19-54632001-C-T

Position:

• chr19-54632001-C-T

Variant summary

Our verdict is Likely benign. Variant got -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. 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

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

Verdict is Likely_benign. Variant got -1 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LILRB1	NM_001081637.3	c.425C>T	p.Thr142Ile	missense_variant	5/15	ENST00000324602.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LILRB1	ENST00000324602.12	c.425C>T	p.Thr142Ile	missense_variant	5/15	5	NM_001081637.3	P4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 65450 AN: 150794 Hom.: 2625 Cov.: 42 FAILED QC

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

Gnomad4 AFR exome AF: 0.387

Gnomad4 AMR exome AF: 0.442

Gnomad4 ASJ exome AF: 0.560

Gnomad4 EAS exome AF: 0.355

Gnomad4 SAS exome AF: 0.602

Gnomad4 FIN exome AF: 0.534

Gnomad4 NFE exome AF: 0.665

Gnomad4 OTH exome AF: 0.584

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

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.438

Alfa AF: 0.693 Hom.: 51367

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	16
DEOGEN2	Benign	0.25	T;T;.;.;T;.;.
LIST_S2	Benign	0.67	T;T;T;T;T;T;.
MetaRNN	Benign	0.30	T;T;T;T;T;T;T
Sift4G	Uncertain	0.039	D;D;D;D;D;D;D
Vest4		0.35
gMVP		0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1061680; hg19: -;