Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 30.6%, 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 | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.39 | GERP -0.32 |
| Non-coding constraint | Z 0.99 | 1 kb window · o/e 0.91 · regional · uncalibrated |
| Overall | ||
| CADD | 11.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
30.6%
African / African-American · 22,745/74,416 alleles
Filtering AF
30.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 30.1%
Overall
5.03%
79,834/1,586,820 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 30.6% | 3 |
| East Asian | 7.34% | 14 |
| Middle Eastern | 6.47% | 15 |
| Remaining individualsnot grpmax-eligible | 6.11% | 16 |
| Ashkenazi Jewishnot grpmax-eligible | 6.06% | 17 |
| Admixed American | 5.24% | 19 |
| European (non-Finnish) | 3.44% | 29 |
| South Asian | 3.43% | 29 |
| Finnishnot grpmax-eligible | 2.81% | 36 |
| Amishnot grpmax-eligible | 2.3% | 43 |
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.-2G>A
- MANE Select
- NM_016579
- dbSNP
- rs2232773
- Type
- single nucleotide variant
- Location
- chr19:8308292 (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-minus-2g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown