rs1061684

Variant names:

• chr19-54636791-C-T
• rs1061684
• NM_001081637.3:c.1872C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001081637.3(LILRB1):​c.1872C>T​(p.Leu624Leu) 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
• Publications: 14 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 -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 rank	MANE	Protein	UniProt
LILRB1	NM_001081637.3	c.1872C>T	p.Leu624Leu	synonymous_variant	Exon 15 of 15	ENST00000324602.12	NP_001075106.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LILRB1	ENST00000324602.12	c.1872C>T	p.Leu624Leu	synonymous_variant	Exon 15 of 15	5	NM_001081637.3	ENSP00000315997.7

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

GnomAD2 exomes AF: 0.151 AC: 37884 AN: 250456 AF XY: 0.148

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 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

African (AFR) AF: 0.0278 AC: 930 AN: 33442

American (AMR) AF: 0.180 AC: 8039 AN: 44700

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 4649 AN: 26134

East Asian (EAS) AF: 0.0859 AC: 3411 AN: 39690

South Asian (SAS) AF: 0.0920 AC: 7934 AN: 86220

European-Finnish (FIN) AF: 0.197 AC: 10528 AN: 53412

Middle Eastern (MID) AF: 0.0867 AC: 500 AN: 5768

European-Non Finnish (NFE) AF: 0.191 AC: 212024 AN: 1111454

Other (OTH) AF: 0.164 AC: 9898 AN: 60368

GnomAD4 genome AF: 0.137 AC: 20709 AN: 150746 Hom.: 1663 Cov.: 29 AF XY: 0.137 AC XY: 10058 AN XY: 73612

African (AFR) AF: 0.0365 AC: 1481 AN: 40614

American (AMR) AF: 0.182 AC: 2763 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3466

East Asian (EAS) AF: 0.0889 AC: 453 AN: 5094

South Asian (SAS) AF: 0.0866 AC: 415 AN: 4792

European-Finnish (FIN) AF: 0.175 AC: 1841 AN: 10498

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12708 AN: 67782

Other (OTH) AF: 0.157 AC: 329 AN: 2098

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
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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