chr14-24317770-T-C

Position:

• chr14-24317770-T-C

Variant summary

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

The NM_001143919.3(LTB4R):​c.*1060T>C 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 167,186 control chromosomes in the GnomAD database, including 55,665 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 (49936 hom., cov: 30)
  • Exomes 𝑓: 0.87 (5729 hom.)
• Consequence: LTB4R NM_001143919.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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=-0.85).
• 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	Protein	UniProt
LTB4R	NM_001143919.3	c.*1060T>C		3_prime_UTR_variant	2/2	ENST00000345363.8	NP_001137391.1
LTB4R	NM_181657.3	c.*1060T>C		3_prime_UTR_variant	2/2		NP_858043.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LTB4R	ENST00000345363.8	c.*1060T>C		3_prime_UTR_variant	2/2	1	NM_001143919.3	ENSP00000307445.3
LTB4R	ENST00000396789.4	c.*1060T>C		3_prime_UTR_variant	2/2	1		ENSP00000380008.4

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122683 AN: 151880 Hom.: 49889 Cov.: 30

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.801

GnomAD4 exome AF: 0.867 AC: 13171 AN: 15188 Hom.: 5729 Cov.: 0 AF XY: 0.867 AC XY: 6271 AN XY: 7230

Gnomad4 AFR exome AF: 0.833

Gnomad4 AMR exome AF: 0.733

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.833

Gnomad4 FIN exome AF: 0.867

Gnomad4 NFE exome AF: 0.877

Gnomad4 OTH exome AF: 0.855

GnomAD4 genome AF: 0.808 AC: 122786 AN: 151998 Hom.: 49936 Cov.: 30 AF XY: 0.814 AC XY: 60455 AN XY: 74272

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.803

Alfa AF: 0.793 Hom.: 75958

Bravo AF: 0.795

Asia WGS AF: 0.935 AC: 3253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.42
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181384; hg19: chr14-24786976;