ASTN2 p.Arg1282=
c.3844C>A · rs73520334 · VCV792133
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.61%, 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 | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -3.5, phastCons 0.97 |
| Overall | ||
| CADD | 5.287 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.61%
African / African-American · 4,960/75,016 alleles
Filtering AF
6.46%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.4%
Overall
0.35%
5,643/1,614,008 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.61% | 15 |
| Remaining individualsnot grpmax-eligible | 0.45% | 222 |
| Admixed American | 0.403% | 248 |
| Middle Eastern | 0.33% | 303 |
| South Asian | 0.0132% | 7,589 |
| Finnishnot grpmax-eligible | 0.011% | 9,130 |
| European (non-Finnish) | 0.0103% | 9,752 |
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.Arg1282=
- Coding
- c.3844C>A
- MANE Select
- NM_001365068
- dbSNP
- rs73520334
- Type
- single nucleotide variant
- Location
- chr9:116426027 (GRCh38)
- Gene constraint
- LOEUF 0.473 · pLI 0.99 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.93 · 3 PDB
Similar variants
- ASTN2 p.Arg1282Gln Uncertain significance ★ ⚠ same residue
- ASTN2 p.Arg1282Trp 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
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-arg1282 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown