ALCAM p.Asp82=
c.246T>C · VCV3904826
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.235%, amr)
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 -1.2 | GERP -5.3, phastCons 0.001 |
| Overall | ||
| CADD | 5.732 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.235%
Admixed American · 141/60,032 alleles
Filtering AF
0.225%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.222%
Overall
0.2%
3,229/1,614,128 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.235% | 426 |
| European (non-Finnish) | 0.233% | 430 |
| Remaining individualsnot grpmax-eligible | 0.187% | 534 |
| Ashkenazi Jewishnot grpmax-eligible | 0.162% | 617 |
| South Asian | 0.148% | 675 |
| Middle Eastern | 0.099% | 1,010 |
| African / African-American | 0.0386% | 2,588 |
| Finnishnot grpmax-eligible | 0.00937% | 10,674 |
| East Asian | 0.00223% | 44,880 |
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
- ALCAM
- Protein
- p.Asp82=
- Coding
- c.246T>C
- MANE Select
- NM_001627
- Type
- single nucleotide variant
- Location
- chr3:105524360 (GRCh38)
- Gene constraint
- LOEUF 0.474 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.13 · 1 PDB
- Residue 82
- a disulfide bond; the ig-like v-type 1 domain
Similar variants
- ALCAM p.Asp82Asn Uncertain significance ★ ⚠ same residue
- ALCAM p.Asp82Val Uncertain significance ★ ⚠ same residue
- ALCAM p.Asp81= Benign ★★ same type
- ALCAM p.His508= Benign/Likely benign ★★ same type
- ALCAM p.Leu254= Benign ★★ same type
- ALCAM p.Pro84Leu Benign ★★ same type
- ALCAM p.Ser454= Benign/Likely benign ★★ same type
- ALCAM p.Thr301Met Benign ★★ 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/alcam-p-asp82 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown