CD33 p.Thr192=
c.576T>C · rs116187588 · VCV783850
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.8%, 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 -8.2 | GERP -3.2 |
| Overall | ||
| CADD | 2.079 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.8%
African / African-American · 2,851/74,984 alleles
Filtering AF
3.69%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.64%
Overall
0.196%
3,165/1,614,060 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.8% | 26 |
| Remaining individualsnot grpmax-eligible | 0.227% | 440 |
| Admixed American | 0.215% | 465 |
| Middle Eastern | 0.0825% | 1,212 |
| South Asian | 0.00439% | 22,770 |
| European (non-Finnish) | 0.0028% | 35,758 |
| East Asian | 0.00223% | 44,880 |
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
- CD33
- Protein
- p.Thr192=
- Coding
- c.576T>C
- MANE Select
- NM_001772
- dbSNP
- rs116187588
- Type
- single nucleotide variant
- Location
- chr19:51225960 (GRCh38)
- Gene constraint
- LOEUF 1.072 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.30 · 11 PDB
- Residue 192
- a disulfide bond; the ig-like c2-type domain
Similar variants
- CD33 p.Asp51Asn Uncertain significance ★★ ⚠ same type
- CD33 c.924+295A>G Benign ★★ same type
- CD33 c.924+296C>T Benign ★★ same type
- CD33 c.924+2T>C Benign ★★ same type
- CD33 c.924+469G>C Benign ★★ same type
- CD33 c.*201G>C Benign ★★ same type
- CD33 p.Ala14Val Benign ★★ same type
- CD33 p.Ala65Pro Benign ★★ ⚠ 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/cd33-p-thr192 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown