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NM_001083961.2(WDR62):c.3033G>A (p.Pro1011=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 29, 2020
Accession:
VCV000160278.5
Variation ID:
160278
Description:
single nucleotide variant
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NM_001083961.2(WDR62):c.3033G>A (p.Pro1011=)

Allele ID
169517
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19q13.12
Genomic location
19: 36101725 (GRCh38) GRCh38 UCSC
19: 36592627 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.10:g.36101725G>A
NC_000019.9:g.36592627G>A
NM_001083961.2:c.3033G>A MANE Select NP_001077430.1:p.Pro1011= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000019.10:36101724:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.01138 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00228
The Genome Aggregation Database (gnomAD) 0.00293
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00024
1000 Genomes Project 0.01138
The Genome Aggregation Database (gnomAD), exomes 0.00438
Trans-Omics for Precision Medicine (TOPMed) 0.00405
Links
ClinGen: CA173925
dbSNP: rs118175551
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Apr 25, 2017 RCV000147948.4
Benign 1 criteria provided, single submitter Oct 29, 2020 RCV000885269.3
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV001128202.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
WDR62 - - GRCh38
GRCh37
479 491

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Apr 25, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000616289.1
Submitted: (Aug 17, 2017)
Evidence details
Benign
(Oct 29, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001028704.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 19, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000515263.4
Submitted: (Mar 26, 2018)
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)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Primary autosomal recessive microcephaly 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001287613.1
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
(-)
no assertion criteria provided
Method: clinical testing
not specified
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000195441.1
Submitted: (Sep 11, 2014)
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs118175551...

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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