C9 p.Thr24=
c.72G>A · rs552482219 · VCV2198270
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.397%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.23 | GERP -4 |
| Overall | ||
| CADD | 3.197 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.397%
South Asian · 359/90,340 alleles
Filtering AF
0.363%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.35%
Overall
0.0264%
417/1,580,192 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.397% | 252 |
| Middle Eastern | 0.0333% | 3,003 |
| Remaining individualsnot grpmax-eligible | 0.0147% | 6,824 |
| European (non-Finnish) | 0.004% | 24,981 |
| Finnishnot grpmax-eligible | 0.00157% | 63,878 |
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
- C9
- Protein
- p.Thr24=
- Coding
- c.72G>A
- MANE Select
- NM_001737
- dbSNP
- rs552482219
- Type
- single nucleotide variant
- Location
- chr5:39364393 (GRCh38)
- Gene constraint
- LOEUF 1.223 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.32 · 9 PDB
Similar variants
- C9 c.871-2A>G Likely pathogenic ★★ same type
- C9 p.Arg116Ter Pathogenic/Likely pathogenic ★★ same type
- C9 p.Arg154Ter Pathogenic/Likely pathogenic ★★ same type
- C9 p.Arg194Ter Pathogenic/Likely pathogenic ★★ same type
- C9 p.Arg86Ter Pathogenic/Likely pathogenic ★★ same type
- C9 p.Cys54Ter Pathogenic/Likely pathogenic ★★ same type
- C9 c.1240+5G>T Uncertain significance ★★ same type
- C9 p.Ala497Val 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/c9-p-thr24 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown