LRBA p.Ala2817=
c.8451G>A · rs566917747 · VCV1116177
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.02 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.29 | GERP -3.5, phastCons 0.021 |
| Overall | ||
| CADD | 1.496 | 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
0.000763%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000605%
Overall
0.00124%
20/1,614,060 alleles · ultra-rare
exomes 19/1,461,818 · genomes 1/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| Admixed American | 0.00333% | 30,014 |
| African / African-American | 0.00133% | 75,014 |
| European (non-Finnish) | 0.00127% | 78,666 |
| South Asian | 0.0011% | 91,070 |
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.Ala2817=
- Coding
- c.8451G>A
- MANE Select
- NM_001364905
- dbSNP
- rs566917747
- Type
- single nucleotide variant
- Location
- chr4:150277870 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI <0.01 (gnomAD)
Similar variants
- LRBA p.Ala2817Val Uncertain significance ★★ ⚠ same residue
- LRBA c.216+1G>C Pathogenic/Likely pathogenic ★★ same condition
- LRBA c.2259-2A>G Likely pathogenic ★★ same condition
- LRBA c.2767-2A>G Likely pathogenic ★★ same condition
- LRBA c.4159-1G>T Likely pathogenic ★★ same condition
- LRBA c.5518+2T>C Likely pathogenic ★★ same condition
- LRBA c.5519-1G>A Likely pathogenic ★★ same condition
- LRBA c.5646-2A>T Pathogenic ★★ 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/lrba-p-ala2817 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown