CD48 p.Thr208=
c.624G>C · VCV4683729
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.908%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -3.3 |
| Overall | ||
| CADD | 0.029 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.908%
Middle Eastern · 55/6,058 alleles
Filtering AF
0.716%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.647%
Overall
0.028%
452/1,614,144 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.908% | 110 |
| Remaining individualsnot grpmax-eligible | 0.0768% | 1,302 |
| Admixed American | 0.0733% | 1,364 |
| African / African-American | 0.028% | 3,573 |
| European (non-Finnish) | 0.0224% | 4,470 |
| South Asian | 0.0165% | 6,072 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0101% | 9,869 |
| Finnishnot grpmax-eligible | 0.00312% | 32,014 |
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
- CD48
- Protein
- p.Thr208=
- Coding
- c.624G>C
- MANE Select
- NM_001778
- Type
- single nucleotide variant
- Location
- chr1:160681230 (GRCh38)
- Gene constraint
- LOEUF 1.31 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.20 · 1 PDB
- Residue 208
- the ig-like c2-type 2 domain
Similar variants
- CD48 p.Thr216Ile Uncertain significance ★★ ⚠ same type
- CD48 c.652+73G>T Benign ★★ same type
- CD48 p.Gln90= Benign ★★ same type
- CD48 p.Leu30= Benign ★★ same type
- CD48 p.Thr233= Benign/Likely benign ★★ same type
- CD48 p.Ala93Thr Uncertain significance ★ ⚠ same type
- CD48 p.Arg192Met Uncertain significance ★ ⚠ same type
- CD48 p.Asn178Lys 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/cd48-p-thr208 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown