Variant rs912278 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CYSLTR2	NM_001308476.3 link	c.*1493A>G		3_prime_UTR_variant	5/5	ENST00000682523.1	NP_001295405.1	Q9NS75Q5KU17A4ZKH2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYSLTR2	ENST00000682523.1 link	c.*1493A>G		3_prime_UTR_variant	5/5		NM_001308476.3	ENSP00000508181.1		Q9NS75
CYSLTR2	ENST00000282018.4 link	c.*1493A>G		3_prime_UTR_variant	1/1	6		ENSP00000282018.3		Q9NS75

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

Gnomad4 AFR exome

AF:

0.750

Gnomad4 AMR exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.467

Gnomad4 NFE exome

AF:

0.520

Gnomad4 OTH exome

AF:

0.400

GnomAD4 genome

AF:

0.390

AC:

59325

AN:

152098

Hom.:

12366

Cov.:

AF XY:

0.395

AC XY:

29343

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.229

Gnomad4 AMR

AF:

0.400

Gnomad4 ASJ

AF:

0.459

Gnomad4 EAS

AF:

0.421

Gnomad4 SAS

AF:

0.505

Gnomad4 FIN

AF:

0.471

Gnomad4 NFE

AF:

0.457

Gnomad4 OTH

AF:

0.412

Alfa

AF:

0.442

Hom.:

21732

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

DANN

Benign

0.55

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over