rs112549096

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001081442.3(LILRB5):​c.1666G>T​(p.Ala556Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000278 in 1,440,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A556T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 26)
Exomes 𝑓: 0.0000028 ( 0 hom. )

Consequence

LILRB5
NM_001081442.3 missense

Scores

1
3
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33
Variant links:
Genes affected
LILRB5 (HGNC:6609): (leukocyte immunoglobulin like receptor B5) 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). Several other LIR subfamily B receptors are expressed on immune cells where they bind to MHC class I molecules on antigen-presenting cells and inhibit stimulation of an immune response. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.1584506).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LILRB5NM_001081442.3 linkc.1666G>T p.Ala556Ser missense_variant Exon 13 of 13 ENST00000449561.3 NP_001074911.2 O75023-3
LILRB5NM_001304457.3 linkc.1876G>T p.Ala626Ser missense_variant Exon 13 of 13 NP_001291386.2 O75023
LILRB5NM_006840.5 linkc.1663G>T p.Ala555Ser missense_variant Exon 13 of 13 NP_006831.2 O75023-1
LILRB5NM_001081443.3 linkc.1366G>T p.Ala456Ser missense_variant Exon 12 of 12 NP_001074912.2 O75023-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LILRB5ENST00000449561.3 linkc.1666G>T p.Ala556Ser missense_variant Exon 13 of 13 1 NM_001081442.3 ENSP00000406478.1 O75023-3

Frequencies

GnomAD3 genomes
Cov.:
26
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251232
Hom.:
0
AF XY:
0.00000736
AC XY:
1
AN XY:
135840
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.00000278
AC:
4
AN:
1440584
Hom.:
0
Cov.:
36
AF XY:
0.00000419
AC XY:
3
AN XY:
716708
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000765
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000170
GnomAD4 genome
Cov.:
26
Alfa
AF:
0.0000171
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.19
BayesDel_addAF
Benign
-0.17
T
BayesDel_noAF
Benign
-0.49
CADD
Benign
20
DANN
Uncertain
0.99
Eigen
Benign
-0.39
Eigen_PC
Benign
-0.67
FATHMM_MKL
Benign
0.036
N
M_CAP
Benign
0.0049
T
MetaRNN
Benign
0.16
T;T;T
MetaSVM
Benign
-0.99
T
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-1.9
N;N;N
REVEL
Benign
0.055
Sift
Uncertain
0.0010
D;D;D
Sift4G
Pathogenic
0.0010
D;D;D
Vest4
0.23
MutPred
0.39
Gain of phosphorylation at A555 (P = 0.0528);.;.;
MVP
0.13
MPC
0.29
ClinPred
0.72
D
GERP RS
-0.70
gMVP
0.12

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs112549096; hg19: chr19-54754760; API