Genetic Variant CYSLTR2:c.*1493A>G (chr13-48709351-A-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_001308476.3(CYSLTR2):c.*1493A>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 0.397 in 166,990 control chromosomes in the GnomAD database, including 14,008 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 ( 12366 hom., cov: 32)

Exomes 𝑓: 0.47 ( 1642 hom. )

Consequence

CYSLTR2
NM_001308476.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46

Publications

20 publications found

Variant links:

Genes affected

CYSLTR2 (HGNC:18274): (cysteinyl leukotriene receptor 2) The cysteinyl leukotrienes LTC4, LTD4, and LTE4 are important mediators of human bronchial asthma. Pharmacologic studies have determined that cysteinyl leukotrienes activate at least 2 receptors, the protein encoded by this gene and CYSLTR1. This encoded receptor is a member of the superfamily of G protein-coupled receptors. It seems to play a major role in endocrine and cardiovascular systems. [provided by RefSeq, Jul 2008]

CYSLTR2 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYSLTR2	NM_001308476.3 link	c.*1493A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000682523.1	NP_001295405.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYSLTR2	ENST00000682523.1 link	c.*1493A>G		3_prime_UTR_variant	Exon 5 of 5		NM_001308476.3	ENSP00000508181.1
CYSLTR2	ENST00000282018.4 link	c.*1493A>G		3_prime_UTR_variant	Exon 1 of 1	6		ENSP00000282018.3

Frequencies

GnomAD3 genomes

AF:

0.390

AC:

59279

AN:

151980

Hom.:

12351

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.471

Gnomad AMR

AF:

0.400

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.421

Gnomad SAS

AF:

0.505

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.457

Gnomad OTH

AF:

0.410

GnomAD4 exome

AF:

0.466

AC:

6946

AN:

14892

Hom.:

1642

Cov.:

AF XY:

0.468

AC XY:

3309

AN XY:

7068

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.467

AC:

6853

AN:

14688

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.520

AC:

AN:

100

Other (OTH)

AF:

0.400

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

201

402

602

803

1004

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.390

AC:

59325

AN:

152098

Hom.:

12366

Cov.:

AF XY:

0.395

AC XY:

29343

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.229

AC:

9523

AN:

41520

American (AMR)

AF:

0.400

AC:

6115

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.459

AC:

1592

AN:

3470

East Asian (EAS)

AF:

0.421

AC:

2174

AN:

5166

South Asian (SAS)

AF:

0.505

AC:

2436

AN:

4820

European-Finnish (FIN)

AF:

0.471

AC:

4978

AN:

10568

Middle Eastern (MID)

AF:

0.480

AC:

141

AN:

294

European-Non Finnish (NFE)

AF:

0.457

AC:

31067

AN:

67956

Other (OTH)

AF:

0.412

AC:

869

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1783

3566

5348

7131

8914

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

584

1168

1752

2336

2920

<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:

0.435

Hom.:

27151

Bravo

AF:

0.375

Asia WGS

AF:

0.462

AC:

1608

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.33

(source)

DANN

Benign

0.55

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over