rs1061684

chr19-54636791-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001081637.3(LILRB1):c.1872C>T(p.Leu624=) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

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

ACMG classification

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	UniProt
LILRB1	NM_001081637.3	c.1872C>T	p.Leu624=	synonymous_variant	15/15	ENST00000324602.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LILRB1	ENST00000324602.12	c.1872C>T	p.Leu624=	synonymous_variant	15/15	5	NM_001081637.3	P4
LILRB1-AS1	ENST00000456337.1	n.200-715G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20695 AN: 150630 Hom.: 1662 Cov.: 29

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

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.: 44 AF XY: 0.173 AC XY: 125890 AN XY: 726940

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.: 29 AF XY: 0.137 AC XY: 10058 AN XY: 73612

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

Other links and lift over

dbSNP: rs1061684; hg19: chr19-55148242; COSMIC: COSV61116038; COSMIC: COSV61116038;