CHD7 p.Pro174=
c.522G>A · rs577112542 · VCV695969
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0245%, eas)
Conditions
2
Inborn genetic diseases
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 -14 | GERP -4.8 |
| Overall | ||
| CADD | 0.046 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0245%
East Asian · 11/44,880 alleles
Filtering AF
0.0137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.00186%
30/1,613,636 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0245% | 4,080 |
| Admixed American | 0.0133% | 7,496 |
| African / African-American | 0.008% | 12,503 |
| South Asian | 0.0011% | 91,054 |
| European (non-Finnish) | 0.000339% | 294,945 |
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.Pro174=
- Coding
- c.522G>A
- MANE Select
- NM_017780
- dbSNP
- rs577112542
- Type
- single nucleotide variant
- Location
- chr8:60741954 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 174
- the 'disordered' region
Similar variants
- CHD7 p.Pro174Leu Benign/Likely benign ★★ same residue
- CHD7 p.Pro174Ser Uncertain significance ★ ⚠ same residue
- CHD7 p.Pro174fs Pathogenic ★★ 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
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-pro174 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown