rs2407249

chr13-48709659-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001308476.3(CYSLTR2):c.*1801A>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 0.163 in 152,210 control chromosomes in the GnomAD database, including 2,146 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 0.16 (2146 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CYSLTR2 NM_001308476.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYSLTR2	NM_001308476.3	c.*1801A>G		3_prime_UTR_variant	5/5	ENST00000682523.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYSLTR2	ENST00000682523.1	c.*1801A>G		3_prime_UTR_variant	5/5		NM_001308476.3	P1
CYSLTR2	ENST00000282018.4	c.*1801A>G		3_prime_UTR_variant	1/1			P1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24746 AN: 152092 Hom.: 2143 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0803

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.176

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.163 AC: 24774 AN: 152210 Hom.: 2146 Cov.: 32 AF XY: 0.161 AC XY: 12013 AN XY: 74422

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0799

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.179

Alfa AF: 0.184 Hom.: 4473

Bravo AF: 0.162

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.5
Dann	Benign	0.63

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

LitVar

Other links and lift over

dbSNP: rs2407249; hg19: chr13-49283795;