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NM_194248.3(OTOF):c.2215-80T>C

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Dec 11, 2020)
Last evaluated:
Aug 9, 2019
Accession:
VCV000048189.5
Variation ID:
48189
Description:
single nucleotide variant
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NM_194248.3(OTOF):c.2215-80T>C

Allele ID
57353
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p23.3
Genomic location
2: 26477829 (GRCh38) GRCh38 UCSC
2: 26700697 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.26700697A>G
NC_000002.12:g.26477829A>G
NG_009937.1:g.85870T>C
... more HGVS
Protein change
L22P
Other names
-
Canonical SPDI
NC_000002.12:26477828:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00140 (G)

Allele frequency
1000 Genomes Project 0.00140
Exome Aggregation Consortium (ExAC) 0.00264
The Genome Aggregation Database (gnomAD) 0.00201
Trans-Omics for Precision Medicine (TOPMed) 0.00293
The Genome Aggregation Database (gnomAD), exomes 0.00267
Links
ClinGen: CA248653
dbSNP: rs143141993
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 Jun 9, 2016 RCV000041485.7
Likely benign 1 criteria provided, single submitter Aug 9, 2019 RCV001283164.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Mar 26, 2018 RCV000731859.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
OTOF - - GRCh38
GRCh37
751 771

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jul 17, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia
Accession: SCV000258277.2
Submitted: (Aug 10, 2015)
Evidence details
Uncertain significance
(Feb 16, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000859715.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jun 09, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000065180.6
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Leu22Pro in exon 1A of OTOF: This variant is not expected to have clinical sig nificance because it has been identified in 0.5% (130/28336) of … (more)
Likely benign
(Mar 26, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000982986.1
Submitted: (Apr 12, 2019)
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)
Likely benign
(Aug 09, 2019)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001159906.2
Submitted: (Dec 11, 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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=OTOF - - - -

Text-mined citations for rs143141993...

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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 11, 2021