19-54630503-A-T

Variant names:

• chr19-54630503-A-T
• rs3760860
• NM_001081637.3:c.-179A>T

Variant summary

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

The NM_001081637.3(LILRB1):​c.-179A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000324 in 308,168 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: 37)
  • Exomes 𝑓: 0.0000032 (0 hom.)
• Consequence: LILRB1 NM_001081637.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 0 publications found

Genes affected

LILRB1 (HGNC:6605): (leukocyte immunoglobulin like receptor B1) 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 (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001081637.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRB1	NM_001081637.3	MANE Select	c.-179A>T		5_prime_UTR	Exon 1 of 15	NP_001075106.2
	LILRB1	NM_001081638.4		c.-179A>T		5_prime_UTR	Exon 1 of 15	NP_001075107.2
	LILRB1	NM_001081639.4		c.-179A>T		5_prime_UTR	Exon 1 of 15	NP_001075108.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRB1	ENST00000324602.12	TSL:5 MANE Select	c.-179A>T		5_prime_UTR	Exon 1 of 15	ENSP00000315997.7
	LILRB1	ENST00000396327.7	TSL:1	c.-179A>T		5_prime_UTR	Exon 1 of 15	ENSP00000379618.3
	LILRB1	ENST00000396331.5	TSL:1	c.-165-14A>T		intron	N/A	ENSP00000379622.1

Frequencies

GnomAD3 genomes Cov.: 37

GnomAD4 exome AF: 0.00000324 AC: 1 AN: 308168 Hom.: 0 Cov.: 3 AF XY: 0.00000578 AC XY: 1 AN XY: 172868

African (AFR) AF: 0.00 AC: 0 AN: 9188

American (AMR) AF: 0.00 AC: 0 AN: 25474

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10576

East Asian (EAS) AF: 0.00 AC: 0 AN: 10176

South Asian (SAS) AF: 0.00 AC: 0 AN: 57752

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 14200

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2512

European-Non Finnish (NFE) AF: 0.00000612 AC: 1 AN: 163450

Other (OTH) AF: 0.00 AC: 0 AN: 14840

GnomAD4 genome Cov.: 37

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
PhyloP100		-0.38
PromoterAI		-0.028	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3760860; hg19: chr19-55141954;