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NM_206933.4(USH2A):c.2109T>C (p.Asp703=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
11 (Most recent: Sep 30, 2021)
Last evaluated:
Jul 1, 2021
Accession:
VCV000048483.9
Variation ID:
48483
Description:
single nucleotide variant
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NM_206933.4(USH2A):c.2109T>C (p.Asp703=)

Allele ID
57645
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q41
Genomic location
1: 216250961 (GRCh38) GRCh38 UCSC
1: 216424303 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.216424303A>G
NC_000001.11:g.216250961A>G
NG_009497.1:g.177436T>C
... more HGVS
Protein change
-
Other names
p.D703D:GAT>GAC
Canonical SPDI
NC_000001.11:216250960:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00739 (G)

Allele frequency
1000 Genomes Project 0.00739
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01292
Trans-Omics for Precision Medicine (TOPMed) 0.01203
The Genome Aggregation Database (gnomAD) 0.01627
Exome Aggregation Consortium (ExAC) 0.01581
The Genome Aggregation Database (gnomAD), exomes 0.01698
Links
ClinGen: CA143435
dbSNP: rs45555435
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 4 criteria provided, multiple submitters, no conflicts Aug 25, 2011 RCV000041806.5
Benign 3 criteria provided, multiple submitters, no conflicts Dec 8, 2020 RCV000993540.3
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Jul 1, 2021 RCV001097278.3
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV001097277.1
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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
3452 4058

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000317198.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Nov 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001146607.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (2)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2A
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001253541.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001732134.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 01, 2021)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2A
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001750420.1
Submitted: (Jul 14, 2021)
Evidence details
Benign
(Aug 25, 2011)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000169734.10
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
(Jul 17, 2009)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000065502.6
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (4)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Retinitis pigmentosa
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001253540.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 2A
Allele origin: germline
Natera, Inc.
Accession: SCV001452249.1
Submitted: (Dec 28, 2020)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001959335.1
Submitted: (Sep 30, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001973100.1
Submitted: (Sep 21, 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
Mutational screening of the USH2A gene in Spanish USH patients reveals 23 novel pathogenic mutations. Garcia-Garcia G Orphanet journal of rare diseases 2011 PMID: 22004887
Spectrum of USH2A mutations in Scandinavian patients with Usher syndrome type II. Dreyer B Human mutation 2008 PMID: 18273898
Novel USH2A mutations in Israeli patients with retinitis pigmentosa and Usher syndrome type 2. Kaiserman N Archives of ophthalmology (Chicago, Ill. : 1960) 2007 PMID: 17296898
Three novel mutations and twelve polymorphisms identified in the USH2A gene in Israeli USH2 families. Adato A Human mutation 2000 PMID: 10738000
Genomic structure and identification of novel mutations in usherin, the gene responsible for Usher syndrome type IIa. Weston MD American journal of human genetics 2000 PMID: 10729113

Text-mined citations for rs45555435...

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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 20, 2021