CD33 c.*201G>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 34.8%, amr) — 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 0.085 | GERP -2.3 |
| Non-coding constraint | Z 1.48 | 1 kb window · o/e 0.89 · regional · uncalibrated |
| Overall | ||
| CADD | 1.742 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
34.8%
Admixed American · 8,153/23,444 alleles
Filtering AF
34.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 33.9%
Overall
12.5%
54,034/433,648 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 34.8% | 3 |
| East Asian | 28.5% | 4 |
| African / African-American | 27.6% | 4 |
| Remaining individualsnot grpmax-eligible | 12.3% | 8 |
| South Asian | 9.71% | 10 |
| Middle Eastern | 7.85% | 13 |
| Ashkenazi Jewishnot grpmax-eligible | 7.18% | 14 |
| European (non-Finnish) | 7.05% | 14 |
| Finnishnot grpmax-eligible | 5.89% | 17 |
| Amishnot grpmax-eligible | 3.51% | 29 |
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
- Coding
- c.*201G>C
- MANE Select
- NM_001772
- dbSNP
- rs1803254
- Type
- single nucleotide variant
- Location
- chr19:51239889 (GRCh38)
- Gene constraint
- LOEUF 1.072 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.30 · 11 PDB
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 p.Ala14Val Benign ★★ ⚠ same type
- CD33 p.Ala65Pro Benign ★★ ⚠ same type
- CD33 p.Arg62Gln Likely 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-c-star-201g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown