HSPH1 p.Asp32=
c.96C>T · rs149981680 · VCV736620
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.198%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 5.951 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.198%
Middle Eastern · 12/6,062 alleles
Filtering AF
0.114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0895%
Overall
0.0201%
325/1,614,052 alleles · rare
exomes 285/1,461,776 · genomes 40/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.198% | 505 |
| Admixed American | 0.09% | 1,112 |
| Remaining individualsnot grpmax-eligible | 0.0576% | 1,736 |
| European (non-Finnish) | 0.0176% | 5,673 |
| African / African-American | 0.016% | 6,253 |
| South Asian | 0.0022% | 45,537 |
| Finnishnot grpmax-eligible | 0.00156% | 64,028 |
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
- HSPH1
- Protein
- p.Asp32=
- Coding
- c.96C>T
- MANE Select
- NM_006644
- dbSNP
- rs149981680
- Type
- single nucleotide variant
- Location
- chr13:31161487 (GRCh38)
- Gene constraint
- LOEUF 0.435 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.31 · 1 PDB
Similar variants
- HSPH1 p.Ala344Ser Uncertain significance ★★ ⚠ same type
- HSPH1 p.Arg781His Benign/Likely benign ★★ same type
- HSPH1 p.Glu575= Benign ★★ same type
- HSPH1 p.Leu435Val Benign ★★ same type
- HSPH1 p.Ala18Gly Uncertain significance ★ ⚠ same type
- HSPH1 p.Ala18Ser Uncertain significance ★ ⚠ same type
- HSPH1 p.Ala18Val Uncertain significance ★ ⚠ same type
- HSPH1 p.Ala27Val 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/hsph1-p-asp32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown