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NM_206933.4(USH2A):c.4994T>C (p.Ile1665Thr)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jul 14, 2021)
Last evaluated:
Jul 1, 2021
Accession:
VCV000048525.5
Variation ID:
48525
Description:
single nucleotide variant
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NM_206933.4(USH2A):c.4994T>C (p.Ile1665Thr)

Allele ID
57687
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q41
Genomic location
1: 216084871 (GRCh38) GRCh38 UCSC
1: 216258213 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
O75445:p.Ile1665Thr
NM_206933.4:c.4994T>C MANE Select NP_996816.3:p.Ile1665Thr missense
NC_000001.10:g.216258213A>G
... more HGVS
Protein change
I1665T
Other names
p.I1665T:ATC>ACC
Canonical SPDI
NC_000001.11:216084870:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.06270 (G)

Allele frequency
1000 Genomes Project 0.06270
Trans-Omics for Precision Medicine (TOPMed) 0.09819
Exome Aggregation Consortium (ExAC) 0.11018
The Genome Aggregation Database (gnomAD), exomes 0.11045
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.11368
The Genome Aggregation Database (gnomAD) 0.09464
Links
ClinGen: CA143505
UniProtKB: O75445#VAR_038362
dbSNP: rs56222536
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 Jan 7, 2013 RCV000041851.4
Benign 2 criteria provided, single submitter Jul 1, 2021 RCV001276254.2
Benign 1 criteria provided, single submitter Dec 5, 2020 RCV001513476.1
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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
USH2A-AS2 - - - GRCh38 - 262

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: SCV000317205.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001721095.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Feb 19, 2008)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000065547.6
Submitted: (Mar 21, 2019)
Evidence details
Benign
(Jul 01, 2021)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2A
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001750327.1
Submitted: (Jul 14, 2021)
Evidence details
Benign
(Jan 07, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000169743.10
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
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 2A
Allele origin: germline
Natera, Inc.
Accession: SCV001462262.1
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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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 rs56222536...

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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