CAPN15 p.Pro949=
c.2847G>A · rs768639968 · VCV2645821
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.053%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.067 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.3 | GERP -3.1 |
| Overall | ||
| CADD | 0.139 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.053%
Admixed American · 27/50,942 alleles
Filtering AF
0.0374%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0321%
Overall
0.0156%
241/1,544,346 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.053% | 1,887 |
| Middle Eastern | 0.0411% | 2,431 |
| East Asian | 0.0196% | 5,106 |
| South Asian | 0.0155% | 6,458 |
| Remaining individualsnot grpmax-eligible | 0.015% | 6,652 |
| European (non-Finnish) | 0.0148% | 6,741 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0105% | 9,524 |
| African / African-American | 0.00959% | 10,431 |
| Finnishnot grpmax-eligible | 0.00361% | 27,734 |
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.Pro949=
- Coding
- c.2847G>A
- MANE Select
- NM_005632
- dbSNP
- rs768639968
- Type
- single nucleotide variant
- Location
- chr16:552714 (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-pro949 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown