rs3742510

Positions:

• chr14-24314475-G-C

Variant summary

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

The NM_181657.3(LTB4R):​c.-561G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 152,176 control chromosomes in the GnomAD database, including 223 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 (223 hom., cov: 32)
  • Exomes 𝑓: 0.069 (0 hom.)
• Consequence: LTB4R NM_181657.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LTB4R	NM_001143919.3	c.-15-1162G>C		intron_variant		ENST00000345363.8	NP_001137391.1
LTB4R	NM_181657.3	c.-561G>C		5_prime_UTR_variant	1/2		NP_858043.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LTB4R	ENST00000396789.4	c.-561G>C		5_prime_UTR_variant	1/2	1		ENSP00000380008.4
LTB4R	ENST00000345363.8	c.-15-1162G>C		intron_variant		1	NM_001143919.3	ENSP00000307445.3
LTB4R	ENST00000556141.1	c.-60+520G>C		intron_variant		3		ENSP00000451929.1
LTB4R	ENST00000553481.1	c.-15-1162G>C		intron_variant		2		ENSP00000450457.1

Frequencies

GnomAD3 genomes AF: 0.0487 AC: 7401 AN: 151942 Hom.: 222 Cov.: 32

Gnomad AFR AF: 0.0571

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0690

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0528

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0361

Gnomad OTH AF: 0.0455

GnomAD4 exome AF: 0.0690 AC: 8 AN: 116 Hom.: 0 Cov.: 0 AF XY: 0.0543 AC XY: 5 AN XY: 92

Gnomad4 AMR exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.0700

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0487 AC: 7412 AN: 152060 Hom.: 223 Cov.: 32 AF XY: 0.0495 AC XY: 3676 AN XY: 74322

Gnomad4 AFR AF: 0.0570

Gnomad4 AMR AF: 0.0693

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.0533

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0361

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0426 Hom.: 26

Bravo AF: 0.0526

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	-0.83
CADD	Benign	9.6
DANN	Benign	0.75

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: rs3742510; hg19: chr14-24783681;