rs448083

Variant names:

• chr19-54281065-T-A
• rs448083
• NM_001080978.4:c.-153A>T

Your query was ambiguous. Multiple possible variants found:

• chr19-54281065-T-A
• chr19-54281065-T-C
• chr19-54281065-T-G

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 12 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 -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LILRB2	NM_001080978.4	c.-153A>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 14	ENST00000314446.10	NP_001074447.2
LILRB2	NM_001080978.4	c.-153A>T		5_prime_UTR_variant	Exon 1 of 14	ENST00000314446.10	NP_001074447.2

Ensembl

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0639 AC: 445 AN: 6964

American (AMR) AF: 0.0348 AC: 768 AN: 22038

Ashkenazi Jewish (ASJ) AF: 0.0983 AC: 719 AN: 7312

East Asian (EAS) AF: 0.00957 AC: 81 AN: 8460

South Asian (SAS) AF: 0.0534 AC: 2690 AN: 50358

European-Finnish (FIN) AF: 0.0596 AC: 660 AN: 11074

Middle Eastern (MID) AF: 0.0682 AC: 124 AN: 1818

European-Non Finnish (NFE) AF: 0.0814 AC: 11446 AN: 140534

Other (OTH) AF: 0.0707 AC: 844 AN: 11946

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00275 AC: 104 AN: 37846

American (AMR) AF: 0.00274 AC: 39 AN: 14236

Ashkenazi Jewish (ASJ) AF: 0.00242 AC: 8 AN: 3300

East Asian (EAS) AF: 0.000413 AC: 2 AN: 4840

South Asian (SAS) AF: 0.00291 AC: 13 AN: 4468

European-Finnish (FIN) AF: 0.00244 AC: 24 AN: 9830

Middle Eastern (MID) AF: 0.00735 AC: 2 AN: 272

European-Non Finnish (NFE) AF: 0.00176 AC: 113 AN: 64248

Other (OTH) AF: 0.00463 AC: 9 AN: 1942

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 3867

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.072
PhyloP100		-2.4
PromoterAI		0.022	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: -;