chr19-54630503-A-G

Variant names:

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

Variant summary

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

The NM_001081637.3(LILRB1):​c.-179A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 148,530 control chromosomes in the GnomAD database, including 18,371 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 0.53 (18371 hom., cov: 37)
  • Exomes 𝑓: 0.56 (39416 hom.)
  • Failed GnomAD Quality Control
• Consequence: LILRB1 NM_001081637.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 11 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

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>G		5_prime_UTR	Exon 1 of 15	NP_001075106.2
	LILRB1	NM_001081638.4		c.-179A>G		5_prime_UTR	Exon 1 of 15	NP_001075107.2
	LILRB1	NM_001081639.4		c.-179A>G		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>G		5_prime_UTR	Exon 1 of 15	ENSP00000315997.7
	LILRB1	ENST00000396327.7	TSL:1	c.-179A>G		5_prime_UTR	Exon 1 of 15	ENSP00000379618.3
	LILRB1	ENST00000396331.5	TSL:1	c.-165-14A>G		intron	N/A	ENSP00000379622.1

Frequencies

GnomAD3 genomes AF: 0.532 AC: 78923 AN: 148416 Hom.: 18370 Cov.: 37

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.511

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.560 AC: 171768 AN: 306508 Hom.: 39416 Cov.: 3 AF XY: 0.566 AC XY: 97252 AN XY: 171868

African (AFR) AF: 0.399 AC: 3645 AN: 9144

American (AMR) AF: 0.436 AC: 11057 AN: 25346

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 5802 AN: 10534

East Asian (EAS) AF: 0.384 AC: 3910 AN: 10174

South Asian (SAS) AF: 0.600 AC: 34512 AN: 57542

European-Finnish (FIN) AF: 0.583 AC: 8234 AN: 14120

Middle Eastern (MID) AF: 0.532 AC: 1319 AN: 2480

European-Non Finnish (NFE) AF: 0.586 AC: 95164 AN: 162410

Other (OTH) AF: 0.551 AC: 8125 AN: 14758

GnomAD4 genome AF: 0.532 AC: 78970 AN: 148530 Hom.: 18371 Cov.: 37 AF XY: 0.529 AC XY: 38390 AN XY: 72628

African (AFR) AF: 0.412 AC: 16891 AN: 40950

American (AMR) AF: 0.481 AC: 7244 AN: 15052

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1896 AN: 3372

East Asian (EAS) AF: 0.375 AC: 1932 AN: 5148

South Asian (SAS) AF: 0.634 AC: 2940 AN: 4640

European-Finnish (FIN) AF: 0.594 AC: 6108 AN: 10280

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.609 AC: 40123 AN: 65858

Other (OTH) AF: 0.515 AC: 1064 AN: 2066

Alfa AF: 0.602 Hom.: 2865

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
PhyloP100		-0.38
PromoterAI		0.012	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;