CD80 p.Leu99=
c.297C>G · rs116944420 · VCV780106
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.02%, eas)
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 0.037 | GERP -4.5, phastCons 0.44 |
| Overall | ||
| CADD | 1.516 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.02%
East Asian · 457/44,886 alleles
Filtering AF
0.941%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.911%
Overall
0.0419%
677/1,614,134 alleles · low-frequency
exomes 555/1,461,836 · genomes 122/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.02% | 98 |
| Remaining individualsnot grpmax-eligible | 0.16% | 625 |
| South Asian | 0.0725% | 1,380 |
| African / African-American | 0.0493% | 2,028 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.01% | 10,002 |
| European (non-Finnish) | 0.000847% | 117,998 |
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
- CD80
- Protein
- p.Leu99=
- Coding
- c.297C>G
- MANE Select
- NM_005191
- dbSNP
- rs116944420
- Type
- single nucleotide variant
- Location
- chr3:119544671 (GRCh38)
- Gene constraint
- LOEUF 0.818 · pLI 0.10 (gnomAD)
- Structure
- AlphaFold pLDDT 86.17 · 6 PDB
- Residue 99
- a turn; the ig-like v-type domain
Similar variants
- CD80 c.*214T>G Benign ★★ same type
- CD80 p.His222Tyr Benign ★★ same type
- CD80 p.Arg107His Uncertain significance ★ ⚠ same type
- CD80 p.Arg128Gln Uncertain significance ★ ⚠ same type
- CD80 p.Arg224Lys Uncertain significance ★ ⚠ same type
- CD80 p.Arg286Cys Uncertain significance ★ ⚠ same type
- CD80 p.Arg286His Uncertain significance ★ ⚠ same type
- CD80 p.Arg63Cys 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/cd80-p-leu99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown