4-150872751-T-C

Position:

chr4-150872751-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001364905.1(LRBA):c.2170A>G(p.Ile724Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0259 in 1,550,800 control chromosomes in the GnomAD database, including 615 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 42 hom., cov: 32)

Exomes 𝑓: 0.027 ( 573 hom. )

Consequence

LRBA
NM_001364905.1 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 1.09

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0076279044).

BP6

Variant 4-150872751-T-C is Benign according to our data. Variant chr4-150872751-T-C is described in ClinVar as [Benign]. Clinvar id is 473170.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-150872751-T-C is described in Lovd as [Likely_benign]. Variant chr4-150872751-T-C is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0191 (2910/152228) while in subpopulation NFE AF= 0.0281 (1910/68000). AF 95% confidence interval is 0.027. There are 42 homozygotes in gnomad4. There are 1421 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 42 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRBA	NM_001364905.1 linkuse as main transcript	c.2170A>G	p.Ile724Val	missense_variant	18/57	ENST00000651943.2	NP_001351834.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRBA	ENST00000651943.2 linkuse as main transcript	c.2170A>G	p.Ile724Val	missense_variant	18/57		NM_001364905.1	ENSP00000498582	P3

Frequencies

GnomAD3 genomes

AF:

0.0191

AC:

2910

AN:

152110

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00420

Gnomad AMI

AF:

0.0899

Gnomad AMR

AF:

0.0165

Gnomad ASJ

AF:

0.0265

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0275

Gnomad FIN

AF:

0.0207

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0281

Gnomad OTH

AF:

0.0196

GnomAD3 exomes

AF:

0.0212

AC:

5119

AN:

241228

Hom.:

AF XY:

0.0225

AC XY:

2934

AN XY:

130308

show subpopulations

Gnomad AFR exome

AF:

0.00438

Gnomad AMR exome

AF:

0.0111

Gnomad ASJ exome

AF:

0.0281

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0238

Gnomad FIN exome

AF:

0.0204

Gnomad NFE exome

AF:

0.0286

Gnomad OTH exome

AF:

0.0254

GnomAD4 exome

AF:

0.0267

AC:

37287

AN:

1398572

Hom.:

573

Cov.:

AF XY:

0.0270

AC XY:

18841

AN XY:

698352

show subpopulations

Gnomad4 AFR exome

AF:

0.00393

Gnomad4 AMR exome

AF:

0.0115

Gnomad4 ASJ exome

AF:

0.0277

Gnomad4 EAS exome

AF:

0.0000515

Gnomad4 SAS exome

AF:

0.0251

Gnomad4 FIN exome

AF:

0.0220

Gnomad4 NFE exome

AF:

0.0293

Gnomad4 OTH exome

AF:

0.0246

GnomAD4 genome

AF:

0.0191

AC:

2910

AN:

152228

Hom.:

Cov.:

AF XY:

0.0191

AC XY:

1421

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.00416

Gnomad4 AMR

AF:

0.0165

Gnomad4 ASJ

AF:

0.0265

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0275

Gnomad4 FIN

AF:

0.0207

Gnomad4 NFE

AF:

0.0281

Gnomad4 OTH

AF:

0.0199

Alfa

AF:

0.0260

Hom.:

Bravo

AF:

0.0176

TwinsUK

AF:

0.0318

AC:

118

ALSPAC

AF:

0.0298

AC:

115

ESP6500AA

AF:

0.00590

AC:

ESP6500EA

AF:

0.0306

AC:

263

ExAC

AF:

0.0216

AC:

2629

Asia WGS

AF:

0.00608

AC:

AN:

3470

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Combined immunodeficiency due to LRBA deficiency

Benign:2

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 28, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not provided

Benign:2

Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, no assertion criteria provided

clinical testing

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.073

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.40

CADD

Benign

DANN

Benign

0.95

DEOGEN2

Benign

0.031

.;T;.

Eigen

Benign

-0.40

Eigen_PC

Benign

-0.20

FATHMM_MKL

Benign

0.74

LIST_S2

Uncertain

0.93

D;D;D

MetaRNN

Benign

0.0076

T;T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.36

N;N;.

MutationTaster

Benign

0.75

D;D;D;D

PrimateAI

Benign

0.44

PROVEAN

Benign

-0.58

N;N;N

REVEL

Benign

0.052

Sift

Benign

0.39

T;T;T

Sift4G

Benign

0.43

T;T;T

Polyphen

0.0010

B;B;.

Vest4

0.097

MPC

0.095

ClinPred

0.011

GERP RS

4.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.034

gMVP

0.068

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over