13-48681836-C-T

Variant names:

• chr13-48681836-C-T
• rs17072059
• NM_001308476.3:c.-265-9376C>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.-265-9376C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,076 control chromosomes in the GnomAD database, including 1,440 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 0.11 (1440 hom., cov: 31)
• Consequence: CYSLTR2 NM_001308476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYSLTR2	NM_001308476.3	c.-265-9376C>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.-265-9376C>T		intron_variant	Intron 1 of 4		NM_001308476.3	ENSP00000508181.1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16225 AN: 151958 Hom.: 1433 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0832

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.0871

Gnomad FIN AF: 0.0819

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0445

Gnomad OTH AF: 0.0739

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

GnomAD4 genome AF: 0.107 AC: 16246 AN: 152076 Hom.: 1440 Cov.: 31 AF XY: 0.107 AC XY: 7959 AN XY: 74340

African (AFR) AF: 0.241 AC: 10005 AN: 41446

American (AMR) AF: 0.0833 AC: 1272 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0723 AC: 251 AN: 3470

East Asian (EAS) AF: 0.0442 AC: 229 AN: 5182

South Asian (SAS) AF: 0.0871 AC: 420 AN: 4820

European-Finnish (FIN) AF: 0.0819 AC: 866 AN: 10574

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0445 AC: 3025 AN: 68006

Other (OTH) AF: 0.0741 AC: 156 AN: 2106

Alfa AF: 0.0623 Hom.: 1992

Bravo AF: 0.111

Asia WGS AF: 0.0780 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.73
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs17072059; hg19: chr13-49255972;