CFD c.55+10C>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00117%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +10 | near-intronic (+10 nt from the splice site) |
|---|---|---|
| SpliceAI | Δ0.34 | donor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -2.1 |
| Non-coding constraint | Z -0.19 | 1 kb window · o/e 1.01 · regional · uncalibrated |
| Overall | ||
| CADD | 6.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00117%
South Asian · 1/85,160 alleles
Overall
0.000142%
2/1,409,778 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00117% | 85,160 |
| European (non-Finnish) | 8.68e-05% | 1,152,090 |
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
- CFD
- Coding
- c.55+10C>T
- MANE Select
- NM_001928
- Type
- single nucleotide variant
- Location
- chr19:859754 (GRCh38)
- Gene constraint
- LOEUF 1.948 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 91.19 · 40 PDB
Similar variants
- CFD c.212+2T>G Likely pathogenic ★★ same type
- CFD c.56-1G>C Likely pathogenic ★★ same type
- CFD p.Tyr95Ter Pathogenic ★★ same type
- ELANE p.Gly203Arg Pathogenic ★★ same type
- ELANE p.Ser126Leu Pathogenic ★★ ⚠ same type
- CFD p.Ala100Pro Uncertain significance ★★ same type
- CFD p.Ala129Thr Uncertain significance ★★ ⚠ same type
- CFD p.Ala143Val 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/cfd-c-55-plus-10c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown