chr4-150844184-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001364905.1(LRBA):c.4485C>T(p.Gly1495Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0281 in 1,603,164 control chromosomes in the GnomAD database, including 803 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001364905.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRBA | NM_001364905.1 | c.4485C>T | p.Gly1495Gly | synonymous_variant | Exon 28 of 57 | ENST00000651943.2 | NP_001351834.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRBA | ENST00000651943.2 | c.4485C>T | p.Gly1495Gly | synonymous_variant | Exon 28 of 57 | NM_001364905.1 | ENSP00000498582.2 |
Frequencies
GnomAD3 genomes AF: 0.0208 AC: 3158AN: 151584Hom.: 51 Cov.: 32
GnomAD3 exomes AF: 0.0206 AC: 5167AN: 251252Hom.: 82 AF XY: 0.0210 AC XY: 2849AN XY: 135808
GnomAD4 exome AF: 0.0289 AC: 41946AN: 1451466Hom.: 752 Cov.: 30 AF XY: 0.0280 AC XY: 20252AN XY: 722452
GnomAD4 genome AF: 0.0208 AC: 3159AN: 151698Hom.: 51 Cov.: 32 AF XY: 0.0202 AC XY: 1495AN XY: 74070
ClinVar
Submissions by phenotype
Combined immunodeficiency due to LRBA deficiency Benign:2
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not specified Benign:1
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, silent variant not in splice consensus -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at