CHD5 p.Ser91=
c.273T>C · VCV4533985
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00682%, sas)
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 -3.9 | GERP -3.6 |
| Overall | ||
| CADD | 3.678 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00682%
South Asian · 6/87,946 alleles
Filtering AF
0.00295%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00201%
Overall
0.00245%
39/1,589,230 alleles · very rare
exomes 36/1,437,394 · genomes 3/151,836 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00682% | 14,658 |
| European (non-Finnish) | 0.00257% | 38,836 |
| Admixed American | 0.00174% | 57,626 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,484 |
| African / African-American | 0.00135% | 74,256 |
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.Ser91=
- Coding
- c.273T>C
- MANE Select
- NM_015557
- Type
- single nucleotide variant
- Location
- chr1:6159450 (GRCh38)
- Structure
- AlphaFold pLDDT 78.15 · 4 PDB
- Residue 91
- an α-helix; the 'interaction with get3/trc40' region
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-ser91 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown