chr19-54281065-T-A

Position:

• chr19-54281065-T-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001080978.4(LILRB2):​c.-153A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00223 in 141,826 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: 𝑓 0.0022 (0 hom., cov: 31)
  • Exomes 𝑓: 0.068 (23 hom.)
  • Failed GnomAD Quality Control
• Consequence: LILRB2 NM_001080978.4 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

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]

LILRB2 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.072).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LILRB2	NM_001080978.4	c.-153A>T		5_prime_UTR_premature_start_codon_gain_variant	1/14	ENST00000314446.10	NP_001074447.2
LILRB2	NM_001080978.4	c.-153A>T		5_prime_UTR_variant	1/14	ENST00000314446.10	NP_001074447.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LILRB2	ENST00000314446.10	c.-153A>T		5_prime_UTR_premature_start_codon_gain_variant	1/14	1	NM_001080978.4	ENSP00000319960.5
LILRB2	ENST00000314446.10	c.-153A>T		5_prime_UTR_variant	1/14	1	NM_001080978.4	ENSP00000319960.5

Frequencies

GnomAD3 genomes AF: 0.00222 AC: 315 AN: 141724 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00276

Gnomad AMI AF: 0.00237

Gnomad AMR AF: 0.00274

Gnomad ASJ AF: 0.00242

Gnomad EAS AF: 0.000619

Gnomad SAS AF: 0.00268

Gnomad FIN AF: 0.00244

Gnomad MID AF: 0.00690

Gnomad NFE AF: 0.00176

Gnomad OTH AF: 0.00415

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0682 AC: 17777 AN: 260504 Hom.: 23 Cov.: 4 AF XY: 0.0672 AC XY: 9775 AN XY: 145496

Gnomad4 AFR exome AF: 0.0639

Gnomad4 AMR exome AF: 0.0348

Gnomad4 ASJ exome AF: 0.0983

Gnomad4 EAS exome AF: 0.00957

Gnomad4 SAS exome AF: 0.0534

Gnomad4 FIN exome AF: 0.0596

Gnomad4 NFE exome AF: 0.0814

Gnomad4 OTH exome AF: 0.0707

GnomAD4 genome AF: 0.00223 AC: 316 AN: 141826 Hom.: 0 Cov.: 31 AF XY: 0.00244 AC XY: 169 AN XY: 69212

Gnomad4 AFR AF: 0.00275

Gnomad4 AMR AF: 0.00274

Gnomad4 ASJ AF: 0.00242

Gnomad4 EAS AF: 0.000413

Gnomad4 SAS AF: 0.00291

Gnomad4 FIN AF: 0.00244

Gnomad4 NFE AF: 0.00176

Gnomad4 OTH AF: 0.00463

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.072

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: rs448083; hg19: -;