CD93 p.Thr34=
c.102C>A · VCV3349074
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.347%, sas)
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 -3.4 | GERP -3.8 |
| Overall | ||
| CADD | 0.044 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.347%
South Asian · 313/90,240 alleles
Filtering AF
0.315%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.303%
Overall
0.0352%
562/1,597,926 alleles · rare
exomes 531/1,445,684 · genomes 31/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.347% | 288 |
| Middle Eastern | 0.18% | 555 |
| Remaining individualsnot grpmax-eligible | 0.0322% | 3,108 |
| European (non-Finnish) | 0.0179% | 5,585 |
| Admixed American | 0.00672% | 14,889 |
| African / African-American | 0.004% | 24,991 |
| Finnishnot grpmax-eligible | 0.00192% | 52,020 |
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
- CD93
- Protein
- p.Thr34=
- Coding
- c.102C>A
- MANE Select
- NM_012072
- Type
- single nucleotide variant
- Location
- chr20:23086091 (GRCh38)
- Gene constraint
- LOEUF 1.237 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.07 · 2 PDB
- Residue 34
- the c-type lectin domain
Similar variants
- CD93 p.Arg496= Benign/Likely benign ★★ same type
- CD93 p.Gly448= Benign ★★ same type
- CD93 p.His551= Likely benign ★★ same type
- CD93 p.Pro541Ser Benign/Likely benign ★★ same type
- CD93 p.Ser520Leu Benign ★★ same type
- CD93 p.Thr493Ile Benign/Likely benign ★★ same type
- CD93 p.Val428Leu Benign ★★ same type
- CD93 p.Ala214Val 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/cd93-p-thr34 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown