ASPH c.790+42del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.3%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +42 | near-intronic (+42 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.085 | GERP 0.079, phastCons 0.003 |
| Overall | ||
| CADD | 1.625 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | AluSp sine, simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.3%
Admixed American · 358/15,586 alleles
Filtering AF
2.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.02%
Overall
1.38%
11,705/845,290 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 2.3% | 44 |
| South Asian | 2.02% | 49 |
| Ashkenazi Jewishnot grpmax-eligible | 1.8% | 56 |
| East Asian | 1.79% | 56 |
| Remaining individualsnot grpmax-eligible | 1.59% | 63 |
| Finnishnot grpmax-eligible | 1.37% | 73 |
| European (non-Finnish) | 1.33% | 75 |
| African / African-American | 0.724% | 138 |
| Middle Eastern | 0.657% | 152 |
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
- ASPH
- Coding
- c.790+42del
- MANE Select
- NM_004318
- dbSNP
- rs749849292
- Type
- Deletion
- Location
- chr8:61642846 (GRCh38)
- Gene constraint
- LOEUF 1.011 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.34 · 43 PDB
Similar variants
- ASPH p.Asn637fs Pathogenic ★ same type
- ASPH p.Asp720fs Likely pathogenic ★ same type
- ASPH p.Gly714fs Likely pathogenic ★ same type
- ASPH p.Ile497fs Likely pathogenic ★ same type
- ASPH p.Leu465fs Pathogenic ★ same type
- ASPH p.Lys391fs Likely pathogenic ★ same type
- ASPH p.Tyr583fs Likely pathogenic ★ same type
- ASPH p.Asp173fs Conflicting classifications of pathogenicity ★ 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/asph-c-790-plus-42del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown