CYBB c.141+90C>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 70.3%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +90 | deep intronic (+90 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2 | GERP -3.4, phastCons 0.84 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 1.236 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
70.3%
African / African-American · 32,196/45,799 alleles
Filtering AF
69.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 69.4%
Overall
20.7%
132,392/638,345 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 70.3% | 1 |
| Admixed American | 22.1% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 21.8% | 5 |
| Remaining individualsnot grpmax-eligible | 20.9% | 5 |
| South Asian | 20.2% | 5 |
| European (non-Finnish) | 16.6% | 6 |
| Middle Eastern | 16.2% | 6 |
| Finnishnot grpmax-eligible | 15% | 7 |
| Amishnot grpmax-eligible | 10.1% | 10 |
| East Asian | 5.04% | 20 |
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
- CYBB
- Coding
- c.141+90C>A
- MANE Select
- NM_000397
- dbSNP
- rs4422908
- Type
- single nucleotide variant
- Location
- chrX:37782273 (GRCh38)
- Structure
- AlphaFold pLDDT 90.29 · 6 PDB
Similar variants
- CYBB c.1151+2T>C Pathogenic ★★ same type
- CYBB c.1315-2A>G Pathogenic/Likely pathogenic ★★ same type
- CYBB c.141+1G>T Pathogenic ★★ same type
- CYBB c.252+5G>A Pathogenic ★★ same type
- CYBB c.483+1G>A Pathogenic ★★ same type
- CYBB c.483+1G>T Pathogenic ★★ same type
- CYBB c.483+3A>T Likely pathogenic ★★ same type
- CYBB p.Ala156Thr Pathogenic/Likely pathogenic ★★ ⚠ 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/cybb-c-141-plus-90c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown