CAPN10 p.Thr570=
c.1710C>T · rs139964868 · VCV729047
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.578%, 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 -0.31 | GERP -2.9 |
| Overall | ||
| CADD | 5.086 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.578%
African / African-American · 434/75,062 alleles
Filtering AF
0.533%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.516%
Overall
0.0312%
503/1,613,590 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.578% | 173 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,083 |
| Admixed American | 0.0333% | 3,001 |
| South Asian | 0.00659% | 15,182 |
| European (non-Finnish) | 0.0011% | 90,772 |
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
- CAPN10
- Protein
- p.Thr570=
- Coding
- c.1710C>T
- MANE Select
- NM_023083
- dbSNP
- rs139964868
- Type
- single nucleotide variant
- Location
- chr2:240596909 (GRCh38)
- Gene constraint
- LOEUF 1.121 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.91
- Residue 570
- the 'domain iii 2' region
Similar variants
- CAPN10 p.Arg127Cys Uncertain significance ★★ ⚠ same type
- CAPN10 p.Gly526Ser Uncertain significance ★★ ⚠ same type
- CAPN10 p.Pro46Ser Uncertain significance ★★ ⚠ same type
- CAPN10 p.Thr339Met Uncertain significance ★★ ⚠ same type
- CAPN10 p.Ala477= Benign ★★ same type
- CAPN10 p.Ala477Thr Benign ★★ same type
- CAPN10 p.Arg555Cys Likely benign ★★ same type
- CAPN10 p.Glu276= Benign/Likely benign ★★ 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/capn10-p-thr570 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown