4-150761851-TAAA-TAAAAA

Variant names:

• chr4-150761851-T-TAA
• rs760075270
• NM_001364905.1:c.5581-6_5581-5dupTT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001364905.1(LRBA):​c.5581-6_5581-5dupTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000075 in 1,159,528 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.000075 (0 hom.)
• Consequence: LRBA NM_001364905.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 0 publications found

Genes affected

LRBA (HGNC:1742): (LPS responsive beige-like anchor protein) The protein encoded by this gene is a member of the WDL-BEACH-WD (WBW) gene family. Its expression is induced in B cells and macrophages by bacterial lipopolysaccharides (LPS). The encoded protein associates with protein kinase A and may be involved in leading intracellular vesicles to activated receptor complexes, which aids in the secretion and/or membrane deposition of immune effector molecules. Defects in this gene are associated with the disorder common variable immunodeficiency-8 with autoimmunity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

LRBA Gene-Disease associations (from GenCC):

• combined immunodeficiency due to LRBA deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, ClinGen, Labcorp Genetics (formerly Invitae), Orphanet, Genomics England PanelApp

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRBA	NM_001364905.1	c.5581-6_5581-5dupTT		splice_region_variant, intron_variant	Intron 34 of 56	ENST00000651943.2	NP_001351834.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRBA	ENST00000651943.2	c.5581-6_5581-5dupTT		splice_region_variant, intron_variant	Intron 34 of 56		NM_001364905.1	ENSP00000498582.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.0000658 AC: 8 AN: 121568 AF XY: 0.0000604

Gnomad AFR exome AF: 0.000231

Gnomad AMR exome AF: 0.0000933

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000672

Gnomad NFE exome AF: 0.0000655

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000750 AC: 87 AN: 1159528 Hom.: 0 Cov.: 20 AF XY: 0.0000696 AC XY: 40 AN XY: 575002

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000418 AC: 1 AN: 23922

American (AMR) AF: 0.0000441 AC: 1 AN: 22694

Ashkenazi Jewish (ASJ) AF: 0.0000539 AC: 1 AN: 18562

East Asian (EAS) AF: 0.00 AC: 0 AN: 29126

South Asian (SAS) AF: 0.000103 AC: 6 AN: 58192

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44006

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4674

European-Non Finnish (NFE) AF: 0.0000811 AC: 74 AN: 911892

Other (OTH) AF: 0.0000861 AC: 4 AN: 46460

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs760075270; hg19: chr4-151683003;