19-54281065-T-C

Position:

• chr19-54281065-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

LILRB2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LILRB2	NM_001080978.4	c.-153A>G		5_prime_UTR_variant	1/14	ENST00000314446.10	NP_001074447.2
LILRB2	NM_005874.5	c.-153A>G		5_prime_UTR_variant	1/14		NP_005865.3
LILRB2	NM_001278404.3	c.-350A>G		5_prime_UTR_variant	1/13		NP_001265333.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LILRB2	ENST00000314446.10	c.-153A>G		5_prime_UTR_variant	1/14	1	NM_001080978.4	ENSP00000319960.5
LILRB2	ENST00000391749.4	c.-153A>G		5_prime_UTR_variant	1/14	1		ENSP00000375629.4
LILRB2	ENST00000493242.1	n.33A>G		non_coding_transcript_exon_variant	1/13	1
LILRB2	ENST00000434421.5	c.-350A>G		5_prime_UTR_variant	1/13	2		ENSP00000410117.1

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

Gnomad4 AFR exome AF: 0.782

Gnomad4 AMR exome AF: 0.569

Gnomad4 ASJ exome AF: 0.723

Gnomad4 EAS exome AF: 0.351

Gnomad4 SAS exome AF: 0.732

Gnomad4 FIN exome AF: 0.609

Gnomad4 NFE exome AF: 0.669

Gnomad4 OTH exome AF: 0.674

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

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.812

Alfa AF: 0.761 Hom.: 3867

Bravo AF: 0.819

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.086

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs448083; hg19: -;