14-24317087-T-G

Variant names:

• chr14-24317087-T-G
• rs4981503
• NM_001143919.3:c.*377T>G

Variant summary

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

The NM_001143919.3(LTB4R):​c.*377T>G 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 200,356 control chromosomes in the GnomAD database, including 66,621 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 (49782 hom., cov: 31)
  • Exomes 𝑓: 0.83 (16839 hom.)
• Consequence: LTB4R NM_001143919.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07
• Publications: 7 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=-0.84).
• 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_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.*377T>G		3_prime_UTR	Exon 2 of 2	NP_001137391.1	Q15722
	LTB4R	NM_181657.3		c.*377T>G		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.*377T>G		3_prime_UTR	Exon 2 of 2	ENSP00000307445.3	Q15722
	LTB4R	ENST00000396789.4	TSL:1	c.*377T>G		3_prime_UTR	Exon 2 of 2	ENSP00000380008.4	Q15722
	LTB4R	ENST00000396782.2	TSL:1	c.*377T>G		downstream_gene	N/A	ENSP00000380002.2	Q15722

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122563 AN: 152010 Hom.: 49736 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.893

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.799

GnomAD4 exome AF: 0.832 AC: 40131 AN: 48228 Hom.: 16839 Cov.: 0 AF XY: 0.832 AC XY: 20182 AN XY: 24264

African (AFR) AF: 0.813 AC: 907 AN: 1116

American (AMR) AF: 0.705 AC: 605 AN: 858

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 1070 AN: 1362

East Asian (EAS) AF: 1.00 AC: 2143 AN: 2144

South Asian (SAS) AF: 0.890 AC: 1210 AN: 1360

European-Finnish (FIN) AF: 0.866 AC: 14773 AN: 17058

Middle Eastern (MID) AF: 0.861 AC: 186 AN: 216

European-Non Finnish (NFE) AF: 0.795 AC: 17353 AN: 21828

Other (OTH) AF: 0.824 AC: 1884 AN: 2286

GnomAD4 genome AF: 0.806 AC: 122665 AN: 152128 Hom.: 49782 Cov.: 31 AF XY: 0.812 AC XY: 60423 AN XY: 74372

African (AFR) AF: 0.818 AC: 33902 AN: 41466

American (AMR) AF: 0.709 AC: 10848 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2789 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5162 AN: 5172

South Asian (SAS) AF: 0.894 AC: 4309 AN: 4822

European-Finnish (FIN) AF: 0.866 AC: 9180 AN: 10602

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

European-Non Finnish (NFE) AF: 0.790 AC: 53720 AN: 67982

Other (OTH) AF: 0.802 AC: 1696 AN: 2116

Alfa AF: 0.798 Hom.: 11143

Bravo AF: 0.794

Asia WGS AF: 0.935 AC: 3252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.64
DANN	Benign	0.41
PhyloP100		-3.1
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: rs4981503; hg19: chr14-24786293;