rs2239928
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_181078.3(IL21R):c.*597C>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 0.251 in 233,496 control chromosomes in the GnomAD database, including 7,915 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 0.26 ( 5615 hom., cov: 33)
Exomes 𝑓: 0.23 ( 2300 hom. )
Consequence
IL21R
NM_181078.3 3_prime_UTR
NM_181078.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -5.64
Genes affected
IL21R (HGNC:6006): (interleukin 21 receptor) The protein encoded by this gene is a cytokine receptor for interleukin 21 (IL21). It belongs to the type I cytokine receptors, and has been shown to form a heterodimeric receptor complex with the common gamma-chain, a receptor subunit also shared by the receptors for interleukin 2, 4, 7, 9, and 15. This receptor transduces the growth promoting signal of IL21, and is important for the proliferation and differentiation of T cells, B cells, and natural killer (NK) cells. The ligand binding of this receptor leads to the activation of multiple downstream signaling molecules, including JAK1, JAK3, STAT1, and STAT3. Knockout studies of a similar gene in mouse suggest a role for this gene in regulating immunoglobulin production. Three alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2010]
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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 = 0.373 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL21R | NM_181078.3 | c.*597C>A | 3_prime_UTR_variant | 9/9 | ENST00000337929.8 | ||
IL21R-AS1 | NR_037158.1 | n.478-74G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL21R | ENST00000337929.8 | c.*597C>A | 3_prime_UTR_variant | 9/9 | 1 | NM_181078.3 | P1 | ||
IL21R | ENST00000395754.4 | c.*597C>A | 3_prime_UTR_variant | 9/9 | 1 | P1 | |||
IL21R-AS1 | ENST00000563191.1 | n.478-74G>T | intron_variant, non_coding_transcript_variant | 2 | |||||
IL21R | ENST00000564089.5 | c.*597C>A | 3_prime_UTR_variant | 10/10 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.262 AC: 39843AN: 152012Hom.: 5587 Cov.: 33
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GnomAD4 exome AF: 0.231 AC: 18757AN: 81366Hom.: 2300 Cov.: 0 AF XY: 0.230 AC XY: 8629AN XY: 37474
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GnomAD4 genome ? AF: 0.262 AC: 39901AN: 152130Hom.: 5615 Cov.: 33 AF XY: 0.258 AC XY: 19226AN XY: 74404
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at