CHD7 p.Arg1494=
c.4482A>C · rs1586420262 · VCV790264
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000255%, nfe)
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 0.6 | GERP -0.3, phastCons 0.93 |
| Overall | ||
| CADD | 7.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000255%
European (non-Finnish) · 3/1,174,784 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000187%
3/1,603,222 alleles · very rare
exomes 3/1,450,898 · genomes 0/152,324 · joint denominator
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.Arg1494=
- Coding
- c.4482A>C
- MANE Select
- NM_017780
- dbSNP
- rs1586420262
- Type
- single nucleotide variant
- Location
- chr8:60838204 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Similar variants
- CHD7 p.Arg1494Ter Pathogenic ★★ same residue
- CHD7 c.2097-2A>G Pathogenic ★★ same type
- CHD7 c.2238+1G>A Pathogenic ★★ same type
- CHD7 c.2377-1G>A Likely pathogenic ★★ same type
- CHD7 c.2613+1G>A Pathogenic/Likely pathogenic ★★ same type
- CHD7 c.2836-1G>A Pathogenic/Likely pathogenic ★★ same type
- CHD7 c.2836-2A>T Pathogenic ★★ same type
- CHD7 c.2957+2T>C Pathogenic ★★ same type
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-arg1494 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown