NM_001081637.3:c.-49+17A>T

Variant names:

• chr19-54630650-A-T
• rs3760861
• NM_001081637.3:c.-49+17A>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.-49+17A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LILRB1 NM_001081637.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 8 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=-1.02).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRB1	NM_001081637.3	MANE Select	c.-49+17A>T		intron	N/A	NP_001075106.2	A0A087WSV6
	LILRB1	NM_001388358.1		c.-49+17A>T		intron	N/A	NP_001375287.1	A0A087WSV6
	LILRB1	NM_001081638.4		c.-49+17A>T		intron	N/A	NP_001075107.2	A0A087WSX8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRB1	ENST00000324602.12	TSL:5 MANE Select	c.-49+17A>T		intron	N/A	ENSP00000315997.7	A0A087WSV6
	LILRB1	ENST00000396327.7	TSL:1	c.-49+17A>T		intron	N/A	ENSP00000379618.3	A0A087WSX8
	LILRB1	ENST00000396332.8	TSL:1	c.-49+17A>T		intron	N/A	ENSP00000379623.4	D9IDM5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 680622 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 358940

African (AFR) AF: 0.00 AC: 0 AN: 16524

American (AMR) AF: 0.00 AC: 0 AN: 34202

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18492

East Asian (EAS) AF: 0.00 AC: 0 AN: 25402

South Asian (SAS) AF: 0.00 AC: 0 AN: 66714

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31320

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4044

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 452034

Other (OTH) AF: 0.00 AC: 0 AN: 31890

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 3409

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
PhyloP100		-2.7
PromoterAI		0.019	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: rs3760861; hg19: chr19-55142101;