chr19-54630650-A-G

Variant names:

• chr19-54630650-A-G
• rs3760861
• NM_001081637.3:c.-49+17A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001081637.3(LILRB1):​c.-49+17A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 818,234 control chromosomes in the GnomAD database, including 201,033 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 0.64 (28291 hom., cov: 32)
  • Exomes 𝑓: 0.72 (172742 hom.)
• Consequence: LILRB1 NM_001081637.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 8 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.709 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.-49+17A>G		intron	N/A	NP_001075106.2	A0A087WSV6
	LILRB1	NM_001388358.1		c.-49+17A>G		intron	N/A	NP_001375287.1	A0A087WSV6
	LILRB1	NM_001081638.4		c.-49+17A>G		intron	N/A	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.-49+17A>G		intron	N/A	ENSP00000315997.7	A0A087WSV6
	LILRB1	ENST00000396327.7	TSL:1	c.-49+17A>G		intron	N/A	ENSP00000379618.3	A0A087WSX8
	LILRB1	ENST00000396332.8	TSL:1	c.-49+17A>G		intron	N/A	ENSP00000379623.4	D9IDM5

Frequencies

GnomAD3 genomes AF: 0.641 AC: 91423 AN: 142564 Hom.: 28281 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.615

GnomAD4 exome AF: 0.719 AC: 485865 AN: 675576 Hom.: 172742 Cov.: 9 AF XY: 0.721 AC XY: 256738 AN XY: 356326

African (AFR) AF: 0.563 AC: 9106 AN: 16184

American (AMR) AF: 0.512 AC: 17318 AN: 33800

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 12176 AN: 18308

East Asian (EAS) AF: 0.420 AC: 10544 AN: 25118

South Asian (SAS) AF: 0.735 AC: 48612 AN: 66146

European-Finnish (FIN) AF: 0.703 AC: 21826 AN: 31066

Middle Eastern (MID) AF: 0.694 AC: 2784 AN: 4014

European-Non Finnish (NFE) AF: 0.760 AC: 341455 AN: 449338

Other (OTH) AF: 0.698 AC: 22044 AN: 31602

GnomAD4 genome AF: 0.641 AC: 91484 AN: 142658 Hom.: 28291 Cov.: 32 AF XY: 0.637 AC XY: 44406 AN XY: 69718

African (AFR) AF: 0.540 AC: 20001 AN: 37062

American (AMR) AF: 0.571 AC: 8075 AN: 14142

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2162 AN: 3276

East Asian (EAS) AF: 0.418 AC: 1955 AN: 4676

South Asian (SAS) AF: 0.723 AC: 3365 AN: 4656

European-Finnish (FIN) AF: 0.685 AC: 6931 AN: 10112

Middle Eastern (MID) AF: 0.627 AC: 168 AN: 268

European-Non Finnish (NFE) AF: 0.715 AC: 46878 AN: 65592

Other (OTH) AF: 0.617 AC: 1219 AN: 1976

Alfa AF: 0.644 Hom.: 3409

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
PhyloP100		-2.7
PromoterAI		0.012	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3760861; hg19: chr19-55142101;