Variant 14-24311158-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019839.5(LTB4R2):c.494A>G(p.Asp165Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00692 in 1,602,994 control chromosomes in the GnomAD database, including 717 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 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 0.038 ( 365 hom., cov: 33)

Exomes 𝑓: 0.0037 ( 352 hom. )

Consequence

LTB4R2
NM_019839.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.889

Variant links:

Genes affected

LTB4R2 (HGNC:19260): (leukotriene B4 receptor 2) Predicted to enable G protein-coupled peptide receptor activity and leukotriene B4 receptor activity. Predicted to be involved in inflammatory response and neuropeptide signaling pathway. Predicted to act upstream of or within keratinocyte migration and signal transduction. Located in nucleoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

LTB4R2 links:

CIDEB (HGNC:1977): (cell death inducing DFFA like effector b) Enables identical protein binding activity. Involved in activation of cysteine-type endopeptidase activity; positive regulation of cell death; and positive regulation of release of cytochrome c from mitochondria. Acts upstream of or within apoptotic process. Located in cytosol and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

CIDEB links:

CIDEB (HGNC:):

CIDEB links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001957804).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LTB4R2	NM_019839.5 linkuse as main transcript	c.494A>G	p.Asp165Gly	missense_variant	2/2	ENST00000533293.2	NP_062813.2	Q9NPC1B4E292

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LTB4R2	ENST00000533293.2 linkuse as main transcript	c.494A>G	p.Asp165Gly	missense_variant	2/2	1	NM_019839.5	ENSP00000433290.1		Q9NPC1

Frequencies

GnomAD3 genomes

AF:

0.0376

AC:

5727

AN:

152128

Hom.:

364

Cov.:

show subpopulations

Gnomad AFR

AF:

0.131

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0133

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.000279

Gnomad OTH

AF:

0.0282

GnomAD3 exomes

AF:

0.00767

AC:

1698

AN:

221512

Hom.:

AF XY:

0.00564

AC XY:

688

AN XY:

121886

show subpopulations

Gnomad AFR exome

AF:

0.118

Gnomad AMR exome

AF:

0.00439

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000174

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000114

Gnomad OTH exome

AF:

0.00454

GnomAD4 exome

AF:

0.00369

AC:

5352

AN:

1450758

Hom.:

352

Cov.:

AF XY:

0.00312

AC XY:

2254

AN XY:

721282

show subpopulations

Gnomad4 AFR exome

AF:

0.138

Gnomad4 AMR exome

AF:

0.00574

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000354

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000686

Gnomad4 OTH exome

AF:

0.00778

GnomAD4 genome

AF:

0.0377

AC:

5737

AN:

152236

Hom.:

365

Cov.:

AF XY:

0.0364

AC XY:

2706

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.131

Gnomad4 AMR

AF:

0.0133

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000279

Gnomad4 OTH

AF:

0.0279

Alfa

AF:

0.00965

Hom.:

Bravo

AF:

0.0423

ESP6500AA

AF:

0.103

AC:

450

ESP6500EA

AF:

0.000235

AC:

ExAC

AF:

0.00965

AC:

1151

Asia WGS

AF:

0.00810

AC:

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.087

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.50

CADD

Benign

3.3

DANN

Benign

0.89

DEOGEN2

Benign

0.061

T;.;.;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.046

MetaRNN

Benign

0.0020

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.0

L;.;.;.

PrimateAI

Benign

0.44

PROVEAN

Benign

-1.4

N;N;N;N

REVEL

Benign

0.10

Sift

Benign

0.26

T;T;T;T

Sift4G

Benign

0.41

T;T;T;T

Polyphen

0.0

B;.;.;.

Vest4

0.079

MVP

0.56

MPC

0.70

ClinPred

0.0031

GERP RS

-1.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.26

gMVP

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over