ASPH p.Leu49=
c.147C>T · rs144828443 · VCV774242
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.49%, mid)
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 1.5 | GERP -4.4, phastCons 1 |
| Overall | ||
| CADD | 2.71 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.49%
Middle Eastern · 90/6,058 alleles
Filtering AF
1.24%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.15%
Overall
0.0438%
706/1,613,596 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.49% | 67 |
| South Asian | 0.239% | 418 |
| Remaining individualsnot grpmax-eligible | 0.101% | 992 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0947% | 1,056 |
| Admixed American | 0.06% | 1,666 |
| European (non-Finnish) | 0.022% | 4,555 |
| African / African-American | 0.016% | 6,250 |
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
- Protein
- p.Leu49=
- Coding
- c.147C>T
- MANE Select
- NM_004318
- dbSNP
- rs144828443
- Type
- single nucleotide variant
- Location
- chr8:61684145 (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.Arg735Trp Likely pathogenic ★★ same type
- ASPH p.Tyr565Ter Pathogenic/Likely pathogenic ★★ same type
- ASPH p.Arg425Cys Uncertain significance ★★ ⚠ same type
- ASPH p.Arg753His Uncertain significance ★★ ⚠ same type
- ASPH p.Glu506Val Uncertain significance ★★ same type
- ASPH p.Leu433Arg Uncertain significance ★★ ⚠ same type
- ASPH p.Ser299Asn Uncertain significance ★★ ⚠ same type
- ASPH p.Val214Met 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/asph-p-leu49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown