19-54636880-C-T

Position:

• chr19-54636880-C-T

Variant summary

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

The NM_001081637.3(LILRB1):​c.*2C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,613,340 control chromosomes in the GnomAD database, including 19,341 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 0.16 (2027 hom., cov: 30)
  • Exomes 𝑓: 0.15 (17314 hom.)
• Consequence: LILRB1 NM_001081637.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LILRB1	NM_001081637.3	c.*2C>T		3_prime_UTR_variant	15/15	ENST00000324602.12	NP_001075106.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LILRB1	ENST00000324602.12	c.*2C>T		3_prime_UTR_variant	15/15	5	NM_001081637.3	ENSP00000315997	P4
LILRB1-AS1	ENST00000456337.1	n.200-804G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24102 AN: 151772 Hom.: 2025 Cov.: 30

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0224

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.154

GnomAD3 exomes AF: 0.138 AC: 34664 AN: 251206 Hom.: 2695 AF XY: 0.139 AC XY: 18832 AN XY: 135764

Gnomad AFR exome AF: 0.184

Gnomad AMR exome AF: 0.0812

Gnomad ASJ exome AF: 0.186

Gnomad EAS exome AF: 0.0206

Gnomad SAS exome AF: 0.125

Gnomad FIN exome AF: 0.195

Gnomad NFE exome AF: 0.155

Gnomad OTH exome AF: 0.155

GnomAD4 exome AF: 0.150 AC: 219014 AN: 1461450 Hom.: 17314 Cov.: 37 AF XY: 0.150 AC XY: 108933 AN XY: 727048

Gnomad4 AFR exome AF: 0.185

Gnomad4 AMR exome AF: 0.0846

Gnomad4 ASJ exome AF: 0.192

Gnomad4 EAS exome AF: 0.0223

Gnomad4 SAS exome AF: 0.126

Gnomad4 FIN exome AF: 0.195

Gnomad4 NFE exome AF: 0.155

Gnomad4 OTH exome AF: 0.148

GnomAD4 genome AF: 0.159 AC: 24142 AN: 151890 Hom.: 2027 Cov.: 30 AF XY: 0.157 AC XY: 11644 AN XY: 74238

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.152

Alfa AF: 0.142 Hom.: 783

Bravo AF: 0.154

Asia WGS AF: 0.0770 AC: 269 AN: 3478

EpiCase AF: 0.154

EpiControl AF: 0.144

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.3
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs8101240; hg19: chr19-55148331;