CD248 p.Arg101=
c.303C>T · rs138322044 · VCV707892
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.46%, afr)
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 -4 | GERP -2.7 |
| Overall | ||
| CADD | 3.938 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.46%
African / African-American · 345/74,984 alleles
Filtering AF
0.42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.404%
Overall
0.037%
593/1,604,520 alleles · rare
exomes 375/1,452,182 · genomes 218/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.46% | 217 |
| Remaining individualsnot grpmax-eligible | 0.0482% | 2,075 |
| Admixed American | 0.0317% | 3,157 |
| European (non-Finnish) | 0.0164% | 6,080 |
| South Asian | 0.0044% | 22,747 |
| East Asian | 0.00223% | 44,858 |
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
- CD248
- Protein
- p.Arg101=
- Coding
- c.303C>T
- MANE Select
- NM_020404
- dbSNP
- rs138322044
- Type
- single nucleotide variant
- Location
- chr11:66316725 (GRCh38)
- Gene constraint
- LOEUF 1.594 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.70
- Residue 101
- the c-type lectin domain
Similar variants
- CD248 p.Ala303Val Likely benign ★★ same type
- CD248 p.Ala486Thr Benign ★★ same type
- CD248 p.Asp379= Benign ★★ same type
- CD248 p.Ile485= Benign ★★ same type
- CD248 p.Pro412= Benign ★★ same type
- CD248 p.Ser598= Benign ★★ same type
- CD248 p.Tyr410= Benign ★★ same type
- CD248 p.Val447= 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/cd248-p-arg101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown