CYBC1 p.Ser41=
c.123C>T · rs767051172 · VCV1682733
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.49 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.28 | GERP -3.6, phastCons 0.36 |
| Overall | ||
| CADD | 10.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Middle Eastern · 1/5,986 alleles
Filtering AF
0.00197%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00168%
Overall
0.00256%
41/1,600,714 alleles · ultra-rare
exomes 39/1,448,536 · genomes 2/152,178 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0167% | 5,986 |
| Remaining individualsnot grpmax-eligible | 0.00645% | 15,506 |
| Admixed American | 0.00347% | 28,784 |
| European (non-Finnish) | 0.00272% | 36,741 |
| South Asian | 0.00228% | 43,952 |
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.Ser41=
- Coding
- c.123C>T
- MANE Select
- NM_001033046
- dbSNP
- rs767051172
- Type
- single nucleotide variant
- Location
- chr17:82447584 (GRCh38)
- Gene constraint
- LOEUF 1.556 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.65 · 1 PDB
- Residue 41
- 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-ser41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown