- Residue 153
- a UniProt-annotated variant site (in cgd5; loss of protein expression; decreased pma-induced oxidative burst in neutrophils)
Similar variants
- CYBC1 p.Arg129Trp Uncertain significance ★★ same type
- CYBC1 p.Arg147Cys Uncertain significance ★★ ⚠ same type
- CYBC1 p.Asp43Asn Uncertain significance ★★ ⚠ same type
- CYBC1 p.Asp98Asn Uncertain significance ★★ ⚠ same type
- CYBC1 p.Thr82Met Uncertain significance ★★ ⚠ same type
- CYBC1 c.127+13C>A Benign/Likely benign ★★ same type
- CYBC1 c.127+16C>T Likely benign ★★ same type
- CYBC1 c.128-150G>T Benign ★★ 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/cybc1-p-ile153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown