Genetic Variant LTB4R:c.-828G>C (chr14-24314208-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.-828G>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 0.153 in 152,276 control chromosomes in the GnomAD database, including 2,453 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 0.15 ( 2450 hom., cov: 32)

Exomes 𝑓: 0.29 ( 3 hom. )

Consequence

LTB4R
ENST00000396789.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.65

Publications

12 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 (AMR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LTB4R	NM_001143919.3 link	c.-15-1429G>C		intron_variant	Intron 1 of 1	ENST00000345363.8	NP_001137391.1	Q15722
LTB4R	NM_181657.3 link	c.-828G>C		5_prime_UTR_variant	Exon 1 of 2		NP_858043.1	Q15722

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
LTB4R	ENST00000396789.4 link	c.-828G>C	5_prime_UTR_variant	Exon 1 of 2	1		ENSP00000380008.4	Q15722
LTB4R	ENST00000345363.8 link	c.-15-1429G>C	intron_variant	Intron 1 of 1	1	NM_001143919.3	ENSP00000307445.3	Q15722
LTB4R	ENST00000556141.1 link	c.-60+253G>C	intron_variant	Intron 1 of 1	3		ENSP00000451929.1	G3V4Q5
LTB4R	ENST00000553481.1 link	c.-15-1429G>C	intron_variant	Intron 1 of 1	2		ENSP00000450457.1	G3V244

Frequencies

GnomAD3 genomes

AF:

0.153

AC:

23314

AN:

152122

Hom.:

2449

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0427

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.00192

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.169

GnomAD4 exome

AF:

0.289

AC:

AN:

Hom.:

Cov.:

AF XY:

0.318

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AF:

0.375

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.435

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:

0.153

AC:

23318

AN:

152238

Hom.:

2450

Cov.:

AF XY:

0.149

AC XY:

11097

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.0426

AC:

1770

AN:

41558

American (AMR)

AF:

0.274

AC:

4191

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.196

AC:

681

AN:

3468

East Asian (EAS)

AF:

0.00193

AC:

AN:

5188

South Asian (SAS)

AF:

0.105

AC:

508

AN:

4824

European-Finnish (FIN)

AF:

0.135

AC:

1433

AN:

10620

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.209

AC:

14228

AN:

67978

Other (OTH)

AF:

0.167

AC:

352

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

969

1938

2906

3875

4844

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.180

Hom.:

380

Bravo

AF:

0.159

Asia WGS

AF:

0.0570

AC:

197

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

5.2

(source)

DANN

Benign

0.66

PhyloP100

1.6

PromoterAI

-0.023

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over