chr13-48705999-G-T

Variant names:

• chr13-48705999-G-T
• rs7324991
• NM_001308476.3:c.-1-818G>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.-1-818G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 137,092 control chromosomes in the GnomAD database, including 22,513 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 0.57 (22513 hom., cov: 26)
• Consequence: CYSLTR2 NM_001308476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 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.-1-818G>T		intron	N/A	NP_001295405.1
	CYSLTR2	NM_001308465.3		c.-1-818G>T		intron	N/A	NP_001295394.1
	CYSLTR2	NM_001308467.3		c.-1-818G>T		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.-1-818G>T		intron	N/A	ENSP00000508181.1
	CYSLTR2	ENST00000614739.4	TSL:1	c.-1-818G>T		intron	N/A	ENSP00000477930.1
	CYSLTR2	ENST00000617562.4	TSL:1	c.-1-818G>T		intron	N/A	ENSP00000482041.1

Frequencies

GnomAD3 genomes AF: 0.572 AC: 78449 AN: 137092 Hom.: 22495 Cov.: 26

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.591

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.572 AC: 78475 AN: 137092 Hom.: 22513 Cov.: 26 AF XY: 0.573 AC XY: 37712 AN XY: 65824

African (AFR) AF: 0.745 AC: 27184 AN: 36486

American (AMR) AF: 0.513 AC: 7095 AN: 13818

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1862 AN: 3348

East Asian (EAS) AF: 0.467 AC: 2220 AN: 4756

South Asian (SAS) AF: 0.598 AC: 2721 AN: 4550

European-Finnish (FIN) AF: 0.492 AC: 3343 AN: 6798

Middle Eastern (MID) AF: 0.597 AC: 160 AN: 268

European-Non Finnish (NFE) AF: 0.504 AC: 32405 AN: 64282

Other (OTH) AF: 0.559 AC: 1061 AN: 1898

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.560

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.23
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs7324991; hg19: chr13-49280135;