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NM_194248.3(OTOF):c.1580-6C>T AND Nonsyndromic genetic hearing loss

Germline classification:
Benign (1 submission)
Last evaluated:
May 13, 2022
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV002228679.1

Allele description [Variation Report for NM_194248.3(OTOF):c.1580-6C>T]

NM_194248.3(OTOF):c.1580-6C>T

Gene:
OTOF:otoferlin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p23.3
Genomic location:
Preferred name:
NM_194248.3(OTOF):c.1580-6C>T
HGVS:
  • NC_000002.12:g.26481015G>A
  • NG_009937.1:g.82684C>T
  • NM_001287489.2:c.1580-6C>T
  • NM_194248.3:c.1580-6C>TMANE SELECT
  • NC_000002.11:g.26703883G>A
  • NM_194248.2:c.1580-6C>T
Links:
dbSNP: rs114260271
NCBI 1000 Genomes Browser:
rs114260271
Molecular consequence:
  • NM_001287489.2:c.1580-6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_194248.3:c.1580-6C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Nonsyndromic genetic hearing loss
Synonyms:
Nonsyndromic hearing loss and deafness; Non-syndromic genetic deafness; Nonsyndromic genetic deafness
Identifiers:
MONDO: MONDO:0019497; MedGen: C5680182; Orphanet: 87884

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002512112ClinGen Hearing Loss Variant Curation Expert Panel
reviewed by expert panel

(clingen hl acmg specifications otof myo15a v1)		Benign
(May 13, 2022) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen Hearing Loss Variant Curation Expert Panel, SCV002512112.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The filtering allele frequency (the lower threshold of the 95% CI of 232/24628) of the c.1580-6C>T variant in the OTOF gene is 0.843% for African/African-American chromosomes by gnomAD, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1). Additionally, splice prediction analysis using MaxEntScan and SpliceAI does not suggest an impact to splicing (BP4). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1, BP4.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024