CHD5 p.Ser313=
c.939C>G · rs112932753 · VCV731575
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.31%, 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 -20 | GERP -4 |
| Overall | ||
| CADD | 0.065 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.31%
African / African-American · 979/74,952 alleles
Filtering AF
1.24%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.21%
Overall
0.0721%
1,160/1,608,938 alleles · low-frequency
exomes 593/1,456,662 · genomes 567/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.31% | 77 |
| Admixed American | 0.137% | 727 |
| Middle Eastern | 0.132% | 756 |
| Remaining individualsnot grpmax-eligible | 0.0964% | 1,038 |
| European (non-Finnish) | 0.00263% | 37,977 |
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.Ser313=
- Coding
- c.939C>G
- MANE Select
- NM_015557
- dbSNP
- rs112932753
- Type
- single nucleotide variant
- Location
- chr1:6151087 (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-ser313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown