CHD2 c.2189+99del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 53.2%, 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 +99 | deep intronic (+99 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.16 | GERP -1.4 |
| Non-coding constraint | Z 2.00 | 1 kb window · o/e 0.84 · regional · uncalibrated |
| Overall | ||
| CADD | 0.595 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (T)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
53.2%
East Asian · 12,754/23,952 alleles
Filtering AF
52.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 52.2%
Overall
37.1%
225,779/607,908 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 53.2% | 2 |
| Admixed American | 43.9% | 2 |
| South Asian | 43.3% | 2 |
| Amishnot grpmax-eligible | 42.2% | 2 |
| Finnishnot grpmax-eligible | 41.8% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 40.9% | 2 |
| European (non-Finnish) | 36.4% | 3 |
| Remaining individualsnot grpmax-eligible | 36.2% | 3 |
| Middle Eastern | 33.3% | 3 |
| African / African-American | 26.9% | 4 |
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.2189+99del
- MANE Select
- NM_001271
- dbSNP
- rs144172255
- Type
- Deletion
- Location
- chr15:92967599 (GRCh38)
- Gene constraint
- LOEUF 0.174 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.81
Similar variants
- CHD2 p.Glu1412fs Pathogenic ★★ same type
- CHD2 p.Lys1393fs Pathogenic ★★ same type
- CHD2 p.Lys174_Val175insTer Pathogenic/Likely pathogenic ★★ same type
- CHD2 p.Pro399fs Pathogenic ★★ same type
- CHD2 c.1199-12del Benign/Likely benign ★★ same type
- CHD2 c.381+12del Likely benign ★★ same type
- CHD2 p.Lys1411del Benign/Likely benign ★★ same type
- CHD2 c.1151_1153+4del 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-2189-plus-99del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown