rs320995
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7
The NM_006639.4(CYSLTR1):c.927C>T(p.Phe309=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.73 ( 21100 hom., 22994 hem., cov: 22)
Exomes 𝑓: 0.77 ( 222867 hom. 279930 hem. )
Failed GnomAD Quality Control
Consequence
CYSLTR1
NM_006639.4 synonymous
NM_006639.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.281
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
?
Variant X-78272820-G-A is Benign according to our data. Variant chrX-78272820-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=0.281 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYSLTR1 | NM_006639.4 | c.927C>T | p.Phe309= | synonymous_variant | 3/3 | ENST00000373304.4 | |
CYSLTR1 | NM_001282186.2 | c.927C>T | p.Phe309= | synonymous_variant | 2/2 | ||
CYSLTR1 | NM_001282187.2 | c.927C>T | p.Phe309= | synonymous_variant | 4/4 | ||
CYSLTR1 | NM_001282188.2 | c.927C>T | p.Phe309= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYSLTR1 | ENST00000373304.4 | c.927C>T | p.Phe309= | synonymous_variant | 3/3 | 1 | NM_006639.4 | P1 | |
CYSLTR1 | ENST00000614798.1 | c.927C>T | p.Phe309= | synonymous_variant | 2/2 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.729 AC: 79935AN: 109623Hom.: 21110 Cov.: 22 AF XY: 0.720 AC XY: 22957AN XY: 31897
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GnomAD3 exomes AF: 0.732 AC: 133376AN: 182325Hom.: 31264 AF XY: 0.731 AC XY: 49020AN XY: 67015
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.775 AC: 850271AN: 1097657Hom.: 222867 Cov.: 44 AF XY: 0.771 AC XY: 279930AN XY: 363095
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.729 AC: 79955AN: 109678Hom.: 21100 Cov.: 22 AF XY: 0.719 AC XY: 22994AN XY: 31962
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at