ENST00000414379.5:n.*1469T>C

Variant names:

• chr19-54217027-A-G
• rs3745410
• ENST00000414379.5:n.*1469T>C

Variant summary

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

The ENST00000414379.5(LILRB3):​n.*1469T>C variant causes a non coding transcript exon 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 ENST00000414379.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 10 publications found

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]

ENSG00000300027 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LILRB3	NM_006864.4	c.*66T>C		3_prime_UTR_variant	Exon 13 of 13	ENST00000445347.2	NP_006855.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LILRB3	ENST00000445347.2	c.*66T>C		3_prime_UTR_variant	Exon 13 of 13	2	NM_006864.4	ENSP00000388199.2

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

African (AFR) AF: 0.0101 AC: 337 AN: 33452

American (AMR) AF: 0.0881 AC: 3932 AN: 44640

Ashkenazi Jewish (ASJ) AF: 0.0416 AC: 1085 AN: 26060

East Asian (EAS) AF: 0.285 AC: 11291 AN: 39658

South Asian (SAS) AF: 0.126 AC: 10840 AN: 86188

European-Finnish (FIN) AF: 0.0508 AC: 2713 AN: 53360

Middle Eastern (MID) AF: 0.105 AC: 606 AN: 5766

European-Non Finnish (NFE) AF: 0.0585 AC: 65013 AN: 1110988

Other (OTH) AF: 0.0789 AC: 4758 AN: 60320

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

African (AFR) AF: 0.0125 AC: 518 AN: 41542

American (AMR) AF: 0.0830 AC: 1270 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3464

East Asian (EAS) AF: 0.317 AC: 1634 AN: 5158

South Asian (SAS) AF: 0.141 AC: 679 AN: 4820

European-Finnish (FIN) AF: 0.0458 AC: 485 AN: 10598

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0575 AC: 3913 AN: 67998

Other (OTH) AF: 0.0791 AC: 167 AN: 2110

Alfa AF: 0.0487 Hom.: 64

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
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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