rs11617224

Variant names:

• chr13-48654621-T-C
• rs11617224
• NM_001308476.3:c.-266+604T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020377.5(CYSLTR2):​c.-243+604T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 152,214 control chromosomes in the GnomAD database, including 659 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 0.078 (659 hom., cov: 32)
• Consequence: CYSLTR2 NM_020377.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.982
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020377.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYSLTR2	NM_001308476.3	MANE Select	c.-266+604T>C		intron	N/A	NP_001295405.1
	CYSLTR2	NM_001308465.3		c.-395+604T>C		intron	N/A	NP_001295394.1
	CYSLTR2	NM_001308467.3		c.-372+604T>C		intron	N/A	NP_001295396.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYSLTR2	ENST00000682523.1	MANE Select	c.-266+604T>C		intron	N/A	ENSP00000508181.1
	CYSLTR2	ENST00000614739.4	TSL:1	c.-243+604T>C		intron	N/A	ENSP00000477930.1
	CYSLTR2	ENST00000617562.4	TSL:1	c.-372+604T>C		intron	N/A	ENSP00000482041.1

Frequencies

GnomAD3 genomes AF: 0.0776 AC: 11805 AN: 152098 Hom.: 660 Cov.: 32

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.0775 AC: 11798 AN: 152214 Hom.: 659 Cov.: 32 AF XY: 0.0740 AC XY: 5507 AN XY: 74418

African (AFR) AF: 0.0181 AC: 750 AN: 41542

American (AMR) AF: 0.0674 AC: 1030 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0449 AC: 216 AN: 4816

European-Finnish (FIN) AF: 0.0930 AC: 986 AN: 10598

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8187 AN: 68004

Other (OTH) AF: 0.0870 AC: 184 AN: 2114

Alfa AF: 0.102 Hom.: 216

Bravo AF: 0.0733

Asia WGS AF: 0.0260 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.79
DANN	Benign	0.79
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs11617224; hg19: chr13-49228757;