CYBC1 p.Phe120=
c.360C>T · rs199793460 · VCV1682707
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.207%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.456 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.2 | GERP -3.4 |
| Overall | ||
| CADD | 1.373 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.207%
East Asian · 93/44,868 alleles
Filtering AF
0.173%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.161%
Overall
0.0145%
234/1,613,888 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.207% | 482 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0912% | 1,096 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,944 |
| European (non-Finnish) | 0.00839% | 11,918 |
| South Asian | 0.00439% | 22,766 |
| Finnishnot grpmax-eligible | 0.00313% | 31,967 |
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.Phe120=
- Coding
- c.360C>T
- MANE Select
- NM_001033046
- dbSNP
- rs199793460
- Type
- single nucleotide variant
- Location
- chr17:82444530 (GRCh38)
- Gene constraint
- LOEUF 1.556 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.65 · 1 PDB
- Residue 120
- 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-phe120 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown