CFI c.883+290A>C
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 10.6%, mid) — 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 +290 | deep intronic (+290 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.1 | GERP -0.31 |
| Non-coding constraint | Z -0.60 | 1 kb window · o/e 1.06 · regional · uncalibrated |
| Overall | ||
| CADD | 1.204 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.6%
Middle Eastern · 199/1,874 alleles
Filtering AF
9.41%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.95%
Overall
5.26%
27,455/522,320 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 10.6% | 9 |
| Ashkenazi Jewishnot grpmax-eligible | 7.04% | 14 |
| Finnishnot grpmax-eligible | 6.26% | 16 |
| Remaining individualsnot grpmax-eligible | 6.05% | 17 |
| South Asian | 5.85% | 17 |
| European (non-Finnish) | 5.62% | 18 |
| Admixed American | 4.84% | 21 |
| Amishnot grpmax-eligible | 4.62% | 22 |
| African / African-American | 3.81% | 26 |
| East Asian | 0.0319% | 3,131 |
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
- CFI
- Coding
- c.883+290A>C
- MANE Select
- NM_000204
- dbSNP
- rs116750895
- Type
- single nucleotide variant
- Location
- chr4:109759980 (GRCh38)
- Gene constraint
- LOEUF 1.076 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.50 · 2 PDB
Similar variants
- CFI c.1429+1G>C Pathogenic/Likely pathogenic ★★ same type
- CFI c.57+1G>C Likely pathogenic ★★ same type
- CFI c.658+1G>A Likely pathogenic ★★ same type
- CFI c.905-1G>C Likely pathogenic ★★ same type
- CFI p.Ala258Thr Pathogenic/Likely pathogenic ★★ ⚠ same type
- CFI p.Arg187Ter Pathogenic/Likely pathogenic ★★ same type
- CFI p.Arg474Ter Pathogenic/Likely pathogenic ★★ same type
- CFI p.His380Arg 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/cfi-c-883-plus-290a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown