13-48679835-A-G

Variant names:

• chr13-48679835-A-G
• rs9595961
• NM_001308476.3:c.-265-11377A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001308476.3(CYSLTR2):​c.-265-11377A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,806 control chromosomes in the GnomAD database, including 21,872 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 0.53 (21872 hom., cov: 30)
• Consequence: CYSLTR2 NM_001308476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYSLTR2	NM_001308476.3	c.-265-11377A>G		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.-265-11377A>G		intron_variant	Intron 1 of 4		NM_001308476.3	ENSP00000508181.1

Frequencies

GnomAD3 genomes AF: 0.534 AC: 80954 AN: 151688 Hom.: 21841 Cov.: 30

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.534 AC: 81024 AN: 151806 Hom.: 21872 Cov.: 30 AF XY: 0.535 AC XY: 39705 AN XY: 74162

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.512

Alfa AF: 0.433 Hom.: 1915

Bravo AF: 0.532

Asia WGS AF: 0.537 AC: 1866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.42
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9595961; hg19: chr13-49253971;