chrX-118776495-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001560.3(IL13RA1):c.1175A>G(p.Gln392Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000168 in 832,134 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000056 ( 0 hom., 2 hem., cov: 21)
Exomes 𝑓: 0.000011 ( 0 hom. 0 hem. )
Consequence
IL13RA1
NM_001560.3 missense
NM_001560.3 missense
Scores
4
8
5
Clinical Significance
Conservation
PhyloP100: 4.56
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 Likely_benign. Variant got -4 ACMG points.
BS2
?
High Hemizygotes in GnomAd at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL13RA1 | NM_001560.3 | c.1175A>G | p.Gln392Arg | missense_variant | 10/11 | ENST00000371666.8 | |
IL13RA1 | XM_047442096.1 | c.1175A>G | p.Gln392Arg | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL13RA1 | ENST00000371666.8 | c.1175A>G | p.Gln392Arg | missense_variant | 10/11 | 1 | NM_001560.3 | P1 | |
IL13RA1 | ENST00000652600.1 | c.1169A>G | p.Gln390Arg | missense_variant | 11/12 |
Frequencies
GnomAD3 genomes ? AF: 0.0000556 AC: 6AN: 107863Hom.: 0 Cov.: 21 AF XY: 0.0000654 AC XY: 2AN XY: 30601
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GnomAD3 exomes AF: 0.0000226 AC: 4AN: 176749Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 61791
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GnomAD4 exome AF: 0.0000110 AC: 8AN: 724271Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0AN XY: 200873
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GnomAD4 genome ? AF: 0.0000556 AC: 6AN: 107863Hom.: 0 Cov.: 21 AF XY: 0.0000654 AC XY: 2AN XY: 30601
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.1175A>G (p.Q392R) alteration is located in exon 10 (coding exon 10) of the IL13RA1 gene. This alteration results from a A to G substitution at nucleotide position 1175, causing the glutamine (Q) at amino acid position 392 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
T
PROVEAN
Benign
N
REVEL
Pathogenic
Sift
Uncertain
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Loss of sheet (P = 0.0228);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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