chrX-118776517-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001560.3(IL13RA1):c.1191+6A>G variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00137 in 672,886 control chromosomes in the GnomAD database, including 4 homozygotes. There are 184 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0049 ( 2 hom., 97 hem., cov: 21)
Exomes 𝑓: 0.00071 ( 2 hom. 87 hem. )
Consequence
IL13RA1
NM_001560.3 splice_donor_region, intron
NM_001560.3 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00002288
2
Clinical Significance
Conservation
PhyloP100: -0.427
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant X-118776517-A-G is Benign according to our data. Variant chrX-118776517-A-G is described in ClinVar as [Benign]. Clinvar id is 780734.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00495 (515/104058) while in subpopulation AFR AF= 0.0176 (483/27449). AF 95% confidence interval is 0.0163. There are 2 homozygotes in gnomad4. There are 97 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL13RA1 | NM_001560.3 | c.1191+6A>G | splice_donor_region_variant, intron_variant | ENST00000371666.8 | |||
IL13RA1 | XM_047442096.1 | c.1191+6A>G | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL13RA1 | ENST00000371666.8 | c.1191+6A>G | splice_donor_region_variant, intron_variant | 1 | NM_001560.3 | P1 | |||
IL13RA1 | ENST00000652600.1 | c.1185+6A>G | splice_donor_region_variant, intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00495 AC: 515AN: 104042Hom.: 2 Cov.: 21 AF XY: 0.00357 AC XY: 97AN XY: 27160
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GnomAD3 exomes AF: 0.00181 AC: 273AN: 151112Hom.: 4 AF XY: 0.00108 AC XY: 51AN XY: 47110
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GnomAD4 exome AF: 0.000710 AC: 404AN: 568828Hom.: 2 Cov.: 10 AF XY: 0.000542 AC XY: 87AN XY: 160566
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 26, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at