CD9 c.447+8G>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.41%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +8 | near-intronic (+8 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.5 | GERP -3.4 |
| Overall | ||
| CADD | 0.022 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.41%
African / African-American · 1,060/75,054 alleles
Filtering AF
1.34%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.31%
Overall
0.101%
1,635/1,614,200 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.41% | 71 |
| East Asian | 0.942% | 106 |
| Middle Eastern | 0.198% | 505 |
| Remaining individualsnot grpmax-eligible | 0.0992% | 1,008 |
| Admixed American | 0.075% | 1,334 |
| South Asian | 0.00659% | 15,181 |
| European (non-Finnish) | 0.00229% | 43,705 |
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
- CD9
- Coding
- c.447+8G>A
- MANE Select
- NM_001769
- dbSNP
- rs11568266
- Type
- single nucleotide variant
- Location
- chr12:6235335 (GRCh38)
- Gene constraint
- LOEUF 0.555 · pLI 0.93 (gnomAD)
- Structure
- AlphaFold pLDDT 88.38 · 5 PDB
Similar variants
- CD9 p.Asn51Thr Uncertain significance ★ ⚠ same type
- CD9 p.Glu103Gln Uncertain significance ★ ⚠ same type
- CD9 p.Gly210Ala Uncertain significance ★ ⚠ same type
- CD9 p.Gly80Arg Uncertain significance ★ ⚠ same type
- CD9 p.Leu96Phe Uncertain significance ★ ⚠ same type
- CD9 p.Lys186Glu Uncertain significance ★ ⚠ same type
- CD9 p.Met227Leu Uncertain significance ★ ⚠ same type
- CD9 p.Met70Ile 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/cd9-c-447-plus-8g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown