CALCA p.Arg93Trp
c.277C>T · rs782816793 · VCV2350344
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0217%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.146 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.8 | GERP -1.1 |
| Overall | ||
| CADD | 14.94 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0217%
Admixed American · 13/60,006 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0101%
Overall
0.00192%
31/1,614,068 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0217% | 4,616 |
| East Asian | 0.00445% | 22,450 |
| South Asian | 0.00329% | 30,363 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
| African / African-American | 0.00267% | 37,459 |
| European (non-Finnish) | 0.000763% | 131,116 |
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
- CALCA
- Protein
- p.Arg93Trp
- Coding
- c.277C>T
- MANE Select
- NM_001741 · reported on NM_001033953
- dbSNP
- rs782816793
- Type
- single nucleotide variant
- Location
- chr11:14967805 (GRCh38)
- Gene constraint
- LOEUF 1.186 · pLI 0.13 (gnomAD)
- Structure
- AlphaFold pLDDT 64.12 · 6 PDB
- Residue 93
- an α-helix
Similar variants
- CALCA p.Arg93Gln Uncertain significance ★ same residue
- CALCA p.Phe106= Benign ★★ same type
- CALCA p.Ala118Val Uncertain significance ★ same type
- CALCA p.Ala11Thr Uncertain significance ★ ⚠ same type
- CALCA p.Ala31Ser Uncertain significance ★ ⚠ same type
- CALCA p.Ala47Pro Uncertain significance ★ ⚠ same type
- CALCA p.Ala47Val Uncertain significance ★ ⚠ same type
- CALCA p.Arg123Cys 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/calca-p-arg93trp (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown