rs1046587

Variant names:

• chr14-24316854-G-A
• rs1046587
• NM_001143919.3:c.*144G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 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: Benign. The variant received -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.

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.*144G>A		3_prime_UTR	Exon 2 of 2	NP_001137391.1	Q15722
	LTB4R	NM_181657.3		c.*144G>A		3_prime_UTR	Exon 2 of 2	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.*144G>A		3_prime_UTR	Exon 2 of 2	ENSP00000307445.3	Q15722
	LTB4R	ENST00000396782.2	TSL:1	c.*144G>A		3_prime_UTR	Exon 2 of 2	ENSP00000380002.2	Q15722
	LTB4R	ENST00000396789.4	TSL:1	c.*144G>A		3_prime_UTR	Exon 2 of 2	ENSP00000380008.4	Q15722

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

African (AFR) AF: 0.221 AC: 2149 AN: 9742

American (AMR) AF: 0.308 AC: 2486 AN: 8072

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 4937 AN: 11200

East Asian (EAS) AF: 0.144 AC: 3354 AN: 23238

South Asian (SAS) AF: 0.332 AC: 9992 AN: 30064

European-Finnish (FIN) AF: 0.480 AC: 19713 AN: 41068

Middle Eastern (MID) AF: 0.523 AC: 955 AN: 1826

European-Non Finnish (NFE) AF: 0.496 AC: 160361 AN: 323500

Other (OTH) AF: 0.442 AC: 10659 AN: 24124

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

African (AFR) AF: 0.221 AC: 9160 AN: 41524

American (AMR) AF: 0.344 AC: 5264 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1623 AN: 3472

East Asian (EAS) AF: 0.154 AC: 799 AN: 5172

South Asian (SAS) AF: 0.314 AC: 1513 AN: 4822

European-Finnish (FIN) AF: 0.484 AC: 5125 AN: 10588

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34136 AN: 67968

Other (OTH) AF: 0.411 AC: 869 AN: 2112

Alfa AF: 0.443 Hom.: 9521

Bravo AF: 0.370

Asia WGS AF: 0.217 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.57
PhyloP100		-0.45
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

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

Other links and lift over

dbSNP: rs1046587;

hg19: chr14-24786060;

COSMIC: COSV60253843;

COSMIC: COSV60253843;