Variant 19-54594453-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The ENST00000251372.8(LILRA1):c.47G>A(p.Gly16Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.23 ( 0 hom., cov: 34)

Exomes 𝑓: 0.051 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

LILRA1
ENST00000251372.8 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.402

Variant links:

Genes affected

LILRA1 (HGNC:6602): (leukocyte immunoglobulin like receptor A1) This gene encodes an activating member of the leukocyte immunoglobulin-like receptor (LIR) family, which is found in a gene cluster at chromosomal region 19q13.4. The encoded protein is predominantly expressed in B cells, interacts with major histocompatibility complex class I ligands, and contributes to the regulation of immune responses. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013]

LILRA1 links:

LILRA1 (HGNC:):

LILRA1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.09820765).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LILRA1	NM_006863.4 linkuse as main transcript	c.47G>A	p.Gly16Asp	missense_variant	3/10	ENST00000251372.8	NP_006854.1	O75019-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LILRA1	ENST00000251372.8 linkuse as main transcript	c.47G>A	p.Gly16Asp	missense_variant	3/10	1	NM_006863.4	ENSP00000251372.3		O75019-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

13924

AN:

60326

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.312

Gnomad AMI

AF:

0.312

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.313

Gnomad EAS

AF:

0.0775

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.179

Gnomad MID

AF:

0.349

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.249

GnomAD3 exomes

AF:

0.0000318

AC:

AN:

251430

Hom.:

AF XY:

0.0000221

AC XY:

AN XY:

135896

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000435

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.0506

AC:

25342

AN:

500930

Hom.:

Cov.:

132

AF XY:

0.0544

AC XY:

13563

AN XY:

249428

show subpopulations

Gnomad4 AFR exome

AF:

0.139

Gnomad4 AMR exome

AF:

0.0867

Gnomad4 ASJ exome

AF:

0.105

Gnomad4 EAS exome

AF:

0.0185

Gnomad4 SAS exome

AF:

0.220

Gnomad4 FIN exome

AF:

0.0490

Gnomad4 NFE exome

AF:

0.0374

Gnomad4 OTH exome

AF:

0.0562

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.231

AC:

13934

AN:

60342

Hom.:

Cov.:

AF XY:

0.224

AC XY:

6654

AN XY:

29688

show subpopulations

Gnomad4 AFR

AF:

0.312

Gnomad4 AMR

AF:

0.219

Gnomad4 ASJ

AF:

0.313

Gnomad4 EAS

AF:

0.0774

Gnomad4 SAS

AF:

0.266

Gnomad4 FIN

AF:

0.179

Gnomad4 NFE

AF:

0.206

Gnomad4 OTH

AF:

0.249

Alfa

AF:

0.273

Hom.:

ExAC

AF:

0.00000824

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 07, 2023

The c.47G>A (p.G16D) alteration is located in exon 3 (coding exon 2) of the LILRA1 gene. This alteration results from a G to A substitution at nucleotide position 47, causing the glycine (G) at amino acid position 16 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.096

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.64

CADD

Benign

8.8

DANN

Benign

0.85

DEOGEN2

Benign

0.020

T;.

Eigen

Benign

-0.90

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.013

M_CAP

Benign

0.0038

MetaRNN

Benign

0.098

T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

1.9

L;L

MutationTaster

Benign

1.0

N;N;N;N;N

PrimateAI

Benign

0.31

PROVEAN

Pathogenic

-4.5

D;D

REVEL

Benign

0.043

Sift

Benign

0.081

T;T

Sift4G

Benign

0.083

T;T

Polyphen

0.032

B;B

Vest4

0.33

MutPred

0.54

Loss of methylation at R18 (P = 0.0754);Loss of methylation at R18 (P = 0.0754);

MVP

0.13

MPC

0.030

ClinPred

0.094

GERP RS

-1.9

Varity_R

0.18

gMVP

0.090

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over