14-24315703-TC-AG

Variant names:

• chr14-24315703-TC-AG
• NM_001143919.3:c.52_53delTCinsAG
• LTB4R p.19

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP7

The NM_001143919.3(LTB4R):​c.52_53delTCinsAG​(p.19) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LTB4R NM_001143919.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 0 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 -1 ACMG points.

• BP7: Synonymous conserved (PhyloP=-2.04 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001143919.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LTB4R	NM_001143919.3	MANE Select	c.52_53delTCinsAG	p.19	synonymous	N/A	NP_001137391.1	Q15722
	LTB4R	NM_181657.3		c.52_53delTCinsAG	p.19	synonymous	N/A	NP_858043.1	Q15722

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LTB4R	ENST00000345363.8	TSL:1 MANE Select	c.52_53delTCinsAG	p.19	synonymous	N/A	ENSP00000307445.3	Q15722
	LTB4R	ENST00000396782.2	TSL:1	c.52_53delTCinsAG	p.19	synonymous	N/A	ENSP00000380002.2	Q15722
	LTB4R	ENST00000396789.4	TSL:1	c.52_53delTCinsAG	p.19	synonymous	N/A	ENSP00000380008.4	Q15722

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr14-24784909;