CD81 p.Ala54=
c.162G>A · rs754071503 · VCV3016100
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00407%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.014 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.7 | GERP -3.2 |
| Overall | ||
| CADD | 1.183 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00407%
European (non-Finnish) · 48/1,179,552 alleles
Filtering AF
0.00315%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00279%
Overall
0.00335%
54/1,612,382 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00407% | 24,574 |
| Admixed American | 0.00333% | 30,003 |
| African / African-American | 0.00267% | 37,461 |
| South Asian | 0.0022% | 45,542 |
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
- CD81
- Protein
- p.Ala54=
- Coding
- c.162G>A
- MANE Select
- NM_004356
- dbSNP
- rs754071503
- Type
- single nucleotide variant
- Location
- chr11:2390507 (GRCh38)
- Gene constraint
- LOEUF 0.702 · pLI 0.36 (gnomAD)
- Structure
- AlphaFold pLDDT 87.24 · 16 PDB
Similar variants
- CD81 p.Ala54Val Uncertain significance ★★ ⚠ same residue
- CD81 p.Ala54Thr Uncertain significance ★ ⚠ same residue
- CD81 c.561+5G>A Uncertain significance ★★ same type
- CD81 p.Ala120Thr Uncertain significance ★★ ⚠ same type
- CD81 p.Arg231Gln Uncertain significance ★★ ⚠ same type
- CD81 p.Asn115Ser Uncertain significance ★★ ⚠ same type
- CD81 p.Asn141Lys Uncertain significance ★★ ⚠ same type
- CD81 p.Asn141Ser 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/cd81-p-ala54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown