rs186080
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001364905.1(LRBA):c.4569+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 1,535,700 control chromosomes in the GnomAD database, including 633,998 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001364905.1 intron
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRBA | NM_001364905.1 | c.4569+9C>T | intron_variant | Intron 28 of 56 | ENST00000651943.2 | NP_001351834.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRBA | ENST00000651943.2 | c.4569+9C>T | intron_variant | Intron 28 of 56 | NM_001364905.1 | ENSP00000498582.2 |
Frequencies
GnomAD3 genomes AF: 0.832 AC: 126304AN: 151876Hom.: 53747 Cov.: 30
GnomAD3 exomes AF: 0.862 AC: 216072AN: 250696Hom.: 94363 AF XY: 0.863 AC XY: 116899AN XY: 135530
GnomAD4 exome AF: 0.913 AC: 1262843AN: 1383706Hom.: 580228 Cov.: 20 AF XY: 0.909 AC XY: 629440AN XY: 692668
GnomAD4 genome AF: 0.831 AC: 126375AN: 151994Hom.: 53770 Cov.: 30 AF XY: 0.826 AC XY: 61358AN XY: 74276
ClinVar
Submissions by phenotype
not specified Benign:6
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Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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This variant is classified as Benign based on local population frequency. This variant was detected in 99% of patients studied by a panel of primary immunodeficiencies. Number of patients: 95. Only high quality variants are reported. -
Combined immunodeficiency due to LRBA deficiency Benign:2
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not provided Benign:1Other:1
Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at