chr19-54632001-C-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_001081637.3(LILRB1):​c.425C>T​(p.Thr142Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 4/5 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.43 (2631 hom., cov: 42)
  • Exomes 𝑓: 0.63 (258796 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.30447322).

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>T	p.Thr142Ile	missense	Exon 5 of 15	NP_001075106.2
	LILRB1	NM_001388358.1		c.425C>T	p.Thr142Ile	missense	Exon 6 of 16	NP_001375287.1
	LILRB1	NM_001081638.4		c.425C>T	p.Thr142Ile	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>T	p.Thr142Ile	missense	Exon 5 of 15	ENSP00000315997.7
	LILRB1	ENST00000396315.5	TSL:1	c.425C>T	p.Thr142Ile	missense	Exon 4 of 14	ENSP00000379608.1
	LILRB1	ENST00000396327.7	TSL:1	c.425C>T	p.Thr142Ile	missense	Exon 5 of 15	ENSP00000379618.3

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65450 AN: 150794 Hom.: 2625 Cov.: 42

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.436

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.629 AC: 918571 AN: 1460210 Hom.: 258796 Cov.: 102 AF XY: 0.627 AC XY: 455439 AN XY: 726208

African (AFR) AF: 0.387 AC: 12940 AN: 33466

American (AMR) AF: 0.442 AC: 19732 AN: 44692

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 14592 AN: 26078

East Asian (EAS) AF: 0.355 AC: 14089 AN: 39668

South Asian (SAS) AF: 0.602 AC: 51890 AN: 86168

European-Finnish (FIN) AF: 0.534 AC: 28428 AN: 53258

Middle Eastern (MID) AF: 0.556 AC: 3207 AN: 5766

European-Non Finnish (NFE) AF: 0.665 AC: 738466 AN: 1110794

Other (OTH) AF: 0.584 AC: 35227 AN: 60320

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.434 AC: 65503 AN: 150916 Hom.: 2631 Cov.: 42 AF XY: 0.435 AC XY: 32027 AN XY: 73696

African (AFR) AF: 0.341 AC: 14020 AN: 41116

American (AMR) AF: 0.413 AC: 6251 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1558 AN: 3444

East Asian (EAS) AF: 0.339 AC: 1746 AN: 5158

South Asian (SAS) AF: 0.489 AC: 2335 AN: 4772

European-Finnish (FIN) AF: 0.494 AC: 5181 AN: 10494

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 32911 AN: 67488

Other (OTH) AF: 0.438 AC: 916 AN: 2092

Alfa AF: 0.676 Hom.: 69542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
CADD	Benign	16
DEOGEN2	Benign	0.25	T
LIST_S2	Benign	0.67	T
MetaRNN	Benign	0.30	T
PhyloP100		-0.22
Sift4G	Uncertain	0.039	D
Vest4		0.35
gMVP		0.13

Splicing

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

Other links and lift over

dbSNP: rs1061680;