CD79B c.430+10A>C
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, eas)
Conditions
1
agammaglobulinemia 6, autosomal recessive
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +10 | near-intronic (+10 nt from the splice site) |
|---|---|---|
| SpliceAI | Δ0.37 | donor loss, 1 bp away · masked 0 · deltas |
| Constraint at this position | ||
| Conservation | phyloP -3.3 | GERP -3.5 |
| Overall | ||
| CADD | 0.267 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
East Asian · 5/44,874 alleles
Filtering AF
0.00435%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.000342%
5/1,461,184 alleles · ultra-rare
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
- CD79B
- Coding
- c.430+10A>C
- MANE Select
- NM_000626
- dbSNP
- rs758503702
- Type
- single nucleotide variant
- Location
- chr17:63930064 (GRCh38)
- Gene constraint
- LOEUF 0.421 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.02 · 6 PDB
Similar variants
- CD79B p.Ala5Val Uncertain significance ★★ ⚠ same condition
- CD79B p.Arg36Trp Uncertain significance ★★ ⚠ same condition
- CD79B p.Gly216Arg Uncertain significance ★★ ⚠ same condition
- CD79B p.Leu91Pro Uncertain significance ★★ ⚠ same condition
- CD79B p.Met96Val Uncertain significance ★★ ⚠ same condition
- CD79B p.Thr212Met Uncertain significance ★★ ⚠ same condition
- CD79B p.Val175Met Uncertain significance ★★ ⚠ same condition
- CD79B c.118+12C>T Benign/Likely benign ★★ same condition
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/cd79b-c-430-plus-10a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown