CD33 p.Gly13=
c.39G>A · rs143114570 · VCV717093
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.55%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.25 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.33 | GERP -3.6 |
| Overall | ||
| CADD | 6.664 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.55%
African / African-American · 1,163/75,036 alleles
Filtering AF
1.48%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.45%
Overall
0.0803%
1,295/1,613,328 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.55% | 65 |
| Middle Eastern | 0.099% | 1,010 |
| Admixed American | 0.0833% | 1,200 |
| Remaining individualsnot grpmax-eligible | 0.0832% | 1,201 |
| South Asian | 0.0022% | 45,523 |
| European (non-Finnish) | 0.00178% | 56,167 |
| Finnishnot grpmax-eligible | 0.00156% | 63,898 |
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.Gly13=
- Coding
- c.39G>A
- MANE Select
- NM_001772
- dbSNP
- rs143114570
- Type
- single nucleotide variant
- Location
- chr19:51225219 (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 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-gly13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown