CFP c.403+20C>T
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00437%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +20 | near-intronic (+20 nt from the splice site) |
|---|---|---|
| SpliceAI | Δ0.94 | donor gain · deltas |
| Pangolin | Δ0.70 | gain · loss 0.29 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -0.43 | GERP -3 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 24.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00437%
Admixed American · 2/45,758 alleles
Filtering AF
0.000725%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000271%
Overall
0.000414%
5/1,207,812 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00437% | 22,879 |
| Finnishnot grpmax-eligible | 0.00215% | 46,504 |
| European (non-Finnish) | 0.000224% | 447,035 |
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
- CFP
- Coding
- c.403+20C>T
- MANE Select
- NM_001145252
- dbSNP
- rs1383306170
- Type
- single nucleotide variant
- Location
- chrX:47628082 (GRCh38)
- Structure
- AlphaFold pLDDT 83.75 · 14 PDB
Similar variants
- CFP p.Trp321Gly Pathogenic ★★ same type
- CFP p.Ala402Gly Uncertain significance ★★ ⚠ same type
- CFP p.Arg157Gln Uncertain significance ★★ ⚠ same type
- CFP p.Arg157Trp Uncertain significance ★★ ⚠ same type
- CFP p.Arg159Cys Uncertain significance ★★ ⚠ same type
- CFP p.Arg247Trp Uncertain significance ★★ ⚠ same type
- CFP p.Arg438Trp Uncertain significance ★★ ⚠ same type
- CFP p.Asn307Ser Uncertain significance ★★ ⚠ 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/cfp-c-403-plus-20c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown