CHD2 c.4413+38C>T
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 7.06%, afr) — 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 +38 | near-intronic (+38 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.88 | GERP -2.4 |
| Non-coding constraint | Z 1.92 | 1 kb window · o/e 0.85 · regional · uncalibrated |
| Overall | ||
| CADD | 7.066 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.06%
African / African-American · 5,268/74,626 alleles
Filtering AF
6.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.83%
Overall
0.373%
5,954/1,596,774 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 7.06% | 14 |
| Remaining individualsnot grpmax-eligible | 0.506% | 198 |
| Middle Eastern | 0.354% | 283 |
| Admixed American | 0.348% | 288 |
| South Asian | 0.0124% | 8,057 |
| European (non-Finnish) | 0.0117% | 8,536 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00345% | 28,948 |
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.4413+38C>T
- MANE Select
- NM_001271
- dbSNP
- rs76579099
- Type
- single nucleotide variant
- Location
- chr15:93004789 (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-4413-plus-38c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown