FBXO7 c.417+141del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 50.3%, eas) — 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 +141 | deep intronic (+141 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -3.2 | GERP -0.3 |
| Non-coding constraint | Z 0.64 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 0.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
50.3%
East Asian · 13,242/26,326 alleles
Filtering AF
49.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 49.3%
Overall
36.3%
206,000/566,958 alleles · common
exomes 152,037/435,242 · genomes 53,963/131,716 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 50.3% | 2 |
| African / African-American | 44.8% | 2 |
| Admixed American | 44.3% | 2 |
| South Asian | 39.7% | 3 |
| Finnishnot grpmax-eligible | 39.4% | 3 |
| Remaining individualsnot grpmax-eligible | 36.1% | 3 |
| Middle Eastern | 36.1% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 36% | 3 |
| European (non-Finnish) | 33.1% | 3 |
| Amishnot grpmax-eligible | 31.8% | 3 |
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
- FBXO7
- Coding
- c.417+141del
- MANE Select
- NM_012179
- dbSNP
- rs5845002
- Type
- Deletion
- Location
- chr22:32479402 (GRCh38)
- Gene constraint
- LOEUF 0.955 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 67.13 · 2 PDB
Similar variants
- FBXO7 p.Pro484fs Pathogenic/Likely pathogenic ★★ same type
- FBXO7 p.Arg513fs Uncertain significance ★★ same type
- FBXO7 c.1183-2_1183-1del Likely pathogenic ★ same type
- FBXO7 p.Asn51fs Pathogenic ★ same type
- FBXO7 p.Asp348fs Pathogenic ★ same type
- FBXO7 p.Cys192fs Pathogenic ★ same type
- FBXO7 p.Gly126fs Pathogenic ★ same type
- FBXO7 p.Leu106fs 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/fbxo7-c-417-plus-141del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown