Variant chr19-54666737-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001278426.4(LILRB4):c.1029A>G(p.Glu343Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00194 in 1,614,124 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0019 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0019 ( 17 hom. )

Consequence

LILRB4
NM_001278426.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.445

Variant links:

Genes affected

LILRB4 (HGNC:6608): (leukocyte immunoglobulin like receptor B4) This gene is a member of the leukocyte immunoglobulin-like receptor (LIR) family, which is found in a gene cluster at chromosomal region 19q13.4. The encoded protein belongs to the subfamily B class of LIR receptors which contain two or four extracellular immunoglobulin domains, a transmembrane domain, and two to four cytoplasmic immunoreceptor tyrosine-based inhibitory motifs (ITIMs). The receptor is expressed on immune cells where it binds to MHC class I molecules on antigen-presenting cells and transduces a negative signal that inhibits stimulation of an immune response. The receptor can also function in antigen capture and presentation. It is thought to control inflammatory responses and cytotoxicity to help focus the immune response and limit autoreactivity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

LILRB4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BP6

Variant 19-54666737-A-G is Benign according to our data. Variant chr19-54666737-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2650455.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.445 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LILRB4	NM_001278426.4 link	c.1029A>G	p.Glu343Glu	synonymous_variant	10/12	ENST00000695418.1	NP_001265355.2	Q8NHJ6A0A8Q3SHR1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LILRB4	ENST00000695418.1 link	c.1029A>G	p.Glu343Glu	synonymous_variant	10/12		NM_001278426.4	ENSP00000511897.1		A0A8Q3SHR1

Frequencies

GnomAD3 genomes

AF:

0.00187

AC:

285

AN:

152196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000627

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00164

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.00894

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00160

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00266

AC:

668

AN:

251448

Hom.:

AF XY:

0.00266

AC XY:

361

AN XY:

135886

show subpopulations

Gnomad AFR exome

AF:

0.000369

Gnomad AMR exome

AF:

0.000347

Gnomad ASJ exome

AF:

0.00347

Gnomad EAS exome

AF:

0.000707

Gnomad SAS exome

AF:

0.00258

Gnomad FIN exome

AF:

0.0102

Gnomad NFE exome

AF:

0.00254

Gnomad OTH exome

AF:

0.00212

GnomAD4 exome

AF:

0.00194

AC:

2842

AN:

1461808

Hom.:

Cov.:

AF XY:

0.00198

AC XY:

1442

AN XY:

727210

show subpopulations

Gnomad4 AFR exome

AF:

0.000538

Gnomad4 AMR exome

AF:

0.000537

Gnomad4 ASJ exome

AF:

0.00321

Gnomad4 EAS exome

AF:

0.00237

Gnomad4 SAS exome

AF:

0.00249

Gnomad4 FIN exome

AF:

0.0102

Gnomad4 NFE exome

AF:

0.00156

Gnomad4 OTH exome

AF:

0.00214

GnomAD4 genome

AF:

0.00188

AC:

286

AN:

152316

Hom.:

Cov.:

AF XY:

0.00209

AC XY:

156

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.000626

Gnomad4 AMR

AF:

0.00163

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00249

Gnomad4 FIN

AF:

0.00894

Gnomad4 NFE

AF:

0.00160

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00180

Hom.:

Bravo

AF:

0.00130

Asia WGS

AF:

0.00289

AC:

AN:

3478

EpiCase

AF:

0.00120

EpiControl

AF:

0.00148

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

LILRB4: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.3

DANN

Benign

0.38

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