rs3760860

Positions:

• chr19-54630503-A-G

Variant summary

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

The NM_001081637.3(LILRB1):​c.-179A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 148,530 control chromosomes in the GnomAD database, including 18,371 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 0.53 (18371 hom., cov: 37)
  • Exomes 𝑓: 0.56 (39416 hom.)
  • Failed GnomAD Quality Control
• Consequence: LILRB1 NM_001081637.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LILRB1	NM_001081637.3	c.-179A>G		5_prime_UTR_variant	1/15	ENST00000324602.12	NP_001075106.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LILRB1	ENST00000324602	c.-179A>G		5_prime_UTR_variant	1/15	5	NM_001081637.3	ENSP00000315997.7
LILRB1	ENST00000396327	c.-179A>G		5_prime_UTR_variant	1/15	1		ENSP00000379618.3
LILRB1	ENST00000396331.5	c.-165-14A>G		intron_variant		1		ENSP00000379622.1
LILRB1	ENST00000396332.8	c.-179A>G		upstream_gene_variant		1		ENSP00000379623.4

Frequencies

GnomAD3 genomes AF: 0.532 AC: 78923 AN: 148416 Hom.: 18370 Cov.: 37

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.511

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.560 AC: 171768 AN: 306508 Hom.: 39416 Cov.: 3 AF XY: 0.566 AC XY: 97252 AN XY: 171868

Gnomad4 AFR exome AF: 0.399

Gnomad4 AMR exome AF: 0.436

Gnomad4 ASJ exome AF: 0.551

Gnomad4 EAS exome AF: 0.384

Gnomad4 SAS exome AF: 0.600

Gnomad4 FIN exome AF: 0.583

Gnomad4 NFE exome AF: 0.586

Gnomad4 OTH exome AF: 0.551

GnomAD4 genome AF: 0.532 AC: 78970 AN: 148530 Hom.: 18371 Cov.: 37 AF XY: 0.529 AC XY: 38390 AN XY: 72628

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.515

Alfa AF: 0.602 Hom.: 2865

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760860; hg19: chr19-55141954;