LRBA p.Val2629=
c.7887C>G · rs138897796 · VCV1116598
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00504%, amr)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.256 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3 | GERP -3.8 |
| Overall | ||
| CADD | 0.638 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00504%
Admixed American · 3/59,508 alleles
Filtering AF
0.00134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000671%
Overall
0.000249%
4/1,608,086 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00504% | 19,836 |
| South Asian | 0.00111% | 90,026 |
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.Val2629=
- Coding
- c.7887C>G
- MANE Select
- NM_001364905
- dbSNP
- rs138897796
- Type
- single nucleotide variant
- Location
- chr4:150302755 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI <0.01 (gnomAD)
Similar variants
- 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
- LRBA p.Arg1445Ter 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-val2629 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown