CHD2 c.1809+13T>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.83e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +13 | near-intronic (+13 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.11 | GERP -0.25, phastCons 0.001 |
| Non-coding constraint | Z -0.41 | 1 kb window · o/e 1.03 · regional · uncalibrated |
| Overall | ||
| CADD | 7.523 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.83e-05%
European (non-Finnish) · 1/1,133,024 alleles
Overall
7.19e-05%
1/1,391,440 alleles · very rare
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.1809+13T>C
- MANE Select
- NM_001271
- dbSNP
- rs1555440769
- Type
- single nucleotide variant
- Location
- chr15:92955525 (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-1809-plus-13t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown