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NM_000260.4(MYO7A):c.3086A>G (p.His1029Arg)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(2);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Oct 22, 2021)
Last evaluated:
Sep 23, 2021
Accession:
VCV000178483.9
Variation ID:
178483
Description:
single nucleotide variant
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NM_000260.4(MYO7A):c.3086A>G (p.His1029Arg)

Allele ID
178245
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q13.5
Genomic location
11: 77182132 (GRCh38) GRCh38 UCSC
11: 76893178 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_1420:g.58887A>G
LRG_1420t1:c.3086A>G LRG_1420p1:p.His1029Arg
NC_000011.10:g.77182132A>G
... more HGVS
Protein change
H1029R, H1018R
Other names
-
Canonical SPDI
NC_000011.10:77182131:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00379 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00211
The Genome Aggregation Database (gnomAD), exomes 0.00056
Exome Aggregation Consortium (ExAC) 0.00072
1000 Genomes Project 0.00379
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00142
The Genome Aggregation Database (gnomAD) 0.00160
Links
ClinGen: CA182416
dbSNP: rs60103800
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 Apr 28, 2017 RCV000155231.3
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000288323.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000345669.2
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000388720.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Sep 23, 2021 RCV000974265.7
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MYO7A - - GRCh38
GRCh37
2206 2216

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Aug 11, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000204917.4
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.His1029Arg in Exon 24 of MYO7A: This variant is not expected to have clinical significance because it has been identified in 0.8% (81/8690) of African … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000374330.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000374329.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal dominant 11
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000374331.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Likely benign
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000706180.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001122081.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Sep 23, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001813997.2
Submitted: (Oct 22, 2021)
Evidence details
Comment:
In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our … (more)

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=MYO7A - - - -

Text-mined citations for rs60103800...

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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 Oct 30, 2021