CHD5 p.Thr1815=
c.5445G>A · rs116111541 · VCV782353
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.55%, afr) — too common for a highly-penetrant pathogenic allele
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 1.2 | GERP -3.6, phastCons 1 |
| Overall | ||
| CADD | 14.31 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.55%
African / African-American · 4,898/74,782 alleles
Filtering AF
6.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.33%
Overall
0.356%
5,720/1,605,722 alleles · common
exomes 2,828/1,453,496 · genomes 2,892/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.55% | 15 |
| Admixed American | 0.484% | 207 |
| Remaining individualsnot grpmax-eligible | 0.42% | 238 |
| Middle Eastern | 0.183% | 545 |
| European (non-Finnish) | 0.0214% | 4,669 |
| South Asian | 0.0156% | 6,427 |
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.Thr1815=
- Coding
- c.5445G>A
- MANE Select
- NM_015557
- dbSNP
- rs116111541
- Type
- single nucleotide variant
- Location
- chr1:6109928 (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-thr1815 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown