Genetic Variant NM_001308476.3: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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001308476.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CYSLTR2	NM_001308476.3	MANE Select	c.*1493A>G	3_prime_UTR	Exon 5 of 5	NP_001295405.1
CYSLTR2	NM_001308465.3		c.*1493A>G	3_prime_UTR	Exon 6 of 6	NP_001295394.1
CYSLTR2	NM_001308467.3		c.*1493A>G	3_prime_UTR	Exon 6 of 6	NP_001295396.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYSLTR2	ENST00000682523.1	MANE Select	c.*1493A>G		3_prime_UTR	Exon 5 of 5	ENSP00000508181.1
	CYSLTR2	ENST00000282018.4	TSL:6	c.*1493A>G		3_prime_UTR	Exon 1 of 1	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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over