rs3745410

chr19-54217027-A-G

Variant summary

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

The NM_006864.4(LILRB3):c.*66T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0679 in 1,612,620 control chromosomes in the GnomAD database, including 5,448 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 0.058 (531 hom., cov: 31)
  • Exomes 𝑓: 0.069 (4917 hom.)
• Consequence: LILRB3 NM_006864.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

Genes affected

LILRB3 (HGNC:6607): (leukocyte immunoglobulin like receptor B3) 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]

RPS9 (HGNC:10442): (ribosomal protein S9) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S4P family of ribosomal proteins. It is located in the cytoplasm. Variable expression of this gene in colorectal cancers compared to adjacent normal tissues has been observed, although no correlation between the level of expression and the severity of the disease has been found. As is typical for genes encoding ribosomal proteins, multiple processed pseudogenes derived from this gene are dispersed through the genome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LILRB3	NM_006864.4	c.*66T>C		3_prime_UTR_variant	13/13	ENST00000445347.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LILRB3	ENST00000445347.2	c.*66T>C		3_prime_UTR_variant	13/13	2	NM_006864.4	A2

Frequencies

GnomAD3 genomes AF: 0.0582 AC: 8848 AN: 152068 Hom.: 526 Cov.: 31

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0728

GnomAD4 exome AF: 0.0689 AC: 100575 AN: 1460432 Hom.: 4917 Cov.: 32 AF XY: 0.0704 AC XY: 51146 AN XY: 726314

Gnomad4 AFR exome AF: 0.0101

Gnomad4 AMR exome AF: 0.0881

Gnomad4 ASJ exome AF: 0.0416

Gnomad4 EAS exome AF: 0.285

Gnomad4 SAS exome AF: 0.126

Gnomad4 FIN exome AF: 0.0508

Gnomad4 NFE exome AF: 0.0585

Gnomad4 OTH exome AF: 0.0789

GnomAD4 genome AF: 0.0582 AC: 8861 AN: 152188 Hom.: 531 Cov.: 31 AF XY: 0.0610 AC XY: 4540 AN XY: 74402

Gnomad4 AFR AF: 0.0125

Gnomad4 AMR AF: 0.0830

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0458

Gnomad4 NFE AF: 0.0575

Gnomad4 OTH AF: 0.0791

Alfa AF: 0.0518 Hom.: 55

Bravo AF: 0.0588

Asia WGS AF: 0.206 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.8
Dann	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3745410; hg19: chr19-54720896; COSMIC: COSV54443116; COSMIC: COSV54443116;