CAPN15 p.Phe879=
c.2637C>T · rs148358614 · VCV2645815
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.46%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.2 | GERP -3 |
| Overall | ||
| CADD | 6.053 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.46%
South Asian · 1,325/91,062 alleles
Filtering AF
1.39%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.36%
Overall
0.718%
11,565/1,610,064 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.46% | 69 |
| European (non-Finnish) | 0.734% | 136 |
| Finnishnot grpmax-eligible | 0.728% | 137 |
| East Asian | 0.702% | 142 |
| Ashkenazi Jewishnot grpmax-eligible | 0.653% | 153 |
| Remaining individualsnot grpmax-eligible | 0.58% | 172 |
| Middle Eastern | 0.248% | 404 |
| Admixed American | 0.245% | 408 |
| African / African-American | 0.137% | 728 |
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.Phe879=
- Coding
- c.2637C>T
- MANE Select
- NM_005632
- dbSNP
- rs148358614
- Type
- single nucleotide variant
- Location
- chr16:552430 (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-phe879 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown