CHD7 p.Ser175=
c.525G>A · VCV3667111
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00891%, eas)
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 -1.1 | GERP -4.8 |
| Overall | ||
| CADD | 6.073 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00891%
East Asian · 4/44,882 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.00105%
17/1,613,458 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00891% | 11,220 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,450 |
| European (non-Finnish) | 0.00102% | 98,314 |
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.Ser175=
- Coding
- c.525G>A
- MANE Select
- NM_017780
- Type
- single nucleotide variant
- Location
- chr8:60741957 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 175
- the 'disordered' region
Similar variants
- CHD7 p.Ser175Leu Benign ★ same residue
- 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
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-ser175 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown