Variant rs41308748 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001081637.3(LILRB1):c.1813-7G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 1,191,938 control chromosomes in the GnomAD database, including 1,572 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.070 ( 99 hom., cov: 17)

Exomes 𝑓: 0.061 ( 1473 hom. )

Consequence

LILRB1
NM_001081637.3 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00001099

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.99

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-AS1 (HGNC:53114): (LILRB1 antisense RNA 1)

LILRB1-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0834 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.1813-7G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000324602.12	NP_001075106.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LILRB1	ENST00000324602.12 linkuse as main transcript	c.1813-7G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		5	NM_001081637.3	ENSP00000315997	P4
LILRB1-AS1	ENST00000456337.1 linkuse as main transcript	n.200-649C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.0702

AC:

4967

AN:

70750

Hom.:

100

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0226

Gnomad AMI

AF:

0.0396

Gnomad AMR

AF:

0.0727

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.00308

Gnomad SAS

AF:

0.0916

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.0682

Gnomad NFE

AF:

0.0858

Gnomad OTH

AF:

0.0884

GnomAD3 exomes

AF:

0.0458

AC:

9297

AN:

203086

Hom.:

125

AF XY:

0.0465

AC XY:

5147

AN XY:

110706

show subpopulations

Gnomad AFR exome

AF:

0.00870

Gnomad AMR exome

AF:

0.0298

Gnomad ASJ exome

AF:

0.0799

Gnomad EAS exome

AF:

0.000822

Gnomad SAS exome

AF:

0.0569

Gnomad FIN exome

AF:

0.0434

Gnomad NFE exome

AF:

0.0540

Gnomad OTH exome

AF:

0.0642

GnomAD4 exome

AF:

0.0606

AC:

67946

AN:

1121136

Hom.:

1473

Cov.:

AF XY:

0.0615

AC XY:

33942

AN XY:

551746

show subpopulations

Gnomad4 AFR exome

AF:

0.00881

Gnomad4 AMR exome

AF:

0.0284

Gnomad4 ASJ exome

AF:

0.107

Gnomad4 EAS exome

AF:

0.000752

Gnomad4 SAS exome

AF:

0.0530

Gnomad4 FIN exome

AF:

0.0704

Gnomad4 NFE exome

AF:

0.0635

Gnomad4 OTH exome

AF:

0.0653

GnomAD4 genome

AF:

0.0702

AC:

4967

AN:

70802

Hom.:

Cov.:

AF XY:

0.0698

AC XY:

2291

AN XY:

32824

show subpopulations

Gnomad4 AFR

AF:

0.0227

Gnomad4 AMR

AF:

0.0730

Gnomad4 ASJ

AF:

0.110

Gnomad4 EAS

AF:

0.00309

Gnomad4 SAS

AF:

0.0907

Gnomad4 FIN

AF:

0.127

Gnomad4 NFE

AF:

0.0858

Gnomad4 OTH

AF:

0.0866

Alfa

AF:

0.0391

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.79

DANN

Benign

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000011

dbscSNV1_RF

Benign

0.0020

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