ITGAM p.Ala762=
c.2286C>T · rs376515347 · VCV2085531
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00208%, nfe)
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 -0.49 | GERP -4.4 |
| Overall | ||
| CADD | 3.065 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00208%
European (non-Finnish) · 24/1,154,684 alleles
Filtering AF
0.00141%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00118%
Overall
0.00161%
25/1,557,438 alleles · very rare
exomes 23/1,405,264 · genomes 2/152,174 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00208% | 48,112 |
| African / African-American | 0.00137% | 72,842 |
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.Ala762=
- Coding
- c.2286C>T
- MANE Select
- NM_000632
- dbSNP
- rs376515347
- Type
- single nucleotide variant
- Location
- chr16:31324779 (GRCh38)
- Gene constraint
- LOEUF 0.678 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.30 · 31 PDB
- Residue 762
- a β-strand
Similar variants
- 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
- ITGAM p.Arg224Trp 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-ala762 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown