CD19 p.Glu410=
c.1230G>A · rs534343856 · VCV1555211
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0593%, sas)
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 2.4 | phastCons 1 |
| Overall | ||
| CADD | 5.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0593%
South Asian · 54/91,046 alleles
Filtering AF
0.0466%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0421%
Overall
0.00366%
59/1,613,822 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0593% | 1,686 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,249 |
| European (non-Finnish) | 8.48e-05% | 1,179,824 |
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
- CD19
- Protein
- p.Glu410=
- Coding
- c.1230G>A
- MANE Select
- NM_001770
- dbSNP
- rs534343856
- Type
- single nucleotide variant
- Location
- chr16:28937302 (GRCh38)
- Gene constraint
- LOEUF 0.627 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 62.99 · 4 PDB
- Residue 410
- the 'disordered' region
Similar variants
- CD19 c.835+3A>G Uncertain significance ★★ same type
- CD19 p.Ala191Thr Uncertain significance ★★ ⚠ same type
- CD19 p.Arg123Trp Uncertain significance ★★ ⚠ same type
- CD19 p.Arg163His Uncertain significance ★★ ⚠ same type
- CD19 p.Arg234Cys Uncertain significance ★★ ⚠ same type
- CD19 p.Arg263His Uncertain significance ★★ ⚠ same type
- CD19 p.Arg321Lys Uncertain significance ★★ ⚠ same type
- CD19 p.Arg490Gln 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/cd19-p-glu410 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown