19-54636880-C-T

Variant names:

• chr19-54636880-C-T
• rs8101240
• NM_001081637.3:c.*2C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001081637.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRB1	NM_001081637.3	MANE Select	c.*2C>T		3_prime_UTR	Exon 15 of 15	NP_001075106.2	A0A087WSV6
	LILRB1	NM_001388358.1		c.*2C>T		3_prime_UTR	Exon 16 of 16	NP_001375287.1	A0A087WSV6
	LILRB1	NM_001081638.4		c.*2C>T		3_prime_UTR	Exon 15 of 15	NP_001075107.2	A0A087WSX8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRB1	ENST00000324602.12	TSL:5 MANE Select	c.*2C>T		3_prime_UTR	Exon 15 of 15	ENSP00000315997.7	A0A087WSV6
	LILRB1	ENST00000396315.5	TSL:1	c.*2C>T		3_prime_UTR	Exon 14 of 14	ENSP00000379608.1	A0A087WSV6
	LILRB1	ENST00000396327.7	TSL:1	c.*2C>T		3_prime_UTR	Exon 15 of 15	ENSP00000379618.3	A0A087WSX8

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

GnomAD2 exomes AF: 0.138 AC: 34664 AN: 251206 AF XY: 0.139

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 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

African (AFR) AF: 0.185 AC: 6193 AN: 33456

American (AMR) AF: 0.0846 AC: 3783 AN: 44716

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 5025 AN: 26130

East Asian (EAS) AF: 0.0223 AC: 887 AN: 39698

South Asian (SAS) AF: 0.126 AC: 10885 AN: 86220

European-Finnish (FIN) AF: 0.195 AC: 10438 AN: 53412

Middle Eastern (MID) AF: 0.124 AC: 715 AN: 5768

European-Non Finnish (NFE) AF: 0.155 AC: 172173 AN: 1111680

Other (OTH) AF: 0.148 AC: 8915 AN: 60370

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

African (AFR) AF: 0.187 AC: 7730 AN: 41374

American (AMR) AF: 0.110 AC: 1688 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3468

East Asian (EAS) AF: 0.0226 AC: 116 AN: 5124

South Asian (SAS) AF: 0.114 AC: 546 AN: 4808

European-Finnish (FIN) AF: 0.187 AC: 1978 AN: 10574

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10869 AN: 67940

Other (OTH) AF: 0.152 AC: 321 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.3
DANN	Benign	0.79
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8101240; hg19: chr19-55148331;