rs321090

chrX-78304490-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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

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

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS2: High Homozygotes in GnomAd at 24645 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYSLTR1	NM_006639.4	c.-114-20950C>T		intron_variant		ENST00000373304.4
CYSLTR1	NM_001282186.2	c.-28+22815C>T		intron_variant
CYSLTR1	NM_001282187.2	c.-115+10445C>T		intron_variant
CYSLTR1	NM_001282188.2	c.-115+14120C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYSLTR1	ENST00000373304.4	c.-114-20950C>T		intron_variant		1	NM_006639.4	P1
CYSLTR1	ENST00000614798.1	c.-28+22815C>T		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.786 AC: 86549 AN: 110143 Hom.: 24645 Cov.: 22 AF XY: 0.775 AC XY: 25084 AN XY: 32359

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

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.752

Alfa AF: 0.772 Hom.: 20777

Bravo AF: 0.784

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.87
Dann	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs321090; hg19: chrX-77559987;