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NM_194248.3(OTOF):c.4023+1G>A

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 2, 2021)
Last evaluated:
Apr 7, 2021
Accession:
VCV000048229.8
Variation ID:
48229
Description:
single nucleotide variant
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NM_194248.3(OTOF):c.4023+1G>A

Allele ID
57393
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p23.3
Genomic location
2: 26470592 (GRCh38) GRCh38 UCSC
2: 26693460 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.26693460C>T
NC_000002.12:g.26470592C>T
NG_009937.1:g.93107G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:26470591:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00180 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00088
The Genome Aggregation Database (gnomAD) 0.00064
The Genome Aggregation Database (gnomAD), exomes 0.00090
The Genome Aggregation Database (gnomAD) 0.00031
Exome Aggregation Consortium (ExAC) 0.00078
1000 Genomes Project 0.00180
Links
ClinGen: CA142879
dbSNP: rs186810296
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 Nov 29, 2019 RCV000897451.3
Uncertain significance 1 criteria provided, single submitter Apr 7, 2021 RCV000041538.5
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Apr 27, 2017 RCV000490336.2
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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
754 774

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Mar 18, 2016)
criteria provided, single submitter
Method: reference population
Deafness, autosomal recessive 9
Allele origin: germline
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center
Accession: SCV000267430.1
Submitted: (Apr 14, 2016)
Evidence details
Publications
PubMed (1)
Benign
(Mar 30, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001041596.1
Submitted: (Mar 14, 2019)
Evidence details
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 9
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001302002.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (3)
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)
Likely benign
(Nov 29, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001825083.1
Submitted: (Sep 02, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 33095980, 31130284, 31980526, 31581539, 30096381, 30245029, 26818607, 25262649, 26434960, 21935370, 31095577)
Uncertain significance
(Apr 07, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000065233.8
Submitted: (May 27, 2021)
Evidence details
Publications
PubMed (10)
Comment:
proposed classification - variant undergoing re-assessment, contact laboratory

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
Next-generation sequencing identifies rare pathogenic and novel candidate variants in a cohort of Chinese patients with syndromic or nonsyndromic hearing loss. Xiang YB Molecular genetics & genomic medicine 2020 PMID: 33095980
Precision medicine integrating whole-genome sequencing, comprehensive metabolomics, and advanced imaging. Hou YC Proceedings of the National Academy of Sciences of the United States of America 2020 PMID: 31980526
OTOF mutation analysis with massively parallel DNA sequencing in 2,265 Japanese sensorineural hearing loss patients. Iwasa YI PloS one 2019 PMID: 31095577
Genomic Landscape and Mutational Signatures of Deafness-Associated Genes. Azaiez H American journal of human genetics 2018 PMID: 30245029
Curating Clinically Relevant Transcripts for the Interpretation of Sequence Variants. DiStefano MT The Journal of molecular diagnostics : JMD 2018 PMID: 30096381
Using large sequencing data sets to refine intragenic disease regions and prioritize clinical variant interpretation. Amr SS Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 27657688
High frequency of OTOF mutations in Chinese infants with congenital auditory neuropathy spectrum disorder. Zhang QJ Clinical genetics 2016 PMID: 26818607
Whole-Exome Sequencing of 10 Scientists: Evaluation of the Process and Outcomes. Lindor NM Mayo Clinic proceedings 2015 PMID: 26434960
Utilizing ethnic-specific differences in minor allele frequency to recategorize reported pathogenic deafness variants. Shearer AE American journal of human genetics 2014 PMID: 25262649
Variants of OTOF and PJVK genes in Chinese patients with auditory neuropathy spectrum disorder. Wang J PloS one 2011 PMID: 21935370

Text-mined citations for rs186810296...

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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