14-24316578-C-T

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

2

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]

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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
LTB4RNM_001143919.3 linkc.927C>T p.Gly309Gly synonymous_variant Exon 2 of 2 ENST00000345363.8 NP_001137391.1 Q15722
LTB4RNM_181657.3 linkc.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 Appris UniProt
LTB4RENST00000345363.8 linkc.927C>T p.Gly309Gly synonymous_variant Exon 2 of 2 1 NM_001143919.3 ENSP00000307445.3 Q15722
LTB4RENST00000396782.2 linkc.927C>T p.Gly309Gly synonymous_variant Exon 2 of 2 1 ENSP00000380002.2 Q15722
LTB4RENST00000396789.4 linkc.927C>T p.Gly309Gly synonymous_variant Exon 2 of 2 1 ENSP00000380008.4 Q15722
LTB4RENST00000556141.1 linkc.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.:
33
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.:
32
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.:
33
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.

Other links and lift over

dbSNP: rs1046584; hg19: chr14-24785784; COSMIC: COSV60252897; COSMIC: COSV60252897; API