X-118759603-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001560.3(IL13RA1):c.676+1361C>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 0.89 ( 30536 hom., 27718 hem., cov: 21)
Failed GnomAD Quality Control
Consequence
IL13RA1
NM_001560.3 intron
NM_001560.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.531
Genes affected
IL13RA1 (HGNC:5974): (interleukin 13 receptor subunit alpha 1) The protein encoded by this gene is a subunit of the interleukin 13 receptor. This subunit forms a receptor complex with IL4 receptor alpha, a subunit shared by IL13 and IL4 receptors. This subunit serves as a primary IL13-binding subunit of the IL13 receptor, and may also be a component of IL4 receptors. This protein has been shown to bind tyrosine kinase TYK2, and thus may mediate the signaling processes that lead to the activation of JAK1, STAT3 and STAT6 induced by IL13 and IL4. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BS2
?
High Homozygotes in GnomAd at 30541 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL13RA1 | NM_001560.3 | c.676+1361C>T | intron_variant | ENST00000371666.8 | |||
IL13RA1 | XM_047442096.1 | c.676+1361C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL13RA1 | ENST00000371666.8 | c.676+1361C>T | intron_variant | 1 | NM_001560.3 | P1 | |||
IL13RA1 | ENST00000371642.1 | c.676+1361C>T | intron_variant | 1 | |||||
IL13RA1 | ENST00000652600.1 | c.670+1361C>T | intron_variant | ||||||
IL13RA1 | ENST00000481868.1 | n.369+634C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.887 AC: 96510AN: 108851Hom.: 30541 Cov.: 21 AF XY: 0.890 AC XY: 27664AN XY: 31095
GnomAD3 genomes
?
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.887 AC: 96553AN: 108907Hom.: 30536 Cov.: 21 AF XY: 0.890 AC XY: 27718AN XY: 31161
GnomAD4 genome
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Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at