LRBA p.Arg1812=
c.5436T>G · VCV3778029
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.012 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.33 | GERP -3.3, phastCons 1 |
| Overall | ||
| CADD | 6.545 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
European (non-Finnish) · 390/1,171,462 alleles
Filtering AF
0.0305%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0295%
Overall
0.0271%
434/1,602,970 alleles · ultra-rare
exomes 432/1,450,876 · genomes 2/152,094 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0333% | 3,004 |
| Middle Eastern | 0.033% | 3,029 |
| Remaining individualsnot grpmax-eligible | 0.0258% | 3,878 |
| Ashkenazi Jewishnot grpmax-eligible | 0.017% | 5,896 |
| South Asian | 0.011% | 9,052 |
| African / African-American | 0.00939% | 10,648 |
| East Asian | 0.00899% | 11,123 |
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
- LRBA
- Protein
- p.Arg1812=
- Coding
- c.5436T>G
- MANE Select
- NM_001364905
- Type
- single nucleotide variant
- Location
- chr4:150806353 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI <0.01 (gnomAD)
Similar variants
- LRBA p.Arg1812Cys Uncertain significance ★★ same residue
- LRBA p.Arg1812His Uncertain significance ★ same residue
- LRBA p.Arg1812Pro Uncertain significance ★ ⚠ same residue
- LRBA c.216+1G>C Pathogenic/Likely pathogenic ★★ same type
- LRBA c.2259-2A>G Likely pathogenic ★★ same type
- LRBA c.2767-2A>G Likely pathogenic ★★ same type
- LRBA c.4159-1G>T Likely pathogenic ★★ same type
- LRBA c.5518+2T>C Likely pathogenic ★★ 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/lrba-p-arg1812 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown