CAPN12 p.Phe680=
c.2040C>T · rs139997883 · VCV777472
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.91%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not looked up on this page · why |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.5 | GERP -4.5 |
| Overall | ||
| CADD | 0.029 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.91%
African / African-American · 1,430/75,034 alleles
Filtering AF
1.82%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.79%
Overall
0.108%
1,741/1,612,968 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.91% | 52 |
| Middle Eastern | 0.116% | 863 |
| Remaining individualsnot grpmax-eligible | 0.115% | 868 |
| Admixed American | 0.113% | 882 |
| European (non-Finnish) | 0.0137% | 7,284 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,596 |
| South Asian | 0.0011% | 91,000 |
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
- CAPN12
- Protein
- p.Phe680=
- Coding
- c.2040C>T
- MANE Select
- NM_004924 · reported on NM_144691
- dbSNP
- rs139997883
- Type
- single nucleotide variant
- Location
- chr19:38731141 (GRCh38)
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/capn12-p-phe680 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown