Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.13%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.32 | GERP -0.83 |
| Overall | ||
| CADD | 10.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.13%
African / African-American · 2,343/74,858 alleles
Filtering AF
3.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.98%
Overall
0.164%
2,632/1,609,206 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.13% | 32 |
| Admixed American | 0.208% | 480 |
| Remaining individualsnot grpmax-eligible | 0.194% | 515 |
| Middle Eastern | 0.153% | 654 |
| South Asian | 0.011% | 9,098 |
| European (non-Finnish) | 0.00204% | 48,990 |
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
- CD63
- Coding
- c.426+9G>C
- MANE Select
- NM_001780
- dbSNP
- rs2231466
- Type
- single nucleotide variant
- Location
- chr12:55726691 (GRCh38)
- Gene constraint
- LOEUF 0.8 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.82 · 2 PDB
Similar variants
- CD63 p.Asn129= Benign ★★ same type
- RDH5 c.570-8G>C Benign/Likely benign ★★ same type
- CD63 p.Arg108Ser Uncertain significance ★ ⚠ same type
- CD63 p.Arg164Gln Uncertain significance ★ ⚠ same type
- CD63 p.Asn130His Uncertain significance ★ ⚠ same type
- CD63 p.Gln122His Uncertain significance ★ ⚠ same type
- CD63 p.Glu189Lys Uncertain significance ★ ⚠ same type
- CD63 p.Glu217Lys 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/cd63-c-426-plus-9g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown