Variant rs280501 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The 19-10380646-C-T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 151,158 control chromosomes in the GnomAD database, including 3,549 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 0.20 ( 3549 hom., cov: 31)

Exomes 𝑓: 0.075 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TYK2
ENST00000699360.1 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Variant links:

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]

TYK2 links:

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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=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	Effect	TSL
TYK2	ENST00000525976.6 linkuse as main transcript	upstream_gene_variant	3
TYK2	ENST00000699360.1 linkuse as main transcript	upstream_gene_variant
TYK2	ENST00000527481.3 linkuse as main transcript	upstream_gene_variant	3

Frequencies

GnomAD3 genomes

AF:

0.199

AC:

30043

AN:

151050

Hom.:

3533

Cov.:

show subpopulations

Gnomad AFR

AF:

0.327

Gnomad AMI

AF:

0.0938

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.166

Gnomad EAS

AF:

0.0380

Gnomad SAS

AF:

0.188

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.242

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.184

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0747

AC:

AN:

174

Hom.:

Cov.:

AF XY:

0.0849

AC XY:

AN XY:

106

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0847

Gnomad4 SAS exome

AF:

0.0500

Gnomad4 NFE exome

AF:

0.0625

GnomAD4 genome

AF:

0.199

AC:

30102

AN:

151158

Hom.:

3549

Cov.:

AF XY:

0.197

AC XY:

14510

AN XY:

73770

show subpopulations

Gnomad4 AFR

AF:

0.328

Gnomad4 AMR

AF:

0.130

Gnomad4 ASJ

AF:

0.166

Gnomad4 EAS

AF:

0.0379

Gnomad4 SAS

AF:

0.188

Gnomad4 FIN

AF:

0.181

Gnomad4 NFE

AF:

0.155

Gnomad4 OTH

AF:

0.188

Alfa

AF:

0.162

Hom.:

2759

Bravo

AF:

0.199

Asia WGS

AF:

0.139

AC:

480

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.2

DANN

Benign

0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over