ASTN2 p.Ser489=
c.1467C>T · rs61736198 · VCV773513
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.13%, eas)
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 -3.2 |
| Overall | ||
| CADD | 2.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.13%
East Asian · 947/44,458 alleles
Filtering AF
2.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.97%
Overall
0.567%
9,128/1,609,680 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.13% | 47 |
| Middle Eastern | 1.21% | 83 |
| South Asian | 0.723% | 138 |
| Remaining individualsnot grpmax-eligible | 0.653% | 153 |
| Admixed American | 0.555% | 180 |
| European (non-Finnish) | 0.547% | 183 |
| Ashkenazi Jewishnot grpmax-eligible | 0.542% | 184 |
| African / African-American | 0.121% | 824 |
| Finnishnot grpmax-eligible | 0.0375% | 2,666 |
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
- ASTN2
- Protein
- p.Ser489=
- Coding
- c.1467C>T
- MANE Select
- NM_001365068
- dbSNP
- rs61736198
- Type
- single nucleotide variant
- Location
- chr9:117008216 (GRCh38)
- Gene constraint
- LOEUF 0.473 · pLI 0.99 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.93 · 3 PDB
Similar variants
- TRIM32 p.Glu489Gly Uncertain significance ⚠ same residue
- TRIM32 p.Arg500Ter Pathogenic/Likely pathogenic ★★ same type
- TRIM32 p.Asp487Asn Pathogenic ★★ same type
- TRIM32 p.Lys401Ter Pathogenic ★★ same type
- TRIM32 p.Tyr226Ter Pathogenic/Likely pathogenic ★★ same type
- TRIM32 p.Tyr528Ter Likely pathogenic ★★ same type
- ASTN2 p.Val880Gly Uncertain significance ★★ ⚠ same type
- TRIM32 c.*152T>G 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/astn2-p-ser489 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown