chr13-48664776-A-G

Variant names:

• chr13-48664776-A-G
• rs9568079
• NM_001308476.3:c.-266+10759A>G

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+10759A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,634 control chromosomes in the GnomAD database, including 3,249 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 (3249 hom., cov: 32)
• Consequence: CYSLTR2 NM_001308476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001308476.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYSLTR2	NM_001308476.3	MANE Select	c.-266+10759A>G		intron	N/A	NP_001295405.1
	CYSLTR2	NM_001308465.3		c.-395+10759A>G		intron	N/A	NP_001295394.1
	CYSLTR2	NM_001308467.3		c.-372+10759A>G		intron	N/A	NP_001295396.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYSLTR2	ENST00000682523.1	MANE Select	c.-266+10759A>G		intron	N/A	ENSP00000508181.1
	CYSLTR2	ENST00000614739.4	TSL:1	c.-243+10759A>G		intron	N/A	ENSP00000477930.1
	CYSLTR2	ENST00000617562.4	TSL:1	c.-372+10759A>G		intron	N/A	ENSP00000482041.1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28780 AN: 151516 Hom.: 3251 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.190 AC: 28776 AN: 151634 Hom.: 3249 Cov.: 32 AF XY: 0.194 AC XY: 14376 AN XY: 74106

African (AFR) AF: 0.0579 AC: 2401 AN: 41446

American (AMR) AF: 0.161 AC: 2455 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3464

East Asian (EAS) AF: 0.252 AC: 1301 AN: 5166

South Asian (SAS) AF: 0.274 AC: 1316 AN: 4810

European-Finnish (FIN) AF: 0.283 AC: 2960 AN: 10470

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16907 AN: 67740

Other (OTH) AF: 0.192 AC: 405 AN: 2110

Alfa AF: 0.225 Hom.: 9344

Bravo AF: 0.176

Asia WGS AF: 0.242 AC: 838 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.81
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs9568079; hg19: chr13-49238912;