CA2 c.663+113T>C
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 15.1%, 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 +113 | deep intronic (+113 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.9 | GERP -2.9 |
| Non-coding constraint | Z 1.65 | 1 kb window · o/e 0.87 · regional · uncalibrated |
| Overall | ||
| CADD | 0.012 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
15.1%
African / African-American · 10,152/67,224 alleles
Filtering AF
14.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 14.8%
Overall
0.971%
11,816/1,217,434 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 15.1% | 7 |
| Admixed American | 1.2% | 83 |
| Remaining individualsnot grpmax-eligible | 1.18% | 84 |
| Middle Eastern | 1.02% | 98 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0517% | 1,936 |
| South Asian | 0.0412% | 2,427 |
| European (non-Finnish) | 0.0344% | 2,904 |
| East Asian | 0.00233% | 42,862 |
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+113T>C
- MANE Select
- NM_000067
- dbSNP
- rs76261710
- Type
- single nucleotide variant
- Location
- chr8:85477388 (GRCh38)
- Gene constraint
- LOEUF 1.491 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.38 · 1249 PDB
Similar variants
- CA2 c.232+1G>A Pathogenic ★★ same type
- CA2 p.Gln92Pro Likely pathogenic ★★ same type
- CA2 p.Glu204Ter Pathogenic/Likely pathogenic ★★ same type
- CA2 p.Tyr193Ter Likely pathogenic ★★ same type
- CA2 p.Arg181Cys Uncertain significance ★★ ⚠ same type
- CA2 p.Arg181His Uncertain significance ★★ ⚠ same type
- CA2 p.Arg226His Uncertain significance ★★ ⚠ same type
- CA2 p.Arg245Cys 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/ca2-c-663-plus-113t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown