19-54281065-T-C

Variant names:

• chr19-54281065-T-C
• rs448083
• NM_001080978.4:c.-153A>G

Variant summary

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

The NM_001080978.4(LILRB2):​c.-153A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 148,210 control chromosomes in the GnomAD database, including 46,843 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 0.80 (46843 hom., cov: 31)
  • Exomes 𝑓: 0.67 (59638 hom.)
  • Failed GnomAD Quality Control
• Consequence: LILRB2 NM_001080978.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 12 publications found

Genes affected

LILRB2 (HGNC:6606): (leukocyte immunoglobulin like receptor B2) 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 (Cadd=0.086).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080978.4. 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
	LILRB2	NM_001080978.4	MANE Select	c.-153A>G		5_prime_UTR	Exon 1 of 14	NP_001074447.2	Q8N423-2
	LILRB2	NM_005874.5		c.-153A>G		5_prime_UTR	Exon 1 of 14	NP_005865.3	Q8N423-1
	LILRB2	NM_001278404.3		c.-350A>G		5_prime_UTR	Exon 1 of 13	NP_001265333.2	Q8N423-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRB2	ENST00000314446.10	TSL:1 MANE Select	c.-153A>G		5_prime_UTR	Exon 1 of 14	ENSP00000319960.5	Q8N423-2
	LILRB2	ENST00000391749.4	TSL:1	c.-153A>G		5_prime_UTR	Exon 1 of 14	ENSP00000375629.4	Q8N423-1
	LILRB2	ENST00000493242.1	TSL:1	n.33A>G		non_coding_transcript_exon	Exon 1 of 13

Frequencies

GnomAD3 genomes AF: 0.795 AC: 117734 AN: 148094 Hom.: 46804 Cov.: 31

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.865

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.817

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.667 AC: 194478 AN: 291678 Hom.: 59638 Cov.: 4 AF XY: 0.674 AC XY: 109541 AN XY: 162634

African (AFR) AF: 0.782 AC: 6340 AN: 8106

American (AMR) AF: 0.569 AC: 13795 AN: 24232

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 6495 AN: 8986

East Asian (EAS) AF: 0.351 AC: 3087 AN: 8800

South Asian (SAS) AF: 0.732 AC: 40973 AN: 55950

European-Finnish (FIN) AF: 0.609 AC: 7351 AN: 12070

Middle Eastern (MID) AF: 0.774 AC: 1620 AN: 2092

European-Non Finnish (NFE) AF: 0.669 AC: 105802 AN: 158066

Other (OTH) AF: 0.674 AC: 9015 AN: 13376

GnomAD4 genome AF: 0.795 AC: 117831 AN: 148210 Hom.: 46843 Cov.: 31 AF XY: 0.787 AC XY: 56913 AN XY: 72354

African (AFR) AF: 0.879 AC: 35343 AN: 40230

American (AMR) AF: 0.759 AC: 11294 AN: 14872

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3021 AN: 3410

East Asian (EAS) AF: 0.377 AC: 1863 AN: 4936

South Asian (SAS) AF: 0.790 AC: 3706 AN: 4692

European-Finnish (FIN) AF: 0.686 AC: 7045 AN: 10266

Middle Eastern (MID) AF: 0.868 AC: 250 AN: 288

European-Non Finnish (NFE) AF: 0.794 AC: 52853 AN: 66546

Other (OTH) AF: 0.812 AC: 1685 AN: 2076

Alfa AF: 0.761 Hom.: 3867

Bravo AF: 0.819

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.086
PhyloP100		-2.4
PromoterAI		0.034	Neutral

Splicing

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

Other links and lift over

dbSNP: rs448083;