rs1046587

Positions:

• chr14-24316854-G-A

Variant summary

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

The NM_001143919.3(LTB4R):​c.*144G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 624,980 control chromosomes in the GnomAD database, including 63,856 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 0.39 (12810 hom., cov: 33)
  • Exomes 𝑓: 0.45 (51046 hom.)
• Consequence: LTB4R NM_001143919.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LTB4R	NM_001143919.3	c.*144G>A		3_prime_UTR_variant	2/2	ENST00000345363.8
LTB4R	NM_181657.3	c.*144G>A		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LTB4R	ENST00000345363.8	c.*144G>A		3_prime_UTR_variant	2/2	1	NM_001143919.3	P1
LTB4R	ENST00000396782.2	c.*144G>A		3_prime_UTR_variant	2/2	1		P1
LTB4R	ENST00000396789.4	c.*144G>A		3_prime_UTR_variant	2/2	1		P1

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59091 AN: 152028 Hom.: 12806 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.414

GnomAD4 exome AF: 0.454 AC: 214606 AN: 472834 Hom.: 51046 Cov.: 7 AF XY: 0.451 AC XY: 109047 AN XY: 241618

Gnomad4 AFR exome AF: 0.221

Gnomad4 AMR exome AF: 0.308

Gnomad4 ASJ exome AF: 0.441

Gnomad4 EAS exome AF: 0.144

Gnomad4 SAS exome AF: 0.332

Gnomad4 FIN exome AF: 0.480

Gnomad4 NFE exome AF: 0.496

Gnomad4 OTH exome AF: 0.442

GnomAD4 genome AF: 0.389 AC: 59113 AN: 152146 Hom.: 12810 Cov.: 33 AF XY: 0.383 AC XY: 28483 AN XY: 74388

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.411

Alfa AF: 0.432 Hom.: 6266

Bravo AF: 0.370

Asia WGS AF: 0.217 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.57
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3

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: rs1046587; hg19: chr14-24786060; COSMIC: COSV60253843; COSMIC: COSV60253843;