NM_004999.4(MYO6):c.2078-2A>G AND Autosomal dominant nonsyndromic hearing loss 22

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 29, 2019
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV001255960.2

Allele description [Variation Report for NM_004999.4(MYO6):c.2078-2A>G]

NM_004999.4(MYO6):c.2078-2A>G

Gene:

MYO6:myosin VI [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q14.1

Genomic location:

Preferred name:

NM_004999.4(MYO6):c.2078-2A>G

HGVS:

NC_000006.12:g.75879818A>G
NG_009934.2:g.135626A>G
NM_001300899.2:c.2078-2A>G
NM_001368136.1:c.2078-2A>G
NM_001368137.1:c.2078-2A>G
NM_001368138.1:c.2063-2A>G
NM_001368865.1:c.2078-2A>G
NM_001368866.1:c.2078-2A>G
NM_004999.4:c.2078-2A>GMANE SELECT
LRG_438t1:c.2078-2A>G
LRG_438:g.135626A>G
NC_000006.11:g.76589535A>G
NC_000006.11:g.76589535A>G
NM_004999.3:c.2078-2A>G

Links:

dbSNP: rs1777874560

NCBI 1000 Genomes Browser:

rs1777874560

Molecular consequence:

NM_001300899.2:c.2078-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001368136.1:c.2078-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001368137.1:c.2078-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001368138.1:c.2063-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001368865.1:c.2078-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001368866.1:c.2078-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_004999.4:c.2078-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Autosomal dominant nonsyndromic hearing loss 22
Synonyms:: Deafness, autosomal dominant 22; Autosomal dominant nonsyndromic deafness 22; Deafness, autosomal dominant nonsyndromic sensorineural 22; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011660; MedGen: C2931767; Orphanet: 228012; OMIM: 606346

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001427061	Clinical Genomics Laboratory, Stanford Medicine	no assertion criteria provided	Likely pathogenic (May 29, 2019)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001427061

Clinical Genomics Laboratory, Stanford Medicine

no assertion criteria provided

Likely pathogenic
(May 29, 2019)

germline

clinical testing

Help

Summary from all submissions

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

Details of each submission

From Clinical Genomics Laboratory, Stanford Medicine, SCV001427061.1

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

Description

The c.2078-2A>G variant in the MYO6 gene has not been previously reported in association with disease. This variant was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). The c.2078-2A>G variant alters the canonical acceptor splice site in intron 20, which is predicted to result in abnormal gene splicing. Heterozygous loss of function is an established mechanism of disease for the MYO6 gene. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the c.2078-2A>G variant as likely pathogenic for autosomal dominant nonsydromic sensorineural hearing loss based on the information above. [ACMG evidence codes used: PVS1_Strong; PM2]

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

Last Updated: Sep 29, 2024

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