13-48661258-C-T

Variant names:

• chr13-48661258-C-T
• rs6420296
• NM_001308476.3:c.-266+7241C>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.-266+7241C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,024 control chromosomes in the GnomAD database, including 65,162 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 0.92 (65162 hom., cov: 28)
• Consequence: CYSLTR2 NM_001308476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYSLTR2	NM_001308476.3	c.-266+7241C>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.-266+7241C>T		intron_variant	Intron 1 of 4		NM_001308476.3	ENSP00000508181.1

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140461 AN: 151906 Hom.: 65102 Cov.: 28

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.925 AC: 140583 AN: 152024 Hom.: 65162 Cov.: 28 AF XY: 0.921 AC XY: 68462 AN XY: 74308

African (AFR) AF: 0.983 AC: 40764 AN: 41490

American (AMR) AF: 0.902 AC: 13760 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3172 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5168 AN: 5180

South Asian (SAS) AF: 0.878 AC: 4196 AN: 4780

European-Finnish (FIN) AF: 0.863 AC: 9119 AN: 10562

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.903 AC: 61375 AN: 67974

Other (OTH) AF: 0.925 AC: 1952 AN: 2110

Alfa AF: 0.912 Hom.: 8032

Bravo AF: 0.931

Asia WGS AF: 0.948 AC: 3298 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	0.85
DANN	Benign	0.43
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs6420296; hg19: chr13-49235394; COSMIC: COSV69349677;