CHRM3 p.Ser10=
c.30G>A · VCV4708311
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00401%, 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 0.46 | GERP -0.55, phastCons 0.47 |
| Overall | ||
| CADD | 7.741 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00401%
African / African-American · 3/74,874 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000744%
12/1,613,872 alleles · very rare
exomes 10/1,461,816 · genomes 2/152,056 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00401% | 24,958 |
| Admixed American | 0.00333% | 29,992 |
| European (non-Finnish) | 0.000593% | 168,569 |
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
- CHRM3
- Protein
- p.Ser10=
- Coding
- c.30G>A
- MANE Select
- NM_001375978
- Type
- single nucleotide variant
- Location
- chr1:239907481 (GRCh38)
- Gene constraint
- LOEUF 0.42 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.30 · 5 PDB
Similar variants
- CHRM3 p.Ser10Leu Uncertain significance ★ ⚠ same residue
- CHRM3 p.Ala585Thr Uncertain significance ★★ ⚠ same type
- CHRM3 p.Ala589Asp Uncertain significance ★★ ⚠ same type
- CHRM3 p.Arg310His Uncertain significance ★★ ⚠ same type
- CHRM3 p.Arg44Gln Uncertain significance ★★ ⚠ same type
- CHRM3 p.Arg569Cys Uncertain significance ★★ ⚠ same type
- CHRM3 p.Arg584His Uncertain significance ★★ ⚠ same type
- CHRM3 p.Asn339Lys 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/chrm3-p-ser10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown