CHD7 p.Phe890=
c.2670T>C · rs1285260989 · VCV2885060
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
CHARGE syndrome
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 1.9 | GERP 0.88, phastCons 1 |
| Overall | ||
| CADD | 11.88 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,968 alleles
Overall
0.000124%
2/1,611,182 alleles · very rare
exomes 2/1,458,940 · genomes 0/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 74,968 |
| European (non-Finnish) | 8.49e-05% | 1,178,450 |
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.Phe890=
- Coding
- c.2670T>C
- MANE Select
- NM_017780
- dbSNP
- rs1285260989
- Type
- single nucleotide variant
- Location
- chr8:60820063 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 890
- the chromo 2 domain
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-phe890 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown