rs6570136
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_052962.3(IL22RA2):c.-138C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,134 control chromosomes in the GnomAD database, including 20,738 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 0.50 ( 20738 hom., cov: 33)
Exomes 𝑓: 0.50 ( 0 hom. )
Consequence
IL22RA2
NM_052962.3 5_prime_UTR
NM_052962.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.162
Genes affected
IL22RA2 (HGNC:14901): (interleukin 22 receptor subunit alpha 2) This gene encodes a member of the class II cytokine receptor family. The encoded soluble protein specifically binds to and inhibits interleukin 22 activity by blocking the interaction of interleukin 22 with its cell surface receptor. The encoded protein may be important in the regulation of inflammatory response, and has been implicated in the regulation of tumorigenesis in the colon. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2013]
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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=-0.96).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL22RA2 | NM_052962.3 | c.-138C>T | 5_prime_UTR_variant | 1/7 | ENST00000296980.7 | ||
IL22RA2 | NM_181309.2 | c.-138C>T | 5_prime_UTR_variant | 1/6 | |||
IL22RA2 | NM_181310.2 | c.-138C>T | 5_prime_UTR_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL22RA2 | ENST00000296980.7 | c.-138C>T | 5_prime_UTR_variant | 1/7 | 1 | NM_052962.3 | |||
IL22RA2 | ENST00000339602.3 | c.-138C>T | 5_prime_UTR_variant | 1/5 | 1 | ||||
IL22RA2 | ENST00000349184.9 | c.-138C>T | 5_prime_UTR_variant | 1/6 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.502 AC: 76367AN: 152014Hom.: 20686 Cov.: 33
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GnomAD4 exome AF: 0.500 AC: 1AN: 2Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1AN XY: 2
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GnomAD4 genome ? AF: 0.503 AC: 76473AN: 152132Hom.: 20738 Cov.: 33 AF XY: 0.504 AC XY: 37451AN XY: 74374
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at