C9 p.Asn178=
c.534T>C · rs76184752 · VCV775072
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.74%, nfe)
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 -5.7 | GERP -4.2 |
| Overall | ||
| CADD | 0.199 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.74%
European (non-Finnish) · 20,564/1,178,684 alleles
Filtering AF
1.72%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.72%
Overall
1.39%
22,383/1,612,718 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.74% | 57 |
| Remaining individualsnot grpmax-eligible | 1.04% | 96 |
| Finnishnot grpmax-eligible | 0.561% | 178 |
| Admixed American | 0.503% | 199 |
| Amishnot grpmax-eligible | 0.439% | 228 |
| Middle Eastern | 0.412% | 242 |
| South Asian | 0.303% | 330 |
| African / African-American | 0.249% | 401 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0507% | 1,973 |
| East Asian | 0.00669% | 14,955 |
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.Asn178=
- Coding
- c.534T>C
- MANE Select
- NM_001737
- dbSNP
- rs76184752
- Type
- single nucleotide variant
- Location
- chr5:39331757 (GRCh38)
- Gene constraint
- LOEUF 1.223 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.32 · 9 PDB
- Residue 178
- the macpf domain; a disulfide bond
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-asn178 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown