4-150915601-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001364905.1(LRBA):c.1014+7A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,596,870 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001364905.1 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRBA | NM_001364905.1 | c.1014+7A>C | splice_region_variant, intron_variant | ENST00000651943.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRBA | ENST00000651943.2 | c.1014+7A>C | splice_region_variant, intron_variant | NM_001364905.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000177 AC: 27AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000679 AC: 16AN: 235544Hom.: 0 AF XY: 0.0000630 AC XY: 8AN XY: 127054
GnomAD4 exome AF: 0.000137 AC: 198AN: 1444738Hom.: 1 Cov.: 29 AF XY: 0.000124 AC XY: 89AN XY: 717738
GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74320
ClinVar
Submissions by phenotype
Combined immunodeficiency due to LRBA deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at