CHD5 p.Ala433=
c.1299C>G · rs773642735 · VCV735683
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0103%, 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 0.56 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 11.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0103%
Admixed American · 6/58,124 alleles
Filtering AF
0.0044%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00303%
Overall
0.00094%
15/1,595,328 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0103% | 9,687 |
| African / African-American | 0.00807% | 12,398 |
| Remaining individualsnot grpmax-eligible | 0.00487% | 20,541 |
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
- CHD5
- Protein
- p.Ala433=
- Coding
- c.1299C>G
- MANE Select
- NM_004627 · reported on NM_015557
- dbSNP
- rs773642735
- Type
- single nucleotide variant
- Location
- chr1:6148938 (GRCh38)
- Structure
- AlphaFold pLDDT 78.15 · 4 PDB
Similar variants
- CHD5 p.Ala433Val Uncertain significance ★ ⚠ same residue
- CHD5 c.4171+1G>A Pathogenic/Likely pathogenic ★★ same type
- CHD5 p.Arg1618Ter Pathogenic/Likely pathogenic ★★ same type
- CHD5 p.Arg193Trp Pathogenic/Likely pathogenic ★★ same type
- CHD5 p.Pro1124Leu Pathogenic/Likely pathogenic ★★ same type
- CHD5 p.Ser912Phe Pathogenic/Likely pathogenic ★★ same type
- CHD5 c.2043+4A>T Uncertain significance ★★ same type
- CHD5 c.79+5G>A 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/chd5-p-ala433 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown