Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 16.2%, mid) — 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 +152 | deep intronic (+152 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -4.8 |
| Non-coding constraint | Z -0.22 | 1 kb window · o/e 1.02 · regional · uncalibrated |
| Overall | ||
| CADD | 0.007 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
16.2%
Middle Eastern · 594/3,658 alleles
Filtering AF
15.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 14.7%
Overall
7.12%
40,933/575,074 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 16.2% | 6 |
| African / African-American | 10.4% | 10 |
| Ashkenazi Jewishnot grpmax-eligible | 9.59% | 10 |
| South Asian | 8.95% | 11 |
| Remaining individualsnot grpmax-eligible | 7.81% | 13 |
| European (non-Finnish) | 7.37% | 14 |
| Admixed American | 6.04% | 17 |
| Amishnot grpmax-eligible | 5.15% | 19 |
| Finnishnot grpmax-eligible | 3.58% | 28 |
| East Asian | 0.235% | 426 |
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.551+152A>G
- MANE Select
- NM_001271
- dbSNP
- rs2272463
- Type
- single nucleotide variant
- Location
- chr15:92937777 (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-551-plus-152a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown