CHD7 p.Pro1875=
c.5625T>C · rs764844969 · VCV260909
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.133%, mid)
Conditions
1
CHARGE syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.82 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 7.973 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.133%
Middle Eastern · 8/6,016 alleles
Filtering AF
0.0661%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0482%
Overall
0.00231%
36/1,557,042 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.133% | 752 |
| Admixed American | 0.0193% | 5,170 |
| Remaining individualsnot grpmax-eligible | 0.00497% | 20,123 |
| South Asian | 0.00356% | 28,117 |
| African / African-American | 0.00136% | 73,398 |
| European (non-Finnish) | 0.000957% | 104,505 |
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.Pro1875=
- Coding
- c.5625T>C
- MANE Select
- NM_017780
- dbSNP
- rs764844969
- Type
- single nucleotide variant
- Location
- chr8:60851279 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Similar variants
- CHD7 c.2097-2A>G Pathogenic ★★ same condition
- CHD7 c.2238+1G>A Pathogenic ★★ same condition
- CHD7 c.2377-1G>A Likely pathogenic ★★ same condition
- CHD7 c.2613+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHD7 c.2836-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHD7 c.2836-2A>T Pathogenic ★★ same condition
- CHD7 c.2957+2T>C Pathogenic ★★ same condition
- CHD7 c.3202-3T>G 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-pro1875 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown