chr13-48682339-C-A

Variant names:

• chr13-48682339-C-A
• rs7330127
• NM_001308476.3:c.-265-8873C>A

Variant summary

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

The NM_001308476.3(CYSLTR2):​c.-265-8873C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,024 control chromosomes in the GnomAD database, including 11,576 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 0.37 (11576 hom., cov: 31)
• Consequence: CYSLTR2 NM_001308476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYSLTR2	NM_001308476.3	c.-265-8873C>A		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.-265-8873C>A		intron_variant	Intron 1 of 4		NM_001308476.3	ENSP00000508181.1

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56477 AN: 151906 Hom.: 11566 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.372 AC: 56505 AN: 152024 Hom.: 11576 Cov.: 31 AF XY: 0.377 AC XY: 27984 AN XY: 74292

African (AFR) AF: 0.182 AC: 7545 AN: 41486

American (AMR) AF: 0.389 AC: 5940 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1603 AN: 3468

East Asian (EAS) AF: 0.420 AC: 2169 AN: 5164

South Asian (SAS) AF: 0.494 AC: 2379 AN: 4820

European-Finnish (FIN) AF: 0.469 AC: 4950 AN: 10558

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30552 AN: 67952

Other (OTH) AF: 0.397 AC: 837 AN: 2108

Alfa AF: 0.395 Hom.: 2694

Bravo AF: 0.355

Asia WGS AF: 0.450 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.19
DANN	Benign	0.61
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs7330127; hg19: chr13-49256475;