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NM_003331.5(TYK2):c.2783C>T (p.Ala928Val)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Jul 4, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000287098.12
Variation ID:
287098
Description:
single nucleotide variant
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NM_003331.5(TYK2):c.2783C>T (p.Ala928Val)

Allele ID
271335
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.2
Genomic location
19: 10354167 (GRCh38) GRCh38 UCSC
19: 10464843 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.10:g.10354167G>A
NC_000019.9:g.10464843G>A
NM_003331.5:c.2783C>T MANE Select NP_003322.3:p.Ala928Val missense
... more HGVS
Protein change
A928V
Other names
-
Canonical SPDI
NC_000019.10:10354166:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (A)

Allele frequency
1000 Genomes Project 0.00100
Exome Aggregation Consortium (ExAC) 0.00511
The Genome Aggregation Database (gnomAD), exomes 0.00464
Trans-Omics for Precision Medicine (TOPMed) 0.00475
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00600
The Genome Aggregation Database (gnomAD) 0.00459
Links
ClinGen: CA9192922
UniProtKB: P29597#VAR_041873
dbSNP: rs35018800
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 3 criteria provided, multiple submitters, no conflicts Apr 1, 2020 RCV000513917.6
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 3, 2020 RCV001085272.4
Likely benign 1 criteria provided, single submitter Apr 1, 2016 RCV000284384.1

Clinical features observed in individuals with this variant

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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TYK2 - - GRCh38
GRCh37
475 489

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jun 14, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000609889.1
Submitted: (Oct 05, 2017)
Evidence details
Likely benign
(Apr 01, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000340763.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Aug 28, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000970887.1
Submitted: (Apr 12, 2019)
Evidence details
Comment:
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 … (more)
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Immunodeficiency 35
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001284618.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Likely benign
(Nov 10, 2017)
criteria provided, single submitter
Method: clinical testing
Immunodeficiency 35
Allele origin: germline
Knight Diagnostic Laboratories, Oregon Health and Sciences University
Accession: SCV001448819.1
Submitted: (Sep 02, 2020)
Evidence details
Benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Immunodeficiency 35
Allele origin: germline
Invitae
Accession: SCV000766987.4
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Apr 01, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001249693.5
Submitted: (Jul 04, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=TYK2 - - - -

Text-mined citations for rs35018800...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jul 10, 2021