chr4-150588057-G-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001364905.1(LRBA):c.6321C>T(p.Ile2107Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000484 in 1,611,720 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000049 ( 0 hom. )
Consequence
LRBA
NM_001364905.1 synonymous
NM_001364905.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.226
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]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (REVEL=0.026).
BP6
Variant 4-150588057-G-A is Benign according to our data. Variant chr4-150588057-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 540406.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.226 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LRBA | NM_001364905.1 | c.6321C>T | p.Ile2107Ile | synonymous_variant | Exon 40 of 57 | ENST00000651943.2 | NP_001351834.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| LRBA | ENST00000651943.2 | c.6321C>T | p.Ile2107Ile | synonymous_variant | Exon 40 of 57 | NM_001364905.1 | ENSP00000498582.2 |
Frequencies
GnomAD3 genomes 0.0000395 AC: 6AN: 152006Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
6
AN:
152006
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
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Gnomad AMR
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Gnomad ASJ
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Gnomad NFE
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Gnomad OTH
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GnomAD2 exomes AF: 0.0000762 AC: 19AN: 249450 AF XY: 0.0000742 show subpopulations
GnomAD2 exomes
AF:
AC:
19
AN:
249450
AF XY:
Gnomad AFR exome
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Gnomad ASJ exome
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GnomAD4 exome AF: 0.0000493 AC: 72AN: 1459596Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 725960 show subpopulations
GnomAD4 exome
AF:
AC:
72
AN:
1459596
Hom.:
Cov.:
31
AF XY:
AC XY:
34
AN XY:
725960
show subpopulations
African (AFR)
AF:
AC:
2
AN:
33420
American (AMR)
AF:
AC:
8
AN:
44430
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26082
East Asian (EAS)
AF:
AC:
1
AN:
39644
South Asian (SAS)
AF:
AC:
0
AN:
85564
European-Finnish (FIN)
AF:
AC:
0
AN:
53400
Middle Eastern (MID)
AF:
AC:
0
AN:
5722
European-Non Finnish (NFE)
AF:
AC:
56
AN:
1111006
Other (OTH)
AF:
AC:
5
AN:
60328
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.476
Heterozygous variant carriers
0
4
8
12
16
20
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000394 AC: 6AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74358 show subpopulations
GnomAD4 genome
AF:
AC:
6
AN:
152124
Hom.:
Cov.:
32
AF XY:
AC XY:
3
AN XY:
74358
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41490
American (AMR)
AF:
AC:
1
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5160
South Asian (SAS)
AF:
AC:
0
AN:
4808
European-Finnish (FIN)
AF:
AC:
2
AN:
10590
Middle Eastern (MID)
AF:
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
AC:
3
AN:
68008
Other (OTH)
AF:
AC:
0
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Combined immunodeficiency due to LRBA deficiency Benign:1
Feb 01, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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