CD33 c.924+469G>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 11.7%, afr) — 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 | ||
| Splice region | donor +469 | deep intronic (+469 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -0.43 |
| Non-coding constraint | Z -0.61 | 1 kb window · o/e 1.04 · regional · uncalibrated |
| Overall | ||
| CADD | 0.222 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11.7%
African / African-American · 5,695/48,594 alleles
Filtering AF
11.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 11.4%
Overall
2.02%
7,894/390,330 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 11.7% | 9 |
| Admixed American | 1.57% | 64 |
| Remaining individualsnot grpmax-eligible | 1.56% | 64 |
| Middle Eastern | 1.06% | 94 |
| European (non-Finnish) | 0.69% | 145 |
| Ashkenazi Jewishnot grpmax-eligible | 0.357% | 280 |
| Finnishnot grpmax-eligible | 0.151% | 660 |
| South Asian | 0.0365% | 2,742 |
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.924+469G>C
- MANE Select
- NM_001772
- dbSNP
- rs148707213
- Type
- single nucleotide variant
- Location
- chr19:51236145 (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.*201G>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-924-plus-469g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown