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NM_025132.4(WDR19):c.2715G>A (p.Lys905=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 17, 2020
Accession:
VCV000286679.4
Variation ID:
286679
Description:
single nucleotide variant
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NM_025132.4(WDR19):c.2715G>A (p.Lys905=)

Allele ID
270916
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
4p14
Genomic location
4: 39245438 (GRCh38) GRCh38 UCSC
4: 39247058 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000004.11:g.39247058G>A
NC_000004.12:g.39245438G>A
NM_025132.4:c.2715G>A MANE Select NP_079408.3:p.Lys905= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000004.12:39245437:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00120 (A)

Allele frequency
1000 Genomes Project 0.00120
The Genome Aggregation Database (gnomAD) 0.00073
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00134
Trans-Omics for Precision Medicine (TOPMed) 0.00085
The Genome Aggregation Database (gnomAD), exomes 0.00026
Exome Aggregation Consortium (ExAC) 0.00040
Links
ClinGen: CA2892166
dbSNP: rs200339331
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Nov 17, 2020 RCV001089412.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations May 18, 2018 RCV000271288.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
WDR19 - - GRCh38
GRCh37
419 445

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Mar 22, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000340213.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(May 18, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV000884904.1
Submitted: (Oct 10, 2018)
Evidence details
Comment:
The WDR19 c.2715G>A; p.Lys905Lys variant (rs200339331), to our knowledge, is not described in the medical literature but is reported as a variant of uncertain significance … (more)
Benign
(Nov 17, 2020)
criteria provided, single submitter
Method: clinical testing
Senior-Loken syndrome 8
Asphyxiating thoracic dystrophy 5
Allele origin: germline
Invitae
Accession: SCV001098727.3
Submitted: (Jan 07, 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=WDR19 - - - -

Text-mined citations for rs200339331...

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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 Jun 14, 2021