Genetic Variant LTB4R:c.-561G>C (chr14-24314475-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000396789.4(LTB4R):c.-561G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 152,176 control chromosomes in the GnomAD database, including 223 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 ( 223 hom., cov: 32)

Exomes 𝑓: 0.069 ( 0 hom. )

Consequence

LTB4R
ENST00000396789.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.328

Publications

5 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000396789.4. 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.-15-1162G>C		intron	N/A	NP_001137391.1
	LTB4R	NM_181657.3		c.-561G>C		5_prime_UTR	Exon 1 of 2	NP_858043.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LTB4R	ENST00000396789.4	TSL:1	c.-561G>C	5_prime_UTR	Exon 1 of 2	ENSP00000380008.4
LTB4R	ENST00000345363.8	TSL:1 MANE Select	c.-15-1162G>C	intron	N/A	ENSP00000307445.3
LTB4R	ENST00000556141.1	TSL:3	c.-60+520G>C	intron	N/A	ENSP00000451929.1

Frequencies

GnomAD3 genomes

AF:

0.0487

AC:

7401

AN:

151942

Hom.:

222

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0571

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0690

Gnomad ASJ

AF:

0.0372

Gnomad EAS

AF:

0.150

Gnomad SAS

AF:

0.0528

Gnomad FIN

AF:

0.0238

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0361

Gnomad OTH

AF:

0.0455

GnomAD4 exome

AF:

0.0690

AC:

AN:

116

Hom.:

Cov.:

AF XY:

0.0543

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0700

AC:

AN:

100

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0487

AC:

7412

AN:

152060

Hom.:

223

Cov.:

AF XY:

0.0495

AC XY:

3676

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.0570

AC:

2363

AN:

41450

American (AMR)

AF:

0.0693

AC:

1058

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.0372

AC:

129

AN:

3470

East Asian (EAS)

AF:

0.150

AC:

778

AN:

5180

South Asian (SAS)

AF:

0.0533

AC:

257

AN:

4822

European-Finnish (FIN)

AF:

0.0238

AC:

252

AN:

10572

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0361

AC:

2452

AN:

67990

Other (OTH)

AF:

0.0445

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

368

736

1105

1473

1841

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:

0.0426

Hom.:

Bravo

AF:

0.0526

Asia WGS

AF:

0.0870

AC:

300

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

9.6

(source)

DANN

Benign

0.75

PhyloP100

0.33

PromoterAI

0.020

Neutral

(source)

Mutation Taster

=300/0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over