rs3742511

Variant names:

• chr14-24315705-T-C
• rs3742511
• NM_001143919.3:c.54T>C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001143919.3(LTB4R):​c.54T>C​(p.Ser18Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 1,614,168 control chromosomes in the GnomAD database, including 1,785 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 0.049 (229 hom., cov: 33)
  • Exomes 𝑓: 0.041 (1556 hom.)
• Consequence: LTB4R NM_001143919.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP7: Synonymous conserved (PhyloP=-1.2 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LTB4R	NM_001143919.3	c.54T>C	p.Ser18Ser	synonymous_variant	Exon 2 of 2	ENST00000345363.8	NP_001137391.1
LTB4R	NM_181657.3	c.54T>C	p.Ser18Ser	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.54T>C	p.Ser18Ser	synonymous_variant	Exon 2 of 2	1	NM_001143919.3	ENSP00000307445.3

Frequencies

GnomAD3 genomes AF: 0.0489 AC: 7446 AN: 152190 Hom.: 228 Cov.: 33

Gnomad AFR AF: 0.0578

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.0237

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0361

Gnomad OTH AF: 0.0454

GnomAD3 exomes AF: 0.0501 AC: 12598 AN: 251436 Hom.: 408 AF XY: 0.0495 AC XY: 6723 AN XY: 135890

Gnomad AFR exome AF: 0.0569

Gnomad AMR exome AF: 0.0658

Gnomad ASJ exome AF: 0.0419

Gnomad EAS exome AF: 0.142

Gnomad SAS exome AF: 0.0484

Gnomad FIN exome AF: 0.0240

Gnomad NFE exome AF: 0.0362

Gnomad OTH exome AF: 0.0407

GnomAD4 exome AF: 0.0414 AC: 60448 AN: 1461860 Hom.: 1556 Cov.: 32 AF XY: 0.0416 AC XY: 30274 AN XY: 727232

Gnomad4 AFR exome AF: 0.0560

Gnomad4 AMR exome AF: 0.0667

Gnomad4 ASJ exome AF: 0.0412

Gnomad4 EAS exome AF: 0.146

Gnomad4 SAS exome AF: 0.0469

Gnomad4 FIN exome AF: 0.0246

Gnomad4 NFE exome AF: 0.0364

Gnomad4 OTH exome AF: 0.0443

GnomAD4 genome AF: 0.0490 AC: 7457 AN: 152308 Hom.: 229 Cov.: 33 AF XY: 0.0497 AC XY: 3705 AN XY: 74476

Gnomad4 AFR AF: 0.0578

Gnomad4 AMR AF: 0.0691

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.0536

Gnomad4 FIN AF: 0.0237

Gnomad4 NFE AF: 0.0361

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0398 Hom.: 113

Bravo AF: 0.0528

Asia WGS AF: 0.0870 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.49

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

Other links and lift over

dbSNP: rs3742511; hg19: chr14-24784911; COSMIC: COSV51865114; COSMIC: COSV51865114;