CAPN2 p.Asp48=
c.144C>T · rs28370008 · VCV715900
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.04%, 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 0.29 | GERP 1, phastCons 0.99 |
| Overall | ||
| CADD | 11.84 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.04%
African / African-American · 1,479/72,398 alleles
Filtering AF
1.96%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.92%
Overall
0.102%
1,605/1,578,796 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.04% | 49 |
| Remaining individualsnot grpmax-eligible | 0.101% | 986 |
| Admixed American | 0.0912% | 1,097 |
| Middle Eastern | 0.0334% | 2,990 |
| South Asian | 0.00233% | 42,876 |
| European (non-Finnish) | 0.000773% | 129,445 |
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
- CAPN2
- Protein
- p.Asp48=
- Coding
- c.144C>T
- MANE Select
- NM_001748
- dbSNP
- rs28370008
- Type
- single nucleotide variant
- Location
- chr1:223712784 (GRCh38)
- Gene constraint
- LOEUF 1.026 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.48 · 3 PDB
- Residue 48
- the calpain catalytic domain
Similar variants
- CAPN2 p.Ala248Thr Uncertain significance ★★ ⚠ same type
- CAPN2 p.Gly72Asp Uncertain significance ★★ ⚠ same type
- CAPN2 p.Lys677Gln Benign ★★ same type
- CAPN2 p.Ala101Pro Uncertain significance ★ ⚠ same type
- CAPN2 p.Ala171Asp Uncertain significance ★ ⚠ same type
- CAPN2 p.Ala194Ser Uncertain significance ★ ⚠ same type
- CAPN2 p.Ala247Pro Uncertain significance ★ same type
- CAPN2 p.Ala371Thr 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/capn2-p-asp48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown