CD79A p.Leu153=
c.459G>A · rs1555843760 · VCV743134
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -1.4 | GERP -3 |
| Overall | ||
| CADD | 4.531 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.00188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00164%
Overall
0.00198%
32/1,612,180 alleles · ultra-rare
exomes 32/1,459,920 · genomes 0/152,260 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| European (non-Finnish) | 0.00263% | 38,040 |
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
- CD79A
- Protein
- p.Leu153=
- Coding
- c.459G>A
- MANE Select
- NM_001783
- dbSNP
- rs1555843760
- Type
- single nucleotide variant
- Location
- chr19:41879614 (GRCh38)
- Gene constraint
- LOEUF 0.991 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.56 · 6 PDB
- Residue 153
- an α-helix
Similar variants
- CD79A p.Arg124Cys Uncertain significance ★★ ⚠ same type
- CD79A p.Arg124His Uncertain significance ★★ ⚠ same type
- CD79A p.Arg168Gln Uncertain significance ★★ same type
- CD79A p.Arg204Gln Uncertain significance ★★ ⚠ same type
- CD79A p.Asn60Ser Uncertain significance ★★ ⚠ same type
- CD79A p.Asn63Ser Uncertain significance ★★ ⚠ same type
- CD79A p.Gly179Arg Uncertain significance ★★ ⚠ same type
- CD79A p.Ile151Thr 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/cd79a-p-leu153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown