Genetic Variant LTB4R:p.Gly309Gly (chr14-24316578-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001143919.3(LTB4R):c.927C>T(p.Gly309Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 1,442,756 control chromosomes in the GnomAD database, including 18,843 homozygotes. 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 0.13 ( 1911 hom., cov: 33)

Exomes 𝑓: 0.14 ( 16932 hom. )

Consequence

LTB4R
NM_001143919.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.383

Variant links:

Genes affected

LTB4R (HGNC:6713): (leukotriene B4 receptor) 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 signal transduction. Predicted to be located in plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

LTB4R links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP7

Synonymous conserved (PhyloP=-0.383 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LTB4R	NM_001143919.3 link	c.927C>T	p.Gly309Gly	synonymous_variant	Exon 2 of 2	ENST00000345363.8	NP_001137391.1	Q15722
LTB4R	NM_181657.3 link	c.927C>T	p.Gly309Gly	synonymous_variant	Exon 2 of 2		NP_858043.1	Q15722

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
LTB4R	ENST00000345363.8 link	c.927C>T	p.Gly309Gly	synonymous_variant	Exon 2 of 2	1	NM_001143919.3	ENSP00000307445.3	Q15722
LTB4R	ENST00000396782.2 link	c.927C>T	p.Gly309Gly	synonymous_variant	Exon 2 of 2	1		ENSP00000380002.2	Q15722
LTB4R	ENST00000396789.4 link	c.927C>T	p.Gly309Gly	synonymous_variant	Exon 2 of 2	1		ENSP00000380008.4	Q15722
LTB4R	ENST00000556141.1 link	c.627C>T	p.Gly209Gly	synonymous_variant	Exon 2 of 2	3		ENSP00000451929.1	G3V4Q5

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20325

AN:

151934

Hom.:

1916

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0962

Gnomad AMI

AF:

0.0286

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.517

Gnomad SAS

AF:

0.284

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.124

GnomAD3 exomes

AF:

0.226

AC:

10719

AN:

47400

Hom.:

1596

AF XY:

0.225

AC XY:

6299

AN XY:

27956

show subpopulations

Gnomad AFR exome

AF:

0.123

Gnomad AMR exome

AF:

0.215

Gnomad ASJ exome

AF:

0.176

Gnomad EAS exome

AF:

0.597

Gnomad SAS exome

AF:

0.314

Gnomad FIN exome

AF:

0.209

Gnomad NFE exome

AF:

0.138

Gnomad OTH exome

AF:

0.171

GnomAD4 exome

AF:

0.137

AC:

177265

AN:

1290714

Hom.:

16932

Cov.:

AF XY:

0.141

AC XY:

89116

AN XY:

633110

show subpopulations

Gnomad4 AFR exome

AF:

0.0889

Gnomad4 AMR exome

AF:

0.172

Gnomad4 ASJ exome

AF:

0.149

Gnomad4 EAS exome

AF:

0.608

Gnomad4 SAS exome

AF:

0.271

Gnomad4 FIN exome

AF:

0.191

Gnomad4 NFE exome

AF:

0.113

Gnomad4 OTH exome

AF:

0.145

GnomAD4 genome

AF:

0.134

AC:

20306

AN:

152042

Hom.:

1911

Cov.:

AF XY:

0.143

AC XY:

10616

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.0961

Gnomad4 AMR

AF:

0.131

Gnomad4 ASJ

AF:

0.142

Gnomad4 EAS

AF:

0.517

Gnomad4 SAS

AF:

0.282

Gnomad4 FIN

AF:

0.191

Gnomad4 NFE

AF:

0.110

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.0780

Hom.:

145

Bravo

AF:

0.128

Asia WGS

AF:

0.378

AC:

1310

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

9.5

DANN

Benign

0.94

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