rs9285169

chr13-48676905-C-T

Variant summary

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

The NM_001308476.3(CYSLTR2):c.-265-14307C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,008 control chromosomes in the GnomAD database, including 3,900 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 0.19 (3900 hom., cov: 32)
• Consequence: CYSLTR2 NM_001308476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYSLTR2	NM_001308476.3	c.-265-14307C>T		intron_variant		ENST00000682523.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYSLTR2	ENST00000682523.1	c.-265-14307C>T		intron_variant			NM_001308476.3	P1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28416 AN: 151890 Hom.: 3889 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.0908

Gnomad OTH AF: 0.162

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.187 AC: 28464 AN: 152008 Hom.: 3900 Cov.: 32 AF XY: 0.187 AC XY: 13911 AN XY: 74316

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0908

Gnomad4 OTH AF: 0.164

Alfa AF: 0.116 Hom.: 874

Bravo AF: 0.197

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.20
Dann	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9285169; hg19: chr13-49251041;