CHD3 p.Asp29del
c.84CGA[1] · rs2544589498 · VCV2505752
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.3 | GERP 0.27, phastCons 1 |
| Region caveats | ||
| Repeat context | tandem | GA-rich low complexity, simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
European (non-Finnish) · 11/998,830 alleles
Filtering AF
0.000591%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000432%
Overall
0.000936%
11/1,175,102 alleles · very rare
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.Asp29del
- Coding
- c.84CGA[1]
- MANE Select
- NM_001005273 · reported on NM_001005271
- dbSNP
- rs2544589498
- Type
- Microsatellite
- Location
- chr17:7884890 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 29
- the 'disordered' region
Similar variants
- CHD3 p.Asp29Glu Uncertain significance ★ same residue
- CHD3 p.Glu35del Benign/Likely benign ★★ same type
- CHD3 p.Pro80_Pro82del Likely benign ★★ same type
- CHD3 p.Pro82_Leu83insPro Benign/Likely benign ★★ same type
- CHD3 p.Pro82del Benign/Likely benign ★★ same type
- CHD3 p.Arg933fs Likely pathogenic ★ same type
- CHD3 p.Gln1438fs Likely pathogenic ★ same type
- CHD3 p.Glu549fs Likely pathogenic ★ 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/chd3-p-asp29del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown