rs62344598
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001364905.1(LRBA):āc.1144T>Cā(p.Leu382=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.038 in 1,607,730 control chromosomes in the GnomAD database, including 2,277 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. L382L) has been classified as Likely benign.
Frequency
Consequence
NM_001364905.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRBA | NM_001364905.1 | c.1144T>C | p.Leu382= | synonymous_variant | 9/57 | ENST00000651943.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRBA | ENST00000651943.2 | c.1144T>C | p.Leu382= | synonymous_variant | 9/57 | NM_001364905.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0751 AC: 11412AN: 151928Hom.: 803 Cov.: 31
GnomAD3 exomes AF: 0.0393 AC: 9808AN: 249438Hom.: 437 AF XY: 0.0361 AC XY: 4875AN XY: 134900
GnomAD4 exome AF: 0.0341 AC: 49652AN: 1455684Hom.: 1467 Cov.: 31 AF XY: 0.0332 AC XY: 24036AN XY: 724150
GnomAD4 genome ? AF: 0.0753 AC: 11446AN: 152046Hom.: 810 Cov.: 31 AF XY: 0.0732 AC XY: 5441AN XY: 74352
ClinVar
Submissions by phenotype
Combined immunodeficiency due to LRBA deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at