rs3795302
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021258.4(IL22RA1):c.*179G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 608,064 control chromosomes in the GnomAD database, including 59,303 homozygotes. 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 0.40 ( 13106 hom., cov: 34)
Exomes 𝑓: 0.44 ( 46197 hom. )
Consequence
IL22RA1
NM_021258.4 3_prime_UTR
NM_021258.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0300
Genes affected
IL22RA1 (HGNC:13700): (interleukin 22 receptor subunit alpha 1) The protein encoded by this gene belongs to the class II cytokine receptor family, and has been shown to be a receptor for interleukin 22 (IL22). IL22 receptor is a protein complex that consists of this protein and interleukin 10 receptor, beta (IL10BR/CRFB4), a subunit also shared by the receptor complex for interleukin 10 (IL10). This gene and interleukin 28 receptor, alpha (IL28RA) form a cytokine receptor gene cluster in the chromosomal region 1p36. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL22RA1 | NM_021258.4 | c.*179G>A | 3_prime_UTR_variant | 7/7 | ENST00000270800.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL22RA1 | ENST00000270800.2 | c.*179G>A | 3_prime_UTR_variant | 7/7 | 1 | NM_021258.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.404 AC: 61381AN: 152116Hom.: 13105 Cov.: 34
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GnomAD4 exome AF: 0.437 AC: 199332AN: 455830Hom.: 46197 Cov.: 5 AF XY: 0.439 AC XY: 103335AN XY: 235156
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GnomAD4 genome ? AF: 0.403 AC: 61395AN: 152234Hom.: 13106 Cov.: 34 AF XY: 0.406 AC XY: 30188AN XY: 74420
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ClinVar
Not reported inComputational scores
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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