19-54632001-C-G

Variant names:

• chr19-54632001-C-G
• rs1061680
• NM_001081637.3:c.425C>G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001081637.3(LILRB1):​c.425C>G​(p.Thr142Ser) variant causes a missense 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: 42)
• Consequence: LILRB1 NM_001081637.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 32 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.425C>G	p.Thr142Ser	missense	Exon 5 of 15	NP_001075106.2
	LILRB1	NM_001388358.1		c.425C>G	p.Thr142Ser	missense	Exon 6 of 16	NP_001375287.1
	LILRB1	NM_001081638.4		c.425C>G	p.Thr142Ser	missense	Exon 5 of 15	NP_001075107.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRB1	ENST00000324602.12	TSL:5 MANE Select	c.425C>G	p.Thr142Ser	missense	Exon 5 of 15	ENSP00000315997.7
	LILRB1	ENST00000396315.5	TSL:1	c.425C>G	p.Thr142Ser	missense	Exon 4 of 14	ENSP00000379608.1
	LILRB1	ENST00000396327.7	TSL:1	c.425C>G	p.Thr142Ser	missense	Exon 5 of 15	ENSP00000379618.3

Frequencies

GnomAD3 genomes Cov.: 42

GnomAD4 exome Cov.: 102

GnomAD4 genome Cov.: 42

Alfa AF: 0.00 Hom.: 69542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
CADD	Benign	15
DEOGEN2	Benign	0.21	T
LIST_S2	Benign	0.66	T
MetaRNN	Benign	0.25	T
PhyloP100		-0.22
Sift4G	Benign	0.20	T
Vest4		0.29
gMVP		0.050

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.41		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.41		Position offset: -5

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

Other links and lift over

dbSNP: rs1061680;