CHTF18 p.Leu797=
c.2391C>T · rs114461038 · VCV781318
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.34%, 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 -7 | GERP -2.8 |
| Overall | ||
| CADD | 0.053 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.34%
African / African-American · 3,251/74,888 alleles
Filtering AF
4.22%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.17%
Overall
0.24%
3,850/1,606,944 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.34% | 23 |
| Remaining individualsnot grpmax-eligible | 0.365% | 274 |
| Admixed American | 0.364% | 275 |
| Middle Eastern | 0.182% | 550 |
| European (non-Finnish) | 0.0116% | 8,595 |
| South Asian | 0.00779% | 12,830 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0034% | 29,452 |
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
- CHTF18
- Protein
- p.Leu797=
- Coding
- c.2391C>T
- MANE Select
- NM_022092
- dbSNP
- rs114461038
- Type
- single nucleotide variant
- Location
- chr16:796012 (GRCh38)
- Gene constraint
- LOEUF 1.712 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.97 · 10 PDB
- Residue 797
- an α-helix
Similar variants
- CHTF18 p.Ala770= Benign ★★ same type
- CHTF18 p.Arg804Cys Benign ★★ same type
- CHTF18 p.Asn820= Benign ★★ same type
- CHTF18 p.Asp284Glu Benign ★★ same type
- CHTF18 p.Glu233Lys Benign ★★ same type
- CHTF18 p.His179= Benign ★★ same type
- CHTF18 p.Leu541= Benign ★★ same type
- CHTF18 p.Lys324= Benign ★★ 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/chtf18-p-leu797 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown