Variant rs1061684 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001081637.3(LILRB1):c.1872C>T(p.Leu624Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,611,934 control chromosomes in the GnomAD database, including 25,705 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 1663 hom., cov: 29)

Exomes 𝑓: 0.18 ( 24042 hom. )

Consequence

LILRB1
NM_001081637.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.57

Variant links:

Genes affected

LILRB1 (HGNC:6605): (leukocyte immunoglobulin like receptor B1) 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]

LILRB1 links:

LILRB1 (HGNC:):

LILRB1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP7

Synonymous conserved (PhyloP=-1.57 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LILRB1	NM_001081637.3 linkuse as main transcript	c.1872C>T	p.Leu624Leu	synonymous_variant	15/15	ENST00000324602.12	NP_001075106.2	Q8NHL6A0A087WSV6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LILRB1	ENST00000324602.12 linkuse as main transcript	c.1872C>T	p.Leu624Leu	synonymous_variant	15/15	5	NM_001081637.3	ENSP00000315997.7		A0A087WSV6

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20695

AN:

150630

Hom.:

1662

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0366

Gnomad AMI

AF:

0.131

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.0883

Gnomad SAS

AF:

0.0867

Gnomad FIN

AF:

0.175

Gnomad MID

AF:

0.0955

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.157

GnomAD3 exomes

AF:

0.151

AC:

37884

AN:

250456

Hom.:

1877

AF XY:

0.148

AC XY:

20098

AN XY:

135360

show subpopulations

Gnomad AFR exome

AF:

0.0307

Gnomad AMR exome

AF:

0.174

Gnomad ASJ exome

AF:

0.168

Gnomad EAS exome

AF:

0.0815

Gnomad SAS exome

AF:

0.0909

Gnomad FIN exome

AF:

0.178

Gnomad NFE exome

AF:

0.182

Gnomad OTH exome

AF:

0.163

GnomAD4 exome

AF:

0.177

AC:

257913

AN:

1461188

Hom.:

24042

Cov.:

AF XY:

0.173

AC XY:

125890

AN XY:

726940

show subpopulations

Gnomad4 AFR exome

AF:

0.0278

Gnomad4 AMR exome

AF:

0.180

Gnomad4 ASJ exome

AF:

0.178

Gnomad4 EAS exome

AF:

0.0859

Gnomad4 SAS exome

AF:

0.0920

Gnomad4 FIN exome

AF:

0.197

Gnomad4 NFE exome

AF:

0.191

Gnomad4 OTH exome

AF:

0.164

GnomAD4 genome

AF:

0.137

AC:

20709

AN:

150746

Hom.:

1663

Cov.:

AF XY:

0.137

AC XY:

10058

AN XY:

73612

show subpopulations

Gnomad4 AFR

AF:

0.0365

Gnomad4 AMR

AF:

0.182

Gnomad4 ASJ

AF:

0.164

Gnomad4 EAS

AF:

0.0889

Gnomad4 SAS

AF:

0.0866

Gnomad4 FIN

AF:

0.175

Gnomad4 NFE

AF:

0.187

Gnomad4 OTH

AF:

0.157

Alfa

AF:

0.167

Hom.:

576

Bravo

AF:

0.135

Asia WGS

AF:

0.0910

AC:

316

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.92

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over