CHD5 p.Ala1809=
c.5427C>T · rs201155895 · VCV750465
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0537%, afr)
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 -1.9 | GERP -4 |
| Overall | ||
| CADD | 7.451 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0537%
African / African-American · 40/74,502 alleles
Filtering AF
0.0404%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0359%
Overall
0.0121%
192/1,589,490 alleles · ultra-rare
exomes 159/1,437,220 · genomes 33/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0537% | 1,863 |
| European (non-Finnish) | 0.0121% | 8,232 |
| Remaining individualsnot grpmax-eligible | 0.00975% | 10,256 |
| Admixed American | 0.0035% | 28,575 |
| East Asian | 0.00224% | 44,602 |
| South Asian | 0.00116% | 86,368 |
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
- CHD5
- Protein
- p.Ala1809=
- Coding
- c.5427C>T
- MANE Select
- NM_015557
- dbSNP
- rs201155895
- Type
- single nucleotide variant
- Location
- chr1:6109946 (GRCh38)
- Structure
- AlphaFold pLDDT 78.15 · 4 PDB
Similar variants
- CHD5 c.4171+1G>A Pathogenic/Likely pathogenic ★★ same type
- CHD5 p.Arg1618Ter Pathogenic/Likely pathogenic ★★ same type
- CHD5 p.Arg193Trp Pathogenic/Likely pathogenic ★★ same type
- CHD5 p.Pro1124Leu Pathogenic/Likely pathogenic ★★ same type
- CHD5 p.Ser912Phe Pathogenic/Likely pathogenic ★★ same type
- CHD5 c.2043+4A>T Uncertain significance ★★ same type
- CHD5 c.79+5G>A Uncertain significance ★★ same type
- CHD5 p.Ala1435Thr Uncertain significance ★★ ⚠ 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/chd5-p-ala1809 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown