Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 9 submitters
gnomAD v4.1
Common
common (popmax 99.8%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
2
Inborn genetic diseases
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 1.8 | GERP -3.8, phastCons 1 |
| Overall | ||
| CADD | 7.366 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
99.8%
East Asian · 44,743/44,818 alleles
Filtering AF
99.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 98.7%
Overall
83.7%
1,349,468/1,611,470 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 99.8% | 1 |
| Amishnot grpmax-eligible | 93.5% | 1 |
| Middle Eastern | 92.1% | 1 |
| Admixed American | 90.9% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 90.7% | 1 |
| South Asian | 90% | 1 |
| Remaining individualsnot grpmax-eligible | 84.3% | 1 |
| European (non-Finnish) | 83.9% | 1 |
| Finnishnot grpmax-eligible | 75.9% | 1 |
| African / African-American | 61.6% | 2 |
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
- CHD2
- Protein
- p.Glu683=
- Coding
- c.2049A>G
- MANE Select
- NM_001271
- dbSNP
- rs4777755
- Type
- single nucleotide variant
- Location
- chr15:92967373 (GRCh38)
- Gene constraint
- LOEUF 0.174 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.81
- Residue 683
- a UniProt-annotated variant site (in dee94); a UniProt-annotated variant site (found in a patient with progressive myoclonus epilepsy; uncertain significance)
Similar variants
- CHD2 c.1153+1G>C Pathogenic ★★ same condition
- CHD2 c.1809+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHD2 c.294+1G>T Likely pathogenic ★★ same condition
- CHD2 c.443+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHD2 c.693-1G>A Likely pathogenic ★★ same condition
- CHD2 p.Ala879Val Pathogenic/Likely pathogenic ★★ same condition
- CHD2 p.Arg1072Ter Pathogenic ★★ same condition
- CHD2 p.Arg1137Ter Pathogenic/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/chd2-p-glu683 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown