CHD3 p.Glu35del
c.89AGG[5] · rs770383628 · VCV2647418
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.46%, sas)
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 3.5 | GERP 0.3, phastCons 1 |
| Overall | ||
| CADD | 15.66 | PHRED · no single calibrated threshold — expert panels disagree |
| 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
1.46%
South Asian · 852/58,292 alleles
Filtering AF
1.38%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.35%
Overall
0.619%
7,635/1,232,916 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.46% | 68 |
| Finnishnot grpmax-eligible | 0.926% | 108 |
| Ashkenazi Jewishnot grpmax-eligible | 0.801% | 125 |
| Admixed American | 0.783% | 128 |
| Remaining individualsnot grpmax-eligible | 0.717% | 139 |
| East Asian | 0.619% | 162 |
| European (non-Finnish) | 0.56% | 178 |
| Middle Eastern | 0.532% | 188 |
| African / African-American | 0.306% | 326 |
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.Glu35del
- Coding
- c.89AGG[5]
- MANE Select
- NM_001005273 · reported on NM_001005271
- dbSNP
- rs770383628
- Type
- Microsatellite
- Location
- chr17:7884894 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 35
- the 'disordered' region
Similar variants
- CHD3 p.Lys35Glu Uncertain significance ★ ⚠ same residue
- 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
- CHD3 p.Glu89fs 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-glu35del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown