rs400322

Variant names:

• chr19-54661127-A-G
• rs400322
• ENST00000270452.6:c.-92-1692A>G

Variant summary

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

The ENST00000270452.6(LILRB4):​c.-92-1692A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,914 control chromosomes in the GnomAD database, including 32,137 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 (32137 hom., cov: 31)
• Consequence: LILRB4 ENST00000270452.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 8 publications found

Genes affected

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LILRB4	ENST00000270452.6	c.-92-1692A>G		intron_variant	Intron 1 of 3	5		ENSP00000270452.3

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97349 AN: 151796 Hom.: 32109 Cov.: 31

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.625

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.641 AC: 97421 AN: 151914 Hom.: 32137 Cov.: 31 AF XY: 0.636 AC XY: 47219 AN XY: 74234

African (AFR) AF: 0.588 AC: 24326 AN: 41382

American (AMR) AF: 0.506 AC: 7729 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2019 AN: 3468

East Asian (EAS) AF: 0.298 AC: 1535 AN: 5148

South Asian (SAS) AF: 0.651 AC: 3133 AN: 4816

European-Finnish (FIN) AF: 0.703 AC: 7419 AN: 10546

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49130 AN: 67974

Other (OTH) AF: 0.627 AC: 1323 AN: 2110

Alfa AF: 0.678 Hom.: 120648

Bravo AF: 0.616

Asia WGS AF: 0.529 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.42
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs400322; hg19: chr19-55172578;