CHCHD10 p.Ala9=
c.27C>T · rs2145928012 · VCV3037190
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.81e-05%, nfe)
Conditions
1
CHCHD10-related disorder
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 0.3 | GERP -2.4, phastCons 0.9 |
| Overall | ||
| CADD | 9.44 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.81e-05%
European (non-Finnish) · 1/1,135,108 alleles
Overall
6.57e-05%
1/1,521,262 alleles · very rare
exomes 1/1,368,986 · genomes 0/152,276 · joint denominator
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
- CHCHD10
- Protein
- p.Ala9=
- Coding
- c.27C>T
- MANE Select
- NM_213720
- dbSNP
- rs2145928012
- Type
- single nucleotide variant
- Location
- chr22:23767848 (GRCh38)
- Gene constraint
- LOEUF 1.543 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.01 · 5 PDB
- Residue 9
- the 'disordered' region
Similar variants
- CHCHD10 p.Ala9Val Uncertain significance ★ ⚠ same residue
- CHCHD10 p.Ser59Leu Pathogenic/Likely pathogenic ★★ same condition
- CHCHD10 p.Pro36Ser Uncertain significance ★★ ⚠ same condition
- CHCHD10 c.41+7G>A Benign/Likely benign ★★ same condition
- CHCHD10 c.42-5C>G Conflicting classifications of pathogenicity ★ same condition
- CHCHD10 p.Ser113Cys Uncertain significance ⚠ same condition
- CHCHD10 p.Tyr134His Uncertain significance ⚠ same condition
- CHCHD10 c.-6G>T Likely benign same condition
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/chchd10-p-ala9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown