4-150850854-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001364905.1(LRBA):c.3874G>A(p.Val1292Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,613,900 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001364905.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRBA | NM_001364905.1 | c.3874G>A | p.Val1292Ile | missense_variant | 24/57 | ENST00000651943.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRBA | ENST00000651943.2 | c.3874G>A | p.Val1292Ile | missense_variant | 24/57 | NM_001364905.1 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00754 AC: 1147AN: 152200Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00187 AC: 469AN: 251068Hom.: 8 AF XY: 0.00130 AC XY: 177AN XY: 135672
GnomAD4 exome AF: 0.000763 AC: 1115AN: 1461582Hom.: 14 Cov.: 30 AF XY: 0.000626 AC XY: 455AN XY: 727098
GnomAD4 genome AF: 0.00756 AC: 1152AN: 152318Hom.: 12 Cov.: 32 AF XY: 0.00724 AC XY: 539AN XY: 74482
ClinVar
Submissions by phenotype
Combined immunodeficiency due to LRBA deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 04, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at