CAPN15 p.Asp839=
c.2517C>T · rs376548766 · VCV3025451
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.101%, 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 -0.7 | GERP -3 |
| Overall | ||
| CADD | 4.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.101%
European (non-Finnish) · 1,173/1,158,390 alleles
Filtering AF
0.0964%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0945%
Overall
0.0849%
1,326/1,561,286 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.101% | 988 |
| South Asian | 0.0685% | 1,460 |
| African / African-American | 0.0541% | 1,849 |
| Remaining individualsnot grpmax-eligible | 0.0494% | 2,023 |
| East Asian | 0.0213% | 4,686 |
| Admixed American | 0.0206% | 4,860 |
| Middle Eastern | 0.0167% | 6,004 |
| Finnishnot grpmax-eligible | 0.00394% | 25,394 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00347% | 28,784 |
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
- CAPN15
- Protein
- p.Asp839=
- Coding
- c.2517C>T
- MANE Select
- NM_005632
- dbSNP
- rs376548766
- Type
- single nucleotide variant
- Location
- chr16:552310 (GRCh38)
- Gene constraint
- LOEUF 0.974 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.65
Similar variants
- CAPN15 c.2192+8C>T Uncertain significance ★★ same type
- CAPN15 p.Arg428Trp Uncertain significance ★★ ⚠ same type
- CAPN15 p.Arg867Cys Uncertain significance ★★ ⚠ same type
- CAPN15 p.Arg867His Uncertain significance ★★ ⚠ same type
- CAPN15 p.Cys363Arg Uncertain significance ★★ ⚠ same type
- CAPN15 p.Glu776Ala Uncertain significance ★★ ⚠ same type
- CAPN15 p.Val489Met Uncertain significance ★★ ⚠ same type
- CAPN15 p.Val841Met 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/capn15-p-asp839 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown