Genetic Variant NM_001143919.3:c.*144G>A (chr14-24316854-G-A) – 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.*144G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 624,980 control chromosomes in the GnomAD database, including 63,856 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 0.39 ( 12810 hom., cov: 33)

Exomes 𝑓: 0.45 ( 51046 hom. )

Consequence

LTB4R
NM_001143919.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.446

Publications

20 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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LTB4R	NM_001143919.3 link	c.*144G>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000345363.8	NP_001137391.1	Q15722
LTB4R	NM_181657.3 link	c.*144G>A		3_prime_UTR_variant	Exon 2 of 2		NP_858043.1	Q15722

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
LTB4R	ENST00000345363.8 link	c.*144G>A	3_prime_UTR_variant	Exon 2 of 2	1	NM_001143919.3	ENSP00000307445.3	Q15722
LTB4R	ENST00000396782.2 link	c.*144G>A	3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000380002.2	Q15722
LTB4R	ENST00000396789.4 link	c.*144G>A	3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000380008.4	Q15722
LTB4R	ENST00000556141.1 link	c.*207G>A	downstream_gene_variant		3		ENSP00000451929.1	G3V4Q5

Frequencies

GnomAD3 genomes

AF:

0.389

AC:

59091

AN:

152028

Hom.:

12806

Cov.:

show subpopulations

Gnomad AFR

AF:

0.221

Gnomad AMI

AF:

0.503

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.467

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.313

Gnomad FIN

AF:

0.484

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.502

Gnomad OTH

AF:

0.414

GnomAD4 exome

AF:

0.454

AC:

214606

AN:

472834

Hom.:

51046

Cov.:

AF XY:

0.451

AC XY:

109047

AN XY:

241618

show subpopulations

African (AFR)

AF:

0.221

AC:

2149

AN:

9742

American (AMR)

AF:

0.308

AC:

2486

AN:

8072

Ashkenazi Jewish (ASJ)

AF:

0.441

AC:

4937

AN:

11200

East Asian (EAS)

AF:

0.144

AC:

3354

AN:

23238

South Asian (SAS)

AF:

0.332

AC:

9992

AN:

30064

European-Finnish (FIN)

AF:

0.480

AC:

19713

AN:

41068

Middle Eastern (MID)

AF:

0.523

AC:

955

AN:

1826

European-Non Finnish (NFE)

AF:

0.496

AC:

160361

AN:

323500

Other (OTH)

AF:

0.442

AC:

10659

AN:

24124

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

5680

11360

17041

22721

28401

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2730

5460

8190

10920

13650

<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:

0.389

AC:

59113

AN:

152146

Hom.:

12810

Cov.:

AF XY:

0.383

AC XY:

28483

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.221

AC:

9160

AN:

41524

American (AMR)

AF:

0.344

AC:

5264

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.467

AC:

1623

AN:

3472

East Asian (EAS)

AF:

0.154

AC:

799

AN:

5172

South Asian (SAS)

AF:

0.314

AC:

1513

AN:

4822

European-Finnish (FIN)

AF:

0.484

AC:

5125

AN:

10588

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.502

AC:

34136

AN:

67968

Other (OTH)

AF:

0.411

AC:

869

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1752

3504

5257

7009

8761

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

562

1124

1686

2248

2810

<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:

0.443

Hom.:

9521

Bravo

AF:

0.370

Asia WGS

AF:

0.217

AC:

756

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.7

(source)

DANN

Benign

0.57

PhyloP100

-0.45

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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