C5 c.3864+4del
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +4 | donor splice region (+4, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -2.3 | GERP -4 |
| Non-coding constraint | Z 3.11 | 1 kb window · o/e 0.77 · regional · uncalibrated |
| Overall | ||
| CADD | 15.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,002 alleles
Overall
0.000657%
1/152,176 alleles · very rare
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
- C5
- Coding
- c.3864+4del
- MANE Select
- NM_001735
- dbSNP
- rs2046955615
- Type
- Deletion
- Location
- chr9:120976696 (GRCh38)
- Gene constraint
- LOEUF 0.779 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.67 · 49 PDB
Similar variants
- C5 c.3154+13del Benign/Likely benign ★★ same type
- C5 c.4220+20_4220+27del Likely benign ★★ same type
- C5 p.Ala1155fs Likely pathogenic ★ same type
- C5 p.Gln1504fs Pathogenic ★ same type
- C5 p.Glu1413fs Pathogenic ★ same type
- C5 p.His1390fs Pathogenic ★ same type
- C5 p.Ile509fs Pathogenic ★ same type
- C5 p.Leu1161fs 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/c5-c-3864-plus-4del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown