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NM_194248.3(OTOF):c.245G>A (p.Arg82His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Jul 28, 2021)
Last evaluated:
Jul 8, 2021
Accession:
VCV000048199.10
Variation ID:
48199
Description:
single nucleotide variant
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NM_194248.3(OTOF):c.245G>A (p.Arg82His)

Allele ID
57363
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p23.3
Genomic location
2: 26519092 (GRCh38) GRCh38 UCSC
2: 26741960 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.26741960C>T
NC_000002.12:g.26519092C>T
NG_009937.1:g.44607G>A
... more HGVS
Protein change
R82H
Other names
-
Canonical SPDI
NC_000002.12:26519091:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00220 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00066
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00231
The Genome Aggregation Database (gnomAD), exomes 0.00050
1000 Genomes Project 0.00220
The Genome Aggregation Database (gnomAD) 0.00237
Trans-Omics for Precision Medicine (TOPMed) 0.00250
The Genome Aggregation Database (gnomAD) 0.00198
Trans-Omics for Precision Medicine (TOPMed) 0.00264
Links
ClinGen: CA142807
dbSNP: rs149766574
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 30, 2018 RCV000041499.4
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Jan 1, 2019 RCV000785039.5
Childhood onset hearing loss
Uncertain significance 1 criteria provided, single submitter Jul 8, 2021 RCV001543606.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 31, 2019 RCV000767023.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
OTOF - - GRCh38
GRCh37
754 774

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(May 16, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000065194.6
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Arg82His in Exon 04 of OTOF: This variant is not expected to have clinical signi ficance because it has been identified in 0.6% (24/3738) of … (more)
Likely benign
(Apr 30, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000860989.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001039162.2
Submitted: (Jan 29, 2020)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 9
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000429656.3
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
(Jul 08, 2021)
criteria provided, single submitter
Method: research
Childhood onset hearing loss
(Autosomal recessive inheritance)
Allele origin: germline
National Institute on Deafness and Communication Disorders,National Institutes of Health
Accession: SCV001519356.2
Submitted: (Jul 28, 2021)
Comment:
was found associated with NM_194248.3:c.3917A>C
Evidence details
Comment:
PP3 (non REVEL) / Modifications from PMID: 30311386 for classification: The genetic causes of hearing loss have not yet been well characterized in the Yoruba … (more)
Uncertain significance
(Aug 24, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000620270.2
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The R82H variant in the OTOF gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. It … (more)
Uncertain significance
(Jan 01, 2019)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 9
Allele origin: unknown
Genomic Research Center,Shahid Beheshti University of Medical Sciences
Accession: SCV000923592.1
Submitted: (Apr 08, 2019)
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=OTOF - - - -

Text-mined citations for rs149766574...

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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