Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.54%, 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 0.32 | GERP -1, phastCons 0.95 |
| Overall | ||
| CADD | 2.196 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.54%
African / African-American · 1,108/72,086 alleles
Filtering AF
1.46%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.43%
Overall
0.0794%
1,215/1,529,374 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.54% | 65 |
| Remaining individualsnot grpmax-eligible | 0.097% | 1,031 |
| Admixed American | 0.0798% | 1,253 |
| Middle Eastern | 0.0355% | 2,813 |
| South Asian | 0.00781% | 12,801 |
| European (non-Finnish) | 0.000438% | 228,118 |
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.Ser598=
- Coding
- c.1794C>T
- MANE Select
- NM_020404
- dbSNP
- rs7110351
- Type
- single nucleotide variant
- Location
- chr11:66315234 (GRCh38)
- Gene constraint
- LOEUF 1.594 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.70
Similar variants
- CD248 p.Ala303Val Likely benign ★★ same type
- CD248 p.Ala486Thr Benign ★★ same type
- CD248 p.Arg101= Benign ★★ same type
- CD248 p.Asp379= Benign ★★ same type
- CD248 p.Ile485= Benign ★★ same type
- CD248 p.Pro412= 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-ser598 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown