ASPN p.Asp50del
c.114TGA[12] · VCV3910744
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 19.1%, eas) — 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 | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.12 | GERP -0.84, phastCons 1 |
| Overall | ||
| CADD | 5.846 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (TCA)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
19.1%
East Asian · 7,512/39,294 alleles
Filtering AF
18.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 18.6%
Overall
5.81%
85,246/1,468,376 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 19.1% | 5 |
| South Asian | 9.19% | 11 |
| Ashkenazi Jewishnot grpmax-eligible | 9.18% | 11 |
| Amishnot grpmax-eligible | 8.24% | 12 |
| Remaining individualsnot grpmax-eligible | 6.65% | 15 |
| European (non-Finnish) | 5.53% | 18 |
| Middle Eastern | 4.91% | 20 |
| Admixed American | 3.47% | 29 |
| Finnishnot grpmax-eligible | 2.58% | 39 |
| African / African-American | 0.999% | 100 |
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
- ASPN
- Protein
- p.Asp50del
- Coding
- c.114TGA[12]
- MANE Select
- NM_017680
- Type
- Microsatellite
- Location
- chr9:92474743 (GRCh38)
- Gene constraint
- LOEUF 1.526 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.71
- Residue 50
- the 'disordered' region
Similar variants
- ASPN p.Asp50_Glu51insAspAspAspAsp Uncertain significance ★ same residue
- ASPN p.Asp50_Glu51insAspAsp Benign ★ same residue
- ASPN p.Asp50_Glu51insAspAspAsp Benign ★ same residue
- ASPN p.Asp50_Glu51insAspAspAspAspAspAsp Benign ★ same residue
- ASPN p.Asp38_Glu51= Benign ★ same type
- CENPP c.564+94884TCA[18] Benign 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/aspn-p-asp50del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown