CHAC1 p.Trp93Ter
c.279G>A · rs193920914 · VCV161528
Uncertain significance
No assertion criteria
Classification
Uncertain significance
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
prostate cancer
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (3 of 3) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 42.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CHAC1
- Protein
- p.Trp93Ter
- Coding
- c.279G>A
- MANE Select
- NM_024111
- dbSNP
- rs193920914
- Type
- single nucleotide variant
- Location
- chr15:40955384 (GRCh38)
- Gene constraint
- LOEUF 1.425 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.56
Similar variants
- CHAC1 c.10G>A Uncertain significance ★ same type
- CHAC1 c.8G>T Uncertain significance ★ same type
- CHAC1 c.-101C>G Uncertain significance ★ same type
- CHAC1 c.-101C>T Uncertain significance ★ same type
- CHAC1 c.-102C>G Uncertain significance ★ same type
- CHAC1 c.-15C>A Uncertain significance ★ same type
- CHAC1 c.-15C>G Uncertain significance ★ same type
- CHAC1 c.-32G>A 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/chac1-p-trp93ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown