CAPN12 c.237+207T>C
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 11.2%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +207 | deep intronic (+207 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP -0.59 |
| Overall | ||
| CADD | 4.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11.2%
East Asian · 349/3,110 alleles
Filtering AF
10.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.87%
Overall
3.48%
3,663/105,298 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 11.2% | 9 |
| African / African-American | 9.04% | 11 |
| South Asian | 7.71% | 13 |
| Admixed American | 5.17% | 19 |
| Remaining individualsnot grpmax-eligible | 3.22% | 31 |
| Middle Eastern | 2.98% | 34 |
| Ashkenazi Jewishnot grpmax-eligible | 1.42% | 70 |
| Finnishnot grpmax-eligible | 0.615% | 163 |
| European (non-Finnish) | 0.482% | 208 |
| Amishnot grpmax-eligible | 0.253% | 396 |
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
- Coding
- c.237+207T>C
- MANE Select
- NM_144691
- dbSNP
- rs57341847
- Type
- single nucleotide variant
- Location
- chr19:38743722 (GRCh38)
- Gene constraint
- LOEUF 1.398 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.63
Similar variants
- CAPN12 c.1362+80A>G Benign ★★ same type
- CAPN12 c.1374+85A>C Benign ★★ same type
- CAPN12 c.1583+12G>A Benign ★★ same type
- CAPN12 c.1584-39C>T Benign ★★ same type
- CAPN12 c.1686+152A>G Benign ★★ same type
- CAPN12 c.1745-17C>T Benign ★★ same type
- CAPN12 c.1815+25G>A Benign ★★ same type
- CAPN12 c.1815+57C>T 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/capn12-c-237-plus-207t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown