C3 c.2245+9del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 9.63e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -4.9 | GERP -2.5 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.63e-05%
European (non-Finnish) · 1/1,038,318 alleles
Overall
7.99e-05%
1/1,250,928 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
- C3
- Coding
- c.2245+9del
- MANE Select
- NM_000064
- dbSNP
- rs2512257856
- Type
- Deletion
- Location
- chr19:6707067 (GRCh38)
- Gene constraint
- LOEUF 0.541 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.84 · 80 PDB
Similar variants
- C3 p.Asp1245_Phe1246insTer Pathogenic ★★ same type
- C3 p.Ile1108_Lys1111del Uncertain significance ★★ same type
- C3 p.Arg668fs Pathogenic ★ same type
- C3 p.Asn1229fs Likely pathogenic ★ same type
- C3 p.Asn853fs Pathogenic ★ same type
- C3 p.Asn93fs Likely pathogenic ★ same type
- C3 p.Asp923_Gly924del Likely pathogenic ★ same type
- C3 p.Glu1640fs 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/c3-c-2245-plus-9del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown