rs3760861

Positions:

• chr19-54630650-A-G
• chr19-54630650-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001081637.3(LILRB1):​c.-49+17A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 818,234 control chromosomes in the GnomAD database, including 201,033 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 0.64 (28291 hom., cov: 32)
  • Exomes 𝑓: 0.72 (172742 hom.)
• Consequence: LILRB1 NM_001081637.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LILRB1	NM_001081637.3	c.-49+17A>G		intron_variant		ENST00000324602.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LILRB1	ENST00000324602.12	c.-49+17A>G		intron_variant		5	NM_001081637.3	P4

Frequencies

GnomAD3 genomes AF: 0.641 AC: 91423 AN: 142564 Hom.: 28281 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.615

GnomAD4 exome AF: 0.719 AC: 485865 AN: 675576 Hom.: 172742 Cov.: 9 AF XY: 0.721 AC XY: 256738 AN XY: 356326

Gnomad4 AFR exome AF: 0.563

Gnomad4 AMR exome AF: 0.512

Gnomad4 ASJ exome AF: 0.665

Gnomad4 EAS exome AF: 0.420

Gnomad4 SAS exome AF: 0.735

Gnomad4 FIN exome AF: 0.703

Gnomad4 NFE exome AF: 0.760

Gnomad4 OTH exome AF: 0.698

GnomAD4 genome AF: 0.641 AC: 91484 AN: 142658 Hom.: 28291 Cov.: 32 AF XY: 0.637 AC XY: 44406 AN XY: 69718

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.617

Alfa AF: 0.644 Hom.: 3409

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760861; hg19: chr19-55142101;