14-24317087-T-G

Position:

• chr14-24317087-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001143919.3(LTB4R):​c.*377T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 200,356 control chromosomes in the GnomAD database, including 66,621 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 0.81 (49782 hom., cov: 31)
  • Exomes 𝑓: 0.83 (16839 hom.)
• Consequence: LTB4R NM_001143919.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LTB4R	NM_001143919.3	c.*377T>G		3_prime_UTR_variant	2/2	ENST00000345363.8
LTB4R	NM_181657.3	c.*377T>G		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LTB4R	ENST00000345363.8	c.*377T>G		3_prime_UTR_variant	2/2	1	NM_001143919.3	P1
LTB4R	ENST00000396789.4	c.*377T>G		3_prime_UTR_variant	2/2	1		P1

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122563 AN: 152010 Hom.: 49736 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.893

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.799

GnomAD4 exome AF: 0.832 AC: 40131 AN: 48228 Hom.: 16839 Cov.: 0 AF XY: 0.832 AC XY: 20182 AN XY: 24264

Gnomad4 AFR exome AF: 0.813

Gnomad4 AMR exome AF: 0.705

Gnomad4 ASJ exome AF: 0.786

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.890

Gnomad4 FIN exome AF: 0.866

Gnomad4 NFE exome AF: 0.795

Gnomad4 OTH exome AF: 0.824

GnomAD4 genome AF: 0.806 AC: 122665 AN: 152128 Hom.: 49782 Cov.: 31 AF XY: 0.812 AC XY: 60423 AN XY: 74372

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.802

Alfa AF: 0.798 Hom.: 10890

Bravo AF: 0.794

Asia WGS AF: 0.935 AC: 3252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.64
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4981503; hg19: chr14-24786293;