13-48668470-C-G

Variant names:

• chr13-48668470-C-G
• rs7335898
• NM_001308476.3:c.-266+14453C>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+14453C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 151,996 control chromosomes in the GnomAD database, including 363 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 0.063 (363 hom., cov: 31)
• Consequence: CYSLTR2 NM_001308476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYSLTR2	NM_001308476.3	c.-266+14453C>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.-266+14453C>G		intron_variant	Intron 1 of 4		NM_001308476.3	ENSP00000508181.1

Frequencies

GnomAD3 genomes AF: 0.0633 AC: 9615 AN: 151876 Hom.: 364 Cov.: 31

Gnomad AFR AF: 0.0542

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.0925

Gnomad FIN AF: 0.0738

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0633 AC: 9622 AN: 151996 Hom.: 363 Cov.: 31 AF XY: 0.0649 AC XY: 4824 AN XY: 74282

African (AFR) AF: 0.0542 AC: 2247 AN: 41462

American (AMR) AF: 0.106 AC: 1622 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.0372 AC: 192 AN: 5162

South Asian (SAS) AF: 0.0930 AC: 447 AN: 4808

European-Finnish (FIN) AF: 0.0738 AC: 779 AN: 10554

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0587 AC: 3989 AN: 67942

Other (OTH) AF: 0.0539 AC: 114 AN: 2114

Alfa AF: 0.0226 Hom.: 13

Bravo AF: 0.0636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.53
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs7335898; hg19: chr13-49242606;