CHAD p.Pro349=
c.1047C>T · rs138527449 · VCV786655
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.15%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.358 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not looked up on this page · why |
| Constraint at this position | ||
| Conservation | phyloP 0.87 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 6.684 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.15%
African / African-American · 862/75,014 alleles
Filtering AF
1.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.06%
Overall
0.0603%
973/1,614,076 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.15% | 87 |
| Admixed American | 0.0833% | 1,200 |
| Remaining individualsnot grpmax-eligible | 0.0704% | 1,421 |
| Middle Eastern | 0.0495% | 2,021 |
| European (non-Finnish) | 0.0011% | 90,770 |
| South Asian | 0.0011% | 91,066 |
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
- CHAD
- Protein
- p.Pro349=
- Coding
- c.1047C>T
- MANE Select
- NM_025149 · reported on NM_001267
- dbSNP
- rs138527449
- Type
- single nucleotide variant
- Location
- chr17:50465331 (GRCh38)
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/chad-p-pro349 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown