CD320 c.268+251C>T
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 5.56%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +251 | deep intronic (+251 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP -0.52 |
| Overall | ||
| CADD | 1.348 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.56%
African / African-American · 2,798/50,294 alleles
Filtering AF
5.39%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.32%
Overall
0.619%
2,976/480,958 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.56% | 18 |
| Remaining individualsnot grpmax-eligible | 0.289% | 346 |
| Admixed American | 0.288% | 347 |
| Middle Eastern | 0.061% | 1,640 |
| European (non-Finnish) | 0.01% | 9,998 |
| South Asian | 0.00602% | 16,625 |
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
- CD320
- Coding
- c.268+251C>T
- MANE Select
- NM_016579
- dbSNP
- rs79602478
- Type
- single nucleotide variant
- Location
- chr19:8304780 (GRCh38)
- Gene constraint
- LOEUF 1.488 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.61 · 6 PDB
Similar variants
- CD320 p.Arg129Leu Uncertain significance ★★ ⚠ same type
- CD320 p.Arg138Ser Uncertain significance ★★ ⚠ same type
- CD320 p.Arg254Gln Uncertain significance ★★ ⚠ same type
- CD320 p.Arg258His Uncertain significance ★★ ⚠ same type
- CD320 p.Asn170Ser Uncertain significance ★★ ⚠ same type
- CD320 p.Asp143Asn Uncertain significance ★★ ⚠ same type
- CD320 p.Asp160Asn Uncertain significance ★★ ⚠ same type
- CD320 p.Gly166Val 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/cd320-c-268-plus-251c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown