CHDH p.Val45=
c.135G>A · rs371031612 · VCV720569
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.727%, 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 0.62 | GERP 0.54, phastCons 1 |
| Overall | ||
| CADD | 9.581 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.727%
African / African-American · 543/74,684 alleles
Filtering AF
0.676%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.656%
Overall
0.0385%
612/1,591,500 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.727% | 138 |
| Admixed American | 0.0646% | 1,549 |
| Remaining individualsnot grpmax-eligible | 0.0404% | 2,475 |
| European (non-Finnish) | 0.00051% | 196,056 |
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
- CHDH
- Protein
- p.Val45=
- Coding
- c.135G>A
- MANE Select
- NM_018397
- dbSNP
- rs371031612
- Type
- single nucleotide variant
- Location
- chr3:53823874 (GRCh38)
- Gene constraint
- LOEUF 1.092 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.84
- Residue 45
- a binding site
Similar variants
- CHDH p.Pro396Leu Uncertain significance ★★ ⚠ same type
- CHDH c.704-3C>T Benign ★★ same type
- CHDH p.Gly235= Benign ★★ same type
- CHDH p.Ala13Val Uncertain significance ★ ⚠ same type
- CHDH p.Ala170Thr Uncertain significance ★ ⚠ same type
- CHDH p.Ala177Thr Uncertain significance ★ ⚠ same type
- CHDH p.Ala240Val Uncertain significance ★ ⚠ same type
- CHDH p.Ala31Val 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/chdh-p-val45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown