CHD3 p.Ala211=
c.633G>A · rs750749834 · VCV3037427
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.227%, eas)
Conditions
1
CHD3-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.087 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -9.7 | GERP -3.8 |
| Overall | ||
| CADD | 0.752 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.227%
East Asian · 102/44,844 alleles
Filtering AF
0.192%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.178%
Overall
0.00732%
118/1,611,508 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.227% | 440 |
| Remaining individualsnot grpmax-eligible | 0.00642% | 15,572 |
| Admixed American | 0.00167% | 59,732 |
| African / African-American | 0.00134% | 74,862 |
| European (non-Finnish) | 0.000848% | 117,908 |
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
- CHD3
- Protein
- p.Ala211=
- Coding
- c.633G>A
- MANE Select
- NM_001005273
- dbSNP
- rs750749834
- Type
- single nucleotide variant
- Location
- chr17:7893409 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
Disease context
CHD3-related disorder
Similar variants
- CHD3 p.Ala211Val Conflicting classifications of pathogenicity ★ same residue
- CHD3 p.Arg1172Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg1342Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg985Gln Pathogenic ★★ same condition
- CHD3 p.Arg1491His Uncertain significance ★★ ⚠ same condition
- CHD3 p.Arg684Ter Pathogenic ★ same condition
- CHD3 p.Glu1653Ter Likely pathogenic ★ same condition
- CHD3 p.Met1085Ile Likely pathogenic ★ 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/chd3-p-ala211 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown