19-54281065-T-G

Variant names:

• chr19-54281065-T-G
• rs448083
• ENST00000493242.1:n.33A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000493242.1(LILRB2):​n.33A>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 0.00000338 in 295,432 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: LILRB2 ENST00000493242.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (Cadd=0.077).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LILRB2	NM_001080978.4	c.-153A>C		5_prime_UTR_variant	Exon 1 of 14	ENST00000314446.10	NP_001074447.2
LILRB2	NM_005874.5	c.-153A>C		5_prime_UTR_variant	Exon 1 of 14		NP_005865.3
LILRB2	NM_001278404.3	c.-350A>C		5_prime_UTR_variant	Exon 1 of 13		NP_001265333.2
LILRB2	NM_001278403.3	c.-310A>C		upstream_gene_variant			NP_001265332.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LILRB2	ENST00000314446.10	c.-153A>C		5_prime_UTR_variant	Exon 1 of 14	1	NM_001080978.4	ENSP00000319960.5

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000338 AC: 1 AN: 295432 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 164752

African (AFR) AF: 0.00 AC: 0 AN: 8154

American (AMR) AF: 0.00 AC: 0 AN: 24558

Ashkenazi Jewish (ASJ) AF: 0.000111 AC: 1 AN: 9042

East Asian (EAS) AF: 0.00 AC: 0 AN: 8844

South Asian (SAS) AF: 0.00 AC: 0 AN: 56568

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12300

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2110

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 160276

Other (OTH) AF: 0.00 AC: 0 AN: 13580

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.077
PhyloP100		-2.4
PromoterAI		0.047	Neutral

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: rs448083; hg19: -;