ITGAM p.Thr833=
c.2499G>A · rs1143682 · VCV1164321
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 74.8%, eas) — too common for a highly-penetrant pathogenic allele
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 -2.3 | GERP -4.2 |
| Overall | ||
| CADD | 0.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
74.8%
East Asian · 33,531/44,852 alleles
Filtering AF
74.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 73.8%
Overall
35.2%
567,231/1,612,436 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 74.8% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 51.2% | 2 |
| Middle Eastern | 48% | 2 |
| Remaining individualsnot grpmax-eligible | 36.5% | 3 |
| European (non-Finnish) | 36.1% | 3 |
| Admixed American | 34.6% | 3 |
| Amishnot grpmax-eligible | 34.1% | 3 |
| Finnishnot grpmax-eligible | 33.4% | 3 |
| South Asian | 16.3% | 6 |
| African / African-American | 13% | 8 |
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
- ITGAM
- Protein
- p.Thr833=
- Coding
- c.2499G>A
- MANE Select
- NM_000632
- dbSNP
- rs1143682
- Type
- single nucleotide variant
- Location
- chr16:31325398 (GRCh38)
- Gene constraint
- LOEUF 0.678 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.30 · 31 PDB
Similar variants
- ITGAM p.Thr833Met Uncertain significance ★ ⚠ same residue
- ITGAM c.704+5G>A Uncertain significance ★★ same type
- ITGAM p.Ala31Thr Uncertain significance ★★ ⚠ same type
- ITGAM p.Ala433Val Uncertain significance ★★ ⚠ same type
- ITGAM p.Ala753Val Uncertain significance ★★ ⚠ same type
- ITGAM p.Ala943Val Uncertain significance ★★ ⚠ same type
- ITGAM p.Arg1003His Uncertain significance ★★ ⚠ same type
- ITGAM p.Arg131Trp 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/itgam-p-thr833 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown