rs771721185
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_181078.3(IL21R):c.138G>A(p.Thr46=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,611,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
IL21R
NM_181078.3 synonymous
NM_181078.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.07
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 16-27434435-G-A is Benign according to our data. Variant chr16-27434435-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 541002.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.07 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL21R | NM_181078.3 | c.138G>A | p.Thr46= | synonymous_variant | 3/9 | ENST00000337929.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL21R | ENST00000337929.8 | c.138G>A | p.Thr46= | synonymous_variant | 3/9 | 1 | NM_181078.3 | P1 | |
IL21R | ENST00000395754.4 | c.138G>A | p.Thr46= | synonymous_variant | 3/9 | 1 | P1 | ||
IL21R | ENST00000564089.5 | c.138G>A | p.Thr46= | synonymous_variant | 4/10 | 5 | P1 | ||
IL21R | ENST00000697146.1 | c.138G>A | p.Thr46= | synonymous_variant, NMD_transcript_variant | 2/7 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250706Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135522
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GnomAD4 exome AF: 0.0000117 AC: 17AN: 1459128Hom.: 0 Cov.: 29 AF XY: 0.0000165 AC XY: 12AN XY: 726018
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74296
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cryptosporidiosis-chronic cholangitis-liver disease syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 12, 2021 | - - |
Computational 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