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NM_206933.4(USH2A):c.3621C>T (p.Ile1207=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Sep 27, 2021)
Last evaluated:
Feb 9, 2021
Accession:
VCV000048505.7
Variation ID:
48505
Description:
single nucleotide variant
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NM_206933.4(USH2A):c.3621C>T (p.Ile1207=)

Allele ID
57667
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q41
Genomic location
1: 216199817 (GRCh38) GRCh38 UCSC
1: 216373159 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.216373159G>A
NC_000001.11:g.216199817G>A
NG_009497.1:g.228580C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:216199816:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00160 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00057
1000 Genomes Project 0.00160
The Genome Aggregation Database (gnomAD) 0.00188
Exome Aggregation Consortium (ExAC) 0.00061
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00169
Trans-Omics for Precision Medicine (TOPMed) 0.00206
Trans-Omics for Precision Medicine (TOPMed) 0.00189
The Genome Aggregation Database (gnomAD) 0.00190
Links
ClinGen: CA143465
dbSNP: rs146462407
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 Apr 15, 2016 RCV000041831.4
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Feb 9, 2021 RCV000974887.4
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000394479.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000341412.2
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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
3407 4062
USH2A-AS1 - - - GRCh38 - 337

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Apr 17, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000065527.6
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Ile1207Ile in exon 17 of USH2A: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, … (more)
Benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001122758.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Apr 15, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000340699.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Retinitis pigmentosa
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000354127.3
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)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2A
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000354128.3
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
(Feb 09, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001940530.1
Submitted: (Sep 27, 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=USH2A - - - -

Text-mined citations for rs146462407...

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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 Dec 04, 2021