CHCHD10 p.Pro23=
c.69G>C · rs1298499214 · VCV2652970
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.267%, 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 -1.5 | GERP -4.2 |
| Overall | ||
| CADD | 5.322 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.267%
European (non-Finnish) · 980/367,020 alleles
Filtering AF
0.253%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.248%
Overall
0.201%
1,085/540,608 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.267% | 375 |
| Remaining individualsnot grpmax-eligible | 0.251% | 399 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0868% | 1,152 |
| Middle Eastern | 0.0664% | 1,506 |
| East Asian | 0.0558% | 1,792 |
| South Asian | 0.0537% | 1,864 |
| African / African-American | 0.0328% | 3,052 |
| Finnishnot grpmax-eligible | 0.0128% | 7,833 |
| Admixed American | 0.0105% | 9,505 |
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.Pro23=
- Coding
- c.69G>C
- MANE Select
- NM_213720
- dbSNP
- rs1298499214
- Type
- single nucleotide variant
- Location
- chr22:23767566 (GRCh38)
- Gene constraint
- LOEUF 1.543 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.01 · 5 PDB
- Residue 23
- the 'disordered' region
Similar variants
- CHCHD10 p.Pro23Thr Uncertain significance ★★ ⚠ same residue
- CHCHD10 p.Ser59Leu Pathogenic/Likely pathogenic ★★ same type
- CHCHD10 c.262-3C>G Uncertain significance ★★ same type
- CHCHD10 c.409+1G>A Uncertain significance ★★ same type
- CHCHD10 p.Ala31Val Uncertain significance ★★ ⚠ same type
- CHCHD10 p.Ala35Thr Uncertain significance ★★ ⚠ same type
- CHCHD10 p.Ala49Val Uncertain significance ★★ ⚠ same type
- CHCHD10 p.Arg11Gly 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/chchd10-p-pro23 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown