CHD7 p.Pro2884=
c.8652C>G · rs761229966 · VCV1764191
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 9.117 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,898 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,613,894 alleles · very rare
exomes 2/1,461,682 · genomes 1/152,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,898 |
| European (non-Finnish) | 0.00017% | 589,939 |
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
- CHD7
- Protein
- p.Pro2884=
- Coding
- c.8652C>G
- MANE Select
- NM_017780
- dbSNP
- rs761229966
- Type
- single nucleotide variant
- Location
- chr8:60865591 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Similar variants
- CHD7 p.Pro2884Arg Uncertain significance ★★ ⚠ same residue
- CHD7 p.Arg1494Ter Pathogenic ★★ same condition
- CHD7 p.Arg157Ter Pathogenic ★★ same condition
- CHD7 p.Arg2024Ter Pathogenic ★★ same condition
- CHD7 p.Arg2098Ter Pathogenic ★★ same condition
- CHD7 p.Arg2428Ter Pathogenic ★★ same condition
- CHD7 p.Arg312Ter Pathogenic ★★ same condition
- CHD7 p.Cys1101Tyr Pathogenic/Likely pathogenic ★★ same condition
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/chd7-p-pro2884 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown