APC2 p.Ala229=
c.687G>A · rs80142793 · VCV2043996
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.09%, nfe)
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 -4 | GERP -2.5 |
| Overall | ||
| CADD | 3.931 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.09%
European (non-Finnish) · 24,509/1,171,430 alleles
Filtering AF
2.07%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.06%
Overall
1.67%
26,533/1,591,512 alleles · low-frequency
exomes 24,889/1,439,188 · genomes 1,644/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 2.09% | 48 |
| Remaining individualsnot grpmax-eligible | 1.35% | 74 |
| Finnishnot grpmax-eligible | 0.535% | 187 |
| Ashkenazi Jewishnot grpmax-eligible | 0.483% | 207 |
| Admixed American | 0.353% | 283 |
| South Asian | 0.329% | 304 |
| African / African-American | 0.316% | 317 |
| Middle Eastern | 0.167% | 599 |
| Amishnot grpmax-eligible | 0.11% | 912 |
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
- APC2
- Protein
- p.Ala229=
- Coding
- c.687G>A
- MANE Select
- NM_005883
- dbSNP
- rs80142793
- Type
- single nucleotide variant
- Location
- chr19:1456123 (GRCh38)
- Gene constraint
- LOEUF 0.961 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 48.87
Similar variants
- APC2 p.Ala1059Glu Uncertain significance ★★ ⚠ same type
- APC2 p.Ala1103Thr Uncertain significance ★★ ⚠ same type
- APC2 p.Ala1116Val Uncertain significance ★★ ⚠ same type
- APC2 p.Ala126Ser Uncertain significance ★★ ⚠ same type
- APC2 p.Ala1311Thr Uncertain significance ★★ ⚠ same type
- APC2 p.Ala1359Val Uncertain significance ★★ ⚠ same type
- APC2 p.Ala1438Thr Uncertain significance ★★ ⚠ same type
- APC2 p.Ala1492Glu 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/apc2-p-ala229 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown