rs7359837

Positions:

• chr19-54648797-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000270452.6(LILRB4):​c.-93+4831G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0454 in 152,252 control chromosomes in the GnomAD database, including 228 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 0.045 (228 hom., cov: 32)
  • Exomes 𝑓: 0.038 (0 hom.)
• Consequence: LILRB4 ENST00000270452.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

LILRB4 (HGNC:):

LILRB4 (HGNC:6608): (leukocyte immunoglobulin like receptor B4) 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. The receptor can also function in antigen capture and presentation. 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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VN1R105P		n.54648797G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LILRB4	ENST00000461839.1	n.842G>A		non_coding_transcript_exon_variant	2/2	1
LILRB4	ENST00000270452.6	c.-93+4831G>A		intron_variant		5		ENSP00000270452.3
VN1R105P	ENST00000486595.1	n.854G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.0454 AC: 6902 AN: 152108 Hom.: 228 Cov.: 32

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0369

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0700

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0406

GnomAD4 exome AF: 0.0385 AC: 1 AN: 26 Hom.: 0 Cov.: 0 AF XY: 0.0556 AC XY: 1 AN XY: 18

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0556

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0454 AC: 6909 AN: 152226 Hom.: 228 Cov.: 32 AF XY: 0.0449 AC XY: 3345 AN XY: 74434

Gnomad4 AFR AF: 0.0138

Gnomad4 AMR AF: 0.0371

Gnomad4 ASJ AF: 0.0801

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.0700

Gnomad4 NFE AF: 0.0641

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0625 Hom.: 92

Bravo AF: 0.0401

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7359837; hg19: chr19-55160246;