CHCHD6 p.Val193=
c.579G>A · rs75184196 · VCV783402
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 7.85%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.91 | GERP -3.7, phastCons 0.3 |
| Overall | ||
| CADD | 4.524 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.85%
African / African-American · 5,882/74,924 alleles
Filtering AF
7.68%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.61%
Overall
0.426%
6,865/1,611,352 alleles · common
exomes 3,435/1,459,114 · genomes 3,430/152,238 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 7.85% | 13 |
| Admixed American | 0.681% | 147 |
| Remaining individualsnot grpmax-eligible | 0.63% | 159 |
| Middle Eastern | 0.526% | 190 |
| South Asian | 0.0155% | 6,458 |
| European (non-Finnish) | 0.0115% | 8,671 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,558 |
| East Asian | 0.00223% | 44,762 |
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
- CHCHD6
- Protein
- p.Val193=
- Coding
- c.579G>A
- MANE Select
- NM_032343
- dbSNP
- rs75184196
- Type
- single nucleotide variant
- Location
- chr3:126957428 (GRCh38)
- Gene constraint
- LOEUF 1.211 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.29
Similar variants
- CHCHD6 p.Ala111Ser Uncertain significance ★ ⚠ same type
- CHCHD6 p.Ala167Thr Uncertain significance ★ ⚠ same type
- CHCHD6 p.Ala202Pro Uncertain significance ★ ⚠ same type
- CHCHD6 p.Ala47Thr Uncertain significance ★ ⚠ same type
- CHCHD6 p.Arg136Trp Uncertain significance ★ ⚠ same type
- CHCHD6 p.Arg150Cys Uncertain significance ★ ⚠ same type
- CHCHD6 p.Arg151Cys Uncertain significance ★ ⚠ same type
- CHCHD6 p.Arg161His 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/chchd6-p-val193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown