rs2224122

Positions:

• chr14-24314208-G-C

Variant summary

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

The ENST00000396789.4(LTB4R):​c.-828G>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 0.153 in 152,276 control chromosomes in the GnomAD database, including 2,453 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 0.15 (2450 hom., cov: 32)
  • Exomes 𝑓: 0.29 (3 hom.)
• Consequence: LTB4R ENST00000396789.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65

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 (AMR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LTB4R	NM_001143919.3	c.-15-1429G>C		intron_variant		ENST00000345363.8
LTB4R	NM_181657.3	c.-828G>C		5_prime_UTR_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LTB4R	ENST00000396789.4	c.-828G>C		5_prime_UTR_variant	1/2	1		P1
LTB4R	ENST00000345363.8	c.-15-1429G>C		intron_variant		1	NM_001143919.3	P1
LTB4R	ENST00000553481.1	c.-15-1429G>C		intron_variant		2
LTB4R	ENST00000556141.1	c.-60+253G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23314 AN: 152122 Hom.: 2449 Cov.: 32

Gnomad AFR AF: 0.0427

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.169

GnomAD4 exome AF: 0.289 AC: 11 AN: 38 Hom.: 3 Cov.: 0 AF XY: 0.318 AC XY: 7 AN XY: 22

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.153 AC: 23318 AN: 152238 Hom.: 2450 Cov.: 32 AF XY: 0.149 AC XY: 11097 AN XY: 74442

Gnomad4 AFR AF: 0.0426

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.167

Alfa AF: 0.180 Hom.: 380

Bravo AF: 0.159

Asia WGS AF: 0.0570 AC: 197 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	5.2
DANN	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2224122; hg19: chr14-24783414;