rs12720276
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The ENST00000525621.6(TYK2):āc.1848T>Gā(p.Pro616=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0045 in 1,613,912 control chromosomes in the GnomAD database, including 298 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.025 ( 167 hom., cov: 32)
Exomes š: 0.0024 ( 131 hom. )
Consequence
TYK2
ENST00000525621.6 synonymous
ENST00000525621.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.79
Genes affected
TYK2 (HGNC:12440): (tyrosine kinase 2) This gene encodes a member of the tyrosine kinase and, more specifically, the Janus kinases (JAKs) protein families. This protein associates with the cytoplasmic domain of type I and type II cytokine receptors and promulgate cytokine signals by phosphorylating receptor subunits. It is also a component of both the type I and type III interferon signaling pathways. As such, it may play a role in anti-viral immunity. A mutation in this gene has been associated with Immunodeficiency 35. [provided by RefSeq, Sep 2020]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 19-10361881-A-C is Benign according to our data. Variant chr19-10361881-A-C is described in ClinVar as [Benign]. Clinvar id is 327945.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-10361881-A-C is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-2.79 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0845 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TYK2 | NM_003331.5 | c.1848T>G | p.Pro616= | synonymous_variant | 13/25 | ENST00000525621.6 | NP_003322.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TYK2 | ENST00000525621.6 | c.1848T>G | p.Pro616= | synonymous_variant | 13/25 | 1 | NM_003331.5 | ENSP00000431885 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0250 AC: 3803AN: 151990Hom.: 166 Cov.: 32
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GnomAD3 exomes AF: 0.00602 AC: 1513AN: 251262Hom.: 70 AF XY: 0.00431 AC XY: 586AN XY: 135834
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GnomAD4 exome AF: 0.00236 AC: 3445AN: 1461804Hom.: 131 Cov.: 36 AF XY: 0.00201 AC XY: 1460AN XY: 727208
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GnomAD4 genome AF: 0.0251 AC: 3813AN: 152108Hom.: 167 Cov.: 32 AF XY: 0.0235 AC XY: 1746AN XY: 74368
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Immunodeficiency 35 Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 22, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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