Variant 19-54595357-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_006863.4(LILRA1):c.616C>T(p.His206Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.019 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00024 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

LILRA1
NM_006863.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.15

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0038981438).

BP6

Variant 19-54595357-C-T is Benign according to our data. Variant chr19-54595357-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3118732.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LILRA1	NM_006863.4 linkuse as main transcript	c.616C>T	p.His206Tyr	missense_variant	5/10	ENST00000251372.8	NP_006854.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LILRA1	ENST00000251372.8 linkuse as main transcript	c.616C>T	p.His206Tyr	missense_variant	5/10	1	NM_006863.4	ENSP00000251372	P1	O75019-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

1688

AN:

88082

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0248

Gnomad AMI

AF:

0.0122

Gnomad AMR

AF:

0.0146

Gnomad ASJ

AF:

0.0271

Gnomad EAS

AF:

0.00895

Gnomad SAS

AF:

0.0700

Gnomad FIN

AF:

0.00872

Gnomad MID

AF:

0.00450

Gnomad NFE

AF:

0.0166

Gnomad OTH

AF:

0.0182

GnomAD3 exomes

AF:

0.000386

AC:

AN:

250996

Hom.:

AF XY:

0.000369

AC XY:

AN XY:

135640

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.000347

Gnomad ASJ exome

AF:

0.00399

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000654

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000194

Gnomad OTH exome

AF:

0.000490

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000235

AC:

332

AN:

1411476

Hom.:

Cov.:

AF XY:

0.000236

AC XY:

166

AN XY:

703052

show subpopulations

Gnomad4 AFR exome

AF:

0.00126

Gnomad4 AMR exome

AF:

0.000525

Gnomad4 ASJ exome

AF:

0.00427

Gnomad4 EAS exome

AF:

0.000103

Gnomad4 SAS exome

AF:

0.000110

Gnomad4 FIN exome

AF:

0.0000190

Gnomad4 NFE exome

AF:

0.000103

Gnomad4 OTH exome

AF:

0.000583

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0192

AC:

1688

AN:

88140

Hom.:

Cov.:

AF XY:

0.0206

AC XY:

895

AN XY:

43446

show subpopulations

Gnomad4 AFR

AF:

0.0248

Gnomad4 AMR

AF:

0.0146

Gnomad4 ASJ

AF:

0.0271

Gnomad4 EAS

AF:

0.00897

Gnomad4 SAS

AF:

0.0699

Gnomad4 FIN

AF:

0.00872

Gnomad4 NFE

AF:

0.0166

Gnomad4 OTH

AF:

0.0188

Alfa

AF:

0.102

Hom.:

3193

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.000233

AC:

ExAC

AF:

0.000354

AC:

EpiCase

AF:

0.000273

EpiControl

AF:

0.000119

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 08, 2023

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.048

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.087

DANN

Benign

0.65

DEOGEN2

Benign

0.00036

T;.

Eigen

Benign

-2.1

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.00073

M_CAP

Benign

0.0065

MetaRNN

Benign

0.0039

T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

-2.0

N;N

MutationTaster

Benign

1.0

N;N;N;N;N

PrimateAI

Benign

0.30

PROVEAN

Benign

1.6

N;N

REVEL

Benign

0.0090

Sift

Benign

0.93

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.089

MVP

0.040

MPC

0.025

ClinPred

0.0014

GERP RS

-2.0

Varity_R

0.029

gMVP

0.022

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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