rs321090

Variant names:

• chrX-78304490-G-A
• rs321090
• NM_006639.4:c.-114-20950C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_006639.4(CYSLTR1):​c.-114-20950C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.79 (24639 hom., 25138 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: CYSLTR1 NM_006639.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 2 publications found

Genes affected

CYSLTR1 (HGNC:17451): (cysteinyl leukotriene receptor 1) This gene encodes a member of the G-protein coupled receptor 1 family. The encoded protein is a receptor for cysteinyl leukotrienes, and is involved in mediating bronchoconstriction via activation of a phosphatidylinositol-calcium second messenger system. Activation of the encoded receptor results in contraction and proliferation of bronchial smooth muscle cells, eosinophil migration, and damage to the mucus layer in the lung. Upregulation of this gene is associated with asthma and dysregulation may also be implicated in cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006639.4. 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
	CYSLTR1	NM_006639.4	MANE Select	c.-114-20950C>T		intron	N/A	NP_006630.1
	CYSLTR1	NM_001282186.2		c.-28+22815C>T		intron	N/A	NP_001269115.1
	CYSLTR1	NM_001282187.2		c.-115+10445C>T		intron	N/A	NP_001269116.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYSLTR1	ENST00000373304.4	TSL:1 MANE Select	c.-114-20950C>T		intron	N/A	ENSP00000362401.3
	CYSLTR1	ENST00000614798.1	TSL:1	c.-28+22815C>T		intron	N/A	ENSP00000478492.1

Frequencies

GnomAD3 genomes AF: 0.786 AC: 86549 AN: 110143 Hom.: 24645 Cov.: 22

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.756

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.786 AC: 86591 AN: 110199 Hom.: 24639 Cov.: 22 AF XY: 0.775 AC XY: 25138 AN XY: 32425

African (AFR) AF: 0.903 AC: 27416 AN: 30367

American (AMR) AF: 0.670 AC: 6920 AN: 10325

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2142 AN: 2628

East Asian (EAS) AF: 0.590 AC: 2067 AN: 3506

South Asian (SAS) AF: 0.622 AC: 1590 AN: 2556

European-Finnish (FIN) AF: 0.772 AC: 4398 AN: 5695

Middle Eastern (MID) AF: 0.757 AC: 165 AN: 218

European-Non Finnish (NFE) AF: 0.765 AC: 40326 AN: 52747

Other (OTH) AF: 0.752 AC: 1119 AN: 1488

Alfa AF: 0.775 Hom.: 41647

Bravo AF: 0.784

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.52
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs321090; hg19: chrX-77559987;