CA2 c.663+282del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 9.06%, afr) — 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 +282 | deep intronic (+282 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -1.9 |
| Non-coding constraint | Z 1.65 | 1 kb window · o/e 0.87 · regional · uncalibrated |
| Overall | ||
| CADD | 0.399 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.06%
African / African-American · 3,639/40,148 alleles
Filtering AF
8.82%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.72%
Overall
2.69%
3,944/146,428 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 9.06% | 11 |
| Remaining individualsnot grpmax-eligible | 1.57% | 64 |
| Middle Eastern | 1.41% | 71 |
| Admixed American | 1.17% | 85 |
| South Asian | 0.526% | 190 |
| Finnishnot grpmax-eligible | 0.236% | 424 |
| East Asian | 0.0994% | 1,006 |
| European (non-Finnish) | 0.0677% | 1,477 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0585% | 1,709 |
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
- CA2
- Coding
- c.663+282del
- MANE Select
- NM_000067
- dbSNP
- rs11452517
- Type
- Deletion
- Location
- chr8:85477545 (GRCh38)
- Gene constraint
- LOEUF 1.491 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.38 · 1249 PDB
Similar variants
- CA2 p.Lys227fs Pathogenic/Likely pathogenic ★★ same type
- CA2 p.Lys224fs Likely pathogenic ★ same type
- CA2 p.Gly63_His64del Uncertain significance ★ same type
- CA2 c.35-18_35-17del Likely benign ★ same type
- CA2 c.351+19_351+21del Likely benign ★ same type
- CA2 c.351+21del Benign ★ same type
- CA2 c.352-10del Likely benign ★ same type
- CA2 c.508-204del 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/ca2-c-663-plus-282del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown