chr14-24317770-T-C

Variant names:

• chr14-24317770-T-C
• rs3181384
• NM_001143919.3:c.*1060T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181657.3(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_181657.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 31 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181657.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LTB4R	NM_001143919.3	MANE Select	c.*1060T>C		3_prime_UTR	Exon 2 of 2	NP_001137391.1
	LTB4R	NM_181657.3		c.*1060T>C		3_prime_UTR	Exon 2 of 2	NP_858043.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LTB4R	ENST00000345363.8	TSL:1 MANE Select	c.*1060T>C		3_prime_UTR	Exon 2 of 2	ENSP00000307445.3
	LTB4R	ENST00000396789.4	TSL:1	c.*1060T>C		3_prime_UTR	Exon 2 of 2	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

African (AFR) AF: 0.833 AC: 5 AN: 6

American (AMR) AF: 0.733 AC: 22 AN: 30

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 4 AN: 4

South Asian (SAS) AF: 0.833 AC: 10 AN: 12

European-Finnish (FIN) AF: 0.867 AC: 12734 AN: 14682

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.877 AC: 300 AN: 342

Other (OTH) AF: 0.855 AC: 94 AN: 110

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

African (AFR) AF: 0.824 AC: 34125 AN: 41430

American (AMR) AF: 0.710 AC: 10836 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2786 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5174 AN: 5184

South Asian (SAS) AF: 0.894 AC: 4293 AN: 4802

European-Finnish (FIN) AF: 0.866 AC: 9155 AN: 10568

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53666 AN: 67976

Other (OTH) AF: 0.803 AC: 1692 AN: 2106

Alfa AF: 0.792 Hom.: 107623

Bravo AF: 0.795

Asia WGS AF: 0.935 AC: 3253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.42
DANN	Benign	0.57
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3181384; hg19: chr14-24786976;