C9 p.Asp104=
c.312C>T · rs747790831 · VCV1530768
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00833%, amr)
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 1.4 | GERP -2.6, phastCons 1 |
| Overall | ||
| CADD | 0.959 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00833%
Admixed American · 5/59,996 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.000558%
9/1,613,886 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00833% | 11,999 |
| African / African-American | 0.00534% | 18,722 |
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.Asp104=
- Coding
- c.312C>T
- MANE Select
- NM_001737
- dbSNP
- rs747790831
- Type
- single nucleotide variant
- Location
- chr5:39341572 (GRCh38)
- Gene constraint
- LOEUF 1.223 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.32 · 9 PDB
- Residue 104
- a disulfide bond; a β-strand; the ldl-receptor class a domain
Similar variants
- C9 p.Asp104Glu Uncertain significance ★ ⚠ same residue
- 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
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-asp104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown