Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.977%, afr)
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 -13 | GERP -3.2 |
| Overall | ||
| CADD | 0.008 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.977%
African / African-American · 732/74,934 alleles
Filtering AF
0.918%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.895%
Overall
0.0563%
909/1,613,846 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.977% | 102 |
| Ashkenazi Jewishnot grpmax-eligible | 0.155% | 643 |
| Admixed American | 0.0817% | 1,224 |
| Remaining individualsnot grpmax-eligible | 0.0736% | 1,359 |
| Middle Eastern | 0.066% | 1,516 |
| European (non-Finnish) | 0.00271% | 36,873 |
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
- ITGAL
- Protein
- p.Ser891=
- Coding
- c.2673G>T
- MANE Select
- NM_002209
- dbSNP
- rs7201914
- Type
- single nucleotide variant
- Location
- chr16:30510934 (GRCh38)
- Gene constraint
- LOEUF 0.595 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.77 · 41 PDB
Similar variants
- ITGAL p.Ser891Leu Likely benign ★ same residue
- ITGAL c.1213+9T>G Benign ★★ same type
- ITGAL p.Ala307= Benign ★★ same type
- ITGAL p.Arg1020His Benign/Likely benign ★★ ⚠ same type
- ITGAL p.Pro1152= Benign ★★ same type
- ITGAL p.Ala1045Pro Uncertain significance ★ ⚠ same type
- ITGAL p.Ala1072Thr Uncertain significance ★ ⚠ same type
- ITGAL p.Ala1127Pro 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/itgal-p-ser891 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown