CHRM2 p.Tyr18del
c.52_54del · rs876657763 · VCV228516
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.4, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,062 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000137%
2/1,461,084 alleles · very rare
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
- CHRM2
- Protein
- p.Tyr18del
- Coding
- c.52_54del
- MANE Select
- NM_001006630
- dbSNP
- rs876657763
- Type
- Deletion
- Location
- chr7:137014916 (GRCh38)
- Gene constraint
- LOEUF 0.555 · pLI 0.92 (gnomAD)
- Structure
- AlphaFold pLDDT 72.87 · 17 PDB
- Residue 18
- an α-helix
Similar variants
- CHRM2 p.Tyr18= Likely benign ★★ same residue
- CHRM2 p.Val292_Ser294del Uncertain significance ★★ same type
- CHRM2 p.Asn6fs 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/chrm2-p-tyr18del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown