CHD2 c.3237+285C>T
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 58.5%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +285 | deep intronic (+285 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.051 | GERP -2.1 |
| Non-coding constraint | Z 2.46 | 1 kb window · o/e 0.79 · regional · uncalibrated |
| Overall | ||
| CADD | 4.938 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
58.5%
East Asian · 3,025/5,170 alleles
Filtering AF
56.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 56.1%
Overall
20.1%
30,517/152,182 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 58.5% | 2 |
| Admixed American | 27.7% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 24.3% | 4 |
| South Asian | 23.9% | 4 |
| Remaining individualsnot grpmax-eligible | 20.4% | 5 |
| European (non-Finnish) | 20.1% | 5 |
| Finnishnot grpmax-eligible | 19.7% | 5 |
| Amishnot grpmax-eligible | 17.8% | 6 |
| Middle Eastern | 14.6% | 7 |
| African / African-American | 11.8% | 9 |
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
- Coding
- c.3237+285C>T
- MANE Select
- NM_001271
- dbSNP
- rs12592212
- Type
- single nucleotide variant
- Location
- chr15:92984785 (GRCh38)
- Gene constraint
- LOEUF 0.174 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.81
Similar variants
- CHD2 c.1153+1G>C Pathogenic ★★ same type
- CHD2 c.1809+1G>A Pathogenic/Likely pathogenic ★★ same type
- CHD2 c.294+1G>T Likely pathogenic ★★ same type
- CHD2 c.443+1G>A Pathogenic/Likely pathogenic ★★ same type
- CHD2 c.693-1G>A Likely pathogenic ★★ same type
- CHD2 p.Ala879Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- CHD2 p.Arg1072Ter Pathogenic ★★ same type
- CHD2 p.Arg1137Ter Pathogenic/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/chd2-c-3237-plus-285c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown