Genetic Variant LTB4R:c.*377T>G (chr14-24317087-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.07

Publications

7 publications found

Variant links:

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]

LTB4R links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LTB4R	NM_001143919.3 link	c.*377T>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000345363.8	NP_001137391.1
LTB4R	NM_181657.3 link	c.*377T>G		3_prime_UTR_variant	Exon 2 of 2		NP_858043.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
LTB4R	ENST00000345363.8 link	c.*377T>G	3_prime_UTR_variant	Exon 2 of 2	1	NM_001143919.3	ENSP00000307445.3
LTB4R	ENST00000396789.4 link	c.*377T>G	3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000380008.4
LTB4R	ENST00000396782.2 link	c.*377T>G	downstream_gene_variant		1		ENSP00000380002.2

Frequencies

GnomAD3 genomes

AF:

0.806

AC:

122563

AN:

152010

Hom.:

49736

Cov.:

show subpopulations

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.:

AF XY:

0.832

AC XY:

20182

AN XY:

24264

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

328

657

985

1314

1642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

106

212

318

424

530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.806

AC:

122665

AN:

152128

Hom.:

49782

Cov.:

AF XY:

0.812

AC XY:

60423

AN XY:

74372

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1225

2450

3676

4901

6126

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

880

1760

2640

3520

4400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.64

(source)

DANN

Benign

0.41

PhyloP100

-3.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over