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NM_206933.4(USH2A):c.4758+3A>G

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Sep 27, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000156396.8
Variation ID:
156396
Description:
single nucleotide variant
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NM_206933.4(USH2A):c.4758+3A>G

Allele ID
166176
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q41
Genomic location
1: 216097080 (GRCh38) GRCh38 UCSC
1: 216270422 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.216270422T>C
NC_000001.11:g.216097080T>C
NG_009497.1:g.331317A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:216097079:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00280 (C)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00107
1000 Genomes Project 0.00280
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD) 0.00056
The Genome Aggregation Database (gnomAD), exomes 0.00151
Exome Aggregation Consortium (ExAC) 0.00152
The Genome Aggregation Database (gnomAD) 0.00140
Trans-Omics for Precision Medicine (TOPMed) 0.00192
Links
ClinGen: CA270793
dbSNP: rs117798425
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Nov 22, 2017 RCV000599908.1
Benign 2 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000907794.4
Likely benign 2 criteria provided, single submitter May 28, 2019 RCV000986536.2
Uncertain significance 1 no assertion criteria provided Sep 18, 2014 RCV000144478.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
USH2A - - GRCh38
GRCh37
3406 4061

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Aug 23, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000856091.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Nov 22, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000711239.2
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (3)
Comment:
c.4758+3A>G in intron 22 of USH2A: This variant is not expected to have clinical significance because it has been identified in 1.9% (348/18756) of East … (more)
Likely benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2A
Allele origin: unknown
Mendelics
Accession: SCV001135554.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001052521.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Dec 20, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001941370.1
Submitted: (Sep 27, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 25445212, 25404053, 30245029, 29625443, 31180159, 31904091, 32090030, 32893482, 33090715)
Uncertain significance
(Sep 18, 2014)
no assertion criteria provided
Method: clinical testing
Leber congenital amaurosis
Allele origin: unknown
Molecular Diagnostics Laboratory,Seoul National University Hospital
Accession: SCV000189613.1
Submitted: (Sep 19, 2014)
Evidence details
Benign
(Jun 24, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 2A
Allele origin: germline
Natera, Inc.
Accession: SCV001455638.1
Submitted: (Dec 28, 2020)
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
Diagnostic application of an extensive gene panel for Leber congenital amaurosis with severe genetic heterogeneity. Seong MW The Journal of molecular diagnostics : JMD 2015 PMID: 25445212
Targeted next generation sequencing for molecular diagnosis of Usher syndrome. Aparisi MJ Orphanet journal of rare diseases 2014 PMID: 25404053
Mutation screening of retinal dystrophy patients by targeted capture from tagged pooled DNAs and next generation sequencing. Watson CM PloS one 2014 PMID: 25133751
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=USH2A - - - -

Text-mined citations for rs117798425...

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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 Nov 27, 2021