rs9285169

Variant names:

• chr13-48676905-C-T
• rs9285169
• NM_001308476.3:c.-265-14307C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CYSLTR2	NM_001308476.3	c.-265-14307C>T		intron_variant	Intron 1 of 4	ENST00000682523.1	NP_001295405.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYSLTR2	ENST00000682523.1	c.-265-14307C>T		intron_variant	Intron 1 of 4		NM_001308476.3	ENSP00000508181.1

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

African (AFR) AF: 0.386 AC: 16004 AN: 41426

American (AMR) AF: 0.148 AC: 2263 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3468

East Asian (EAS) AF: 0.215 AC: 1114 AN: 5186

South Asian (SAS) AF: 0.147 AC: 704 AN: 4804

European-Finnish (FIN) AF: 0.114 AC: 1206 AN: 10558

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.0908 AC: 6174 AN: 67988

Other (OTH) AF: 0.164 AC: 345 AN: 2110

Alfa AF: 0.117 Hom.: 975

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
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs9285169; hg19: chr13-49251041;