CALM3 p.Asp57=
c.171T>C · VCV3339755
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000424%, nfe)
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 -9.5 | GERP -3.7 |
| Overall | ||
| CADD | 3.041 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000424%
European (non-Finnish) · 5/1,179,964 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.000342%
5/1,461,806 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
- CALM3
- Protein
- p.Asp57=
- Coding
- c.171T>C
- MANE Select
- NM_005184
- Type
- single nucleotide variant
- Location
- chr19:46608333 (GRCh38)
- Gene constraint
- LOEUF 0.556 · pLI 0.93 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.45 · 26 PDB
- Residue 57
- a binding site; the ef-hand 2 domain; a β-strand
Similar variants
- CALM3 p.Asp94Ala Pathogenic/Likely pathogenic ★★ same type
- CALM3 p.Asp96His Pathogenic/Likely pathogenic ★★ same type
- CALM3 p.Glu141Lys Pathogenic ★★ same type
- CALM3 c.34+3G>A Uncertain significance ★★ same type
- CALM3 c.421+5G>A Uncertain significance ★★ same type
- CALM3 p.Ala103Thr Uncertain significance ★★ ⚠ same type
- CALM3 p.Ala148Thr Uncertain significance ★★ ⚠ same type
- CALM3 p.Arg107Cys 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/calm3-p-asp57 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown