Variant chr19-54276882-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001080978.4(LILRB2):c.1405G>A(p.Val469Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0023 in 1,609,522 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0038 ( 4 hom., cov: 31)

Exomes 𝑓: 0.0022 ( 18 hom. )

Consequence

LILRB2
NM_001080978.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.36

Variant links:

Genes affected

LILRB2 (HGNC:6606): (leukocyte immunoglobulin like receptor B2) 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. 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]

LILRB2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008268654).

BP6

Variant 19-54276882-C-T is Benign according to our data. Variant chr19-54276882-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2650439.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LILRB2	NM_001080978.4 linkuse as main transcript	c.1405G>A	p.Val469Ile	missense_variant	10/14	ENST00000314446.10	NP_001074447.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LILRB2	ENST00000314446.10 linkuse as main transcript	c.1405G>A	p.Val469Ile	missense_variant	10/14	1	NM_001080978.4	ENSP00000319960	A2	Q8N423-2

Frequencies

GnomAD3 genomes

AF:

0.00376

AC:

570

AN:

151732

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000920

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000525

Gnomad ASJ

AF:

0.0148

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0126

Gnomad FIN

AF:

0.00537

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00500

Gnomad OTH

AF:

0.00385

GnomAD3 exomes

AF:

0.00224

AC:

555

AN:

247552

Hom.:

AF XY:

0.00256

AC XY:

343

AN XY:

133892

show subpopulations

Gnomad AFR exome

AF:

0.000677

Gnomad AMR exome

AF:

0.000116

Gnomad ASJ exome

AF:

0.00716

Gnomad EAS exome

AF:

0.000381

Gnomad SAS exome

AF:

0.00905

Gnomad FIN exome

AF:

0.000744

Gnomad NFE exome

AF:

0.00145

Gnomad OTH exome

AF:

0.00197

GnomAD4 exome

AF:

0.00215

AC:

3136

AN:

1457672

Hom.:

Cov.:

AF XY:

0.00243

AC XY:

1761

AN XY:

724938

show subpopulations

Gnomad4 AFR exome

AF:

0.000599

Gnomad4 AMR exome

AF:

0.000268

Gnomad4 ASJ exome

AF:

0.00927

Gnomad4 EAS exome

AF:

0.00128

Gnomad4 SAS exome

AF:

0.00904

Gnomad4 FIN exome

AF:

0.00278

Gnomad4 NFE exome

AF:

0.00153

Gnomad4 OTH exome

AF:

0.00273

GnomAD4 genome

AF:

0.00376

AC:

571

AN:

151850

Hom.:

Cov.:

AF XY:

0.00373

AC XY:

277

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.000917

Gnomad4 AMR

AF:

0.000524

Gnomad4 ASJ

AF:

0.0148

Gnomad4 EAS

AF:

0.00174

Gnomad4 SAS

AF:

0.0128

Gnomad4 FIN

AF:

0.00537

Gnomad4 NFE

AF:

0.00500

Gnomad4 OTH

AF:

0.00381

Alfa

AF:

0.00638

Hom.:

ExAC

AF:

0.00445

AC:

540

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

LILRB2: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.031

DANN

Benign

0.33

Eigen

Benign

-1.9

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.00069

LIST_S2

Benign

0.53

.;.;T;.;.

MetaRNN

Benign

0.0083

T;T;T;T;T

MetaSVM

Benign

-0.94

MutationTaster

Benign

1.0

N;N;N;N;N

PrimateAI

Benign

0.39

PROVEAN

Benign

-0.010

N;N;N;N;N

REVEL

Benign

0.022

Sift

Benign

0.41

T;T;T;T;T

Sift4G

Benign

0.51

T;T;T;T;T

Vest4

0.17

MVP

0.048

MPC

0.040

ClinPred

0.011

GERP RS

-3.0

gMVP

0.071

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