CHTF18 p.Asn820=
c.2460C>T · rs115612427 · VCV711640
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.58%, 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 -8.1 | GERP -2.8 |
| Overall | ||
| CADD | 1.102 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.58%
African / African-American · 1,188/74,984 alleles
Filtering AF
1.51%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.48%
Overall
0.086%
1,375/1,599,062 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.58% | 63 |
| Middle Eastern | 0.149% | 671 |
| Admixed American | 0.109% | 919 |
| Remaining individualsnot grpmax-eligible | 0.101% | 988 |
| Finnishnot grpmax-eligible | 0.00581% | 17,206 |
| European (non-Finnish) | 0.00382% | 26,187 |
| South Asian | 0.0022% | 45,424 |
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.Asn820=
- Coding
- c.2460C>T
- MANE Select
- NM_022092
- dbSNP
- rs115612427
- Type
- single nucleotide variant
- Location
- chr16:796720 (GRCh38)
- Gene constraint
- LOEUF 1.712 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.97 · 10 PDB
Similar variants
- CHTF18 p.Ala770= Benign ★★ same type
- CHTF18 p.Arg804Cys 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.Leu797= 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-asn820 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown