14-24316578-C-G

Variant names:

• chr14-24316578-C-G
• rs1046584
• NM_001143919.3:c.927C>G

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001143919.3(LTB4R):​c.927C>G​(p.Gly309Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: LTB4R NM_001143919.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 14 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BP7: Synonymous conserved (PhyloP=-0.383 with no splicing effect.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	9.2
DANN	Benign	0.81
PhyloP100		-0.38

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

Other links and lift over

dbSNP: rs1046584; hg19: chr14-24785784;