NM_194248.3(OTOF):c.4677G>A (p.Val1559=) AND Autosomal recessive nonsyndromic hearing loss 9

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 12, 2018
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000021064.7

Allele description [Variation Report for NM_194248.3(OTOF):c.4677G>A (p.Val1559=)]

NM_194248.3(OTOF):c.4677G>A (p.Val1559=)

Gene:

OTOF:otoferlin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p23.3

Genomic location:

Preferred name:

NM_194248.3(OTOF):c.4677G>A (p.Val1559=)

HGVS:

NC_000002.12:g.26465794C>T
NG_009937.1:g.97905G>A
NM_001287489.2:c.4677G>A
NM_004802.4:c.2376G>A
NM_194248.3:c.4677G>AMANE SELECT
NM_194322.3:c.2607G>A
NM_194323.3:c.2376G>A
NP_001274418.1:p.Val1559=
NP_004793.2:p.Val792=
NP_919224.1:p.Val1559=
NP_919303.1:p.Val869=
NP_919304.1:p.Val792=
NC_000002.11:g.26688662C>T
NM_194248.1:c.4677G>A
NM_194248.2:c.4677G>A
c.4677G>A
p.Val1559Val

Links:

dbSNP: rs2272071

NCBI 1000 Genomes Browser:

rs2272071

Molecular consequence:

NM_001287489.2:c.4677G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_004802.4:c.2376G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_194248.3:c.4677G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_194322.3:c.2607G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_194323.3:c.2376G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Autosomal recessive nonsyndromic hearing loss 9
Synonyms:: NEUROSENSORY NONSYNDROMIC RECESSIVE DEAFNESS 9; Deafness, autosomal recessive 9; AUDITORY NEUROPATHY, AUTOSOMAL RECESSIVE, 1, TEMPERATURE-SENSITIVE; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010986; MedGen: C1832828; Orphanet: 90636; OMIM: 601071

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000041720	GeneReviews	no classification provided	not provided	unknown	literature only	PubMed (1) [See all records that cite this PMID]
SCV000429600	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Jan 12, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000041720

GeneReviews

no classification provided

not provided

unknown

literature only

PubMed (1)
[See all records that cite this PMID]

SCV000429600

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Jan 12, 2018)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

OTOF-Related Deafness.

Azaiez H, Thorpe RK, Smith RJH.

2008 Feb 29 [updated 2021 Jan 21]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]

PMID:: 20301429

Details of each submission

From GeneReviews, SCV000041720.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	not provided	not provided	not provided	Assert pathogenicity		not provided	not provided	not provided	not provided

From Illumina Laboratory Services, Illumina, SCV000429600.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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