SIAE p.Ile32=
c.96C>T · rs755755030 · VCV2069871
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0072%, nfe)
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 |
|---|---|---|
| Pangolin | Δ0.24 | gain · loss 0.15 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP -0.49 | GERP -3.9 |
| Overall | ||
| CADD | 7.349 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0072%
European (non-Finnish) · 85/1,180,022 alleles
Filtering AF
0.00596%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00549%
Overall
0.00539%
87/1,613,936 alleles · very rare
exomes 76/1,461,806 · genomes 11/152,130 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0072% | 13,883 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| African / African-American | 0.00134% | 74,890 |
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
- SIAE
- Protein
- p.Ile32=
- Coding
- c.96C>T
- MANE Select
- NM_170601
- dbSNP
- rs755755030
- Type
- single nucleotide variant
- Location
- chr11:124669493 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.26
Similar variants
- SIAE p.Ile32Val Uncertain significance ★ ⚠ same residue
- SIAE p.Ala385Thr Uncertain significance ★★ ⚠ same type
- SIAE p.Arg301His Uncertain significance ★★ ⚠ same type
- SIAE p.Arg306Cys Uncertain significance ★★ ⚠ same type
- SIAE p.Cys196Phe Uncertain significance ★★ ⚠ same type
- SIAE p.Cys449Ser Uncertain significance ★★ ⚠ same type
- SIAE p.Gln309Arg Uncertain significance ★★ ⚠ same type
- SIAE p.Glu399Lys 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/siae-p-ile32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown