AZIN2 p.Ser254=
c.762C>T · rs115719263 · VCV788074
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.465%, afr)
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 2.9 | GERP 0.85, phastCons 1 |
| Overall | ||
| CADD | 10.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.465%
African / African-American · 349/75,060 alleles
Filtering AF
0.425%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.409%
Overall
0.0382%
616/1,614,218 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.465% | 215 |
| Admixed American | 0.0466% | 2,144 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,156 |
| South Asian | 0.0242% | 4,140 |
| Middle Eastern | 0.0165% | 6,062 |
| European (non-Finnish) | 0.0154% | 6,484 |
| East Asian | 0.00891% | 11,223 |
| Finnishnot grpmax-eligible | 0.00156% | 64,030 |
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
- AZIN2
- Protein
- p.Ser254=
- Coding
- c.762C>T
- MANE Select
- NM_052998
- dbSNP
- rs115719263
- Type
- single nucleotide variant
- Location
- chr1:33096715 (GRCh38)
- Gene constraint
- LOEUF 0.797 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.94
Similar variants
- TRIM62 p.Arg254Trp Uncertain significance ★ ⚠ same residue
- AZIN2 p.His188Asn Benign ★★ same type
- TRIM62 p.Glu234= Benign ★★ same type
- TRIM62 p.Val473Ile Benign ★★ same type
- AZIN2 p.Ala112Thr Uncertain significance ★ ⚠ same type
- AZIN2 p.Arg217Gln Uncertain significance ★ ⚠ same type
- AZIN2 p.Arg217Trp Uncertain significance ★ ⚠ same type
- AZIN2 p.Arg412Trp 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/azin2-p-ser254 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown