dbSNP rs3742511: LTB4R:p.Ser18Ser (chr14-24315705-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001143919.3(LTB4R):c.54T>C(p.Ser18Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 1,614,168 control chromosomes in the GnomAD database, including 1,785 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 0.049 ( 229 hom., cov: 33)

Exomes 𝑓: 0.041 ( 1556 hom. )

Consequence

LTB4R
NM_001143919.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

Publications

10 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP7

Synonymous conserved (PhyloP=-1.2 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LTB4R	NM_001143919.3 link	c.54T>C	p.Ser18Ser	synonymous_variant	Exon 2 of 2	ENST00000345363.8	NP_001137391.1	Q15722
LTB4R	NM_181657.3 link	c.54T>C	p.Ser18Ser	synonymous_variant	Exon 2 of 2		NP_858043.1	Q15722

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LTB4R	ENST00000345363.8 link	c.54T>C	p.Ser18Ser	synonymous_variant	Exon 2 of 2	1	NM_001143919.3	ENSP00000307445.3		Q15722

Frequencies

GnomAD3 genomes

AF:

0.0489

AC:

7446

AN:

152190

Hom.:

228

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0578

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0688

Gnomad ASJ

AF:

0.0372

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.0532

Gnomad FIN

AF:

0.0237

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0361

Gnomad OTH

AF:

0.0454

GnomAD2 exomes

AF:

0.0501

AC:

12598

AN:

251436

AF XY:

0.0495

show subpopulations

Gnomad AFR exome

AF:

0.0569

Gnomad AMR exome

AF:

0.0658

Gnomad ASJ exome

AF:

0.0419

Gnomad EAS exome

AF:

0.142

Gnomad FIN exome

AF:

0.0240

Gnomad NFE exome

AF:

0.0362

Gnomad OTH exome

AF:

0.0407

GnomAD4 exome

AF:

0.0414

AC:

60448

AN:

1461860

Hom.:

1556

Cov.:

AF XY:

0.0416

AC XY:

30274

AN XY:

727232

show subpopulations

African (AFR)

AF:

0.0560

AC:

1874

AN:

33480

American (AMR)

AF:

0.0667

AC:

2981

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0412

AC:

1077

AN:

26136

East Asian (EAS)

AF:

0.146

AC:

5801

AN:

39700

South Asian (SAS)

AF:

0.0469

AC:

4048

AN:

86258

European-Finnish (FIN)

AF:

0.0246

AC:

1312

AN:

53408

Middle Eastern (MID)

AF:

0.0314

AC:

181

AN:

5768

European-Non Finnish (NFE)

AF:

0.0364

AC:

40497

AN:

1111992

Other (OTH)

AF:

0.0443

AC:

2677

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

3521

7042

10564

14085

17606

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1654

3308

4962

6616

8270

<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:

0.0490

AC:

7457

AN:

152308

Hom.:

229

Cov.:

AF XY:

0.0497

AC XY:

3705

AN XY:

74476

show subpopulations

African (AFR)

AF:

0.0578

AC:

2402

AN:

41566

American (AMR)

AF:

0.0691

AC:

1056

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0372

AC:

129

AN:

3472

East Asian (EAS)

AF:

0.151

AC:

783

AN:

5188

South Asian (SAS)

AF:

0.0536

AC:

259

AN:

4828

European-Finnish (FIN)

AF:

0.0237

AC:

252

AN:

10618

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0361

AC:

2453

AN:

68024

Other (OTH)

AF:

0.0445

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

358

715

1073

1430

1788

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0401

Hom.:

124

Bravo

AF:

0.0528

Asia WGS

AF:

0.0870

AC:

300

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

1.7

(source)

DANN

Benign

0.49

PhyloP100

-1.2

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