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NM_001077365.2(POMT1):c.986+9A>G

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(4);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 26, 2020
Accession:
VCV000211944.6
Variation ID:
211944
Description:
single nucleotide variant
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NM_001077365.2(POMT1):c.986+9A>G

Allele ID
207636
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.13
Genomic location
9: 131511476 (GRCh38) GRCh38 UCSC
9: 134386863 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.134386863A>G
NC_000009.12:g.131511476A>G
NM_001077365.2:c.986+9A>G MANE Select
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000009.12:131511475:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (G)

Allele frequency
1000 Genomes Project 0.00020
The Genome Aggregation Database (gnomAD) 0.00064
Trans-Omics for Precision Medicine (TOPMed) 0.00108
Exome Aggregation Consortium (ExAC) 0.00082
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00092
The Genome Aggregation Database (gnomAD), exomes 0.00088
Links
dbSNP: rs202095070
ClinGen: CA206070
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000349139.2
Benign 1 criteria provided, single submitter Sep 6, 2018 RCV000532464.4
Likely benign 1 criteria provided, single submitter Nov 26, 2020 RCV001085720.2
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Jun 15, 2017 RCV000192918.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
POMT1 - - GRCh38
GRCh37
558 596

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jul 23, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000248580.1
Submitted: (Sep 15, 2015)
Evidence details
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000311726.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Mar 17, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000525354.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Jun 15, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000342841.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Sep 06, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001145174.1
Submitted: (Sep 25, 2019)
Evidence details
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Limb-girdle muscular dystrophy-dystroglycanopathy, type C1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000477657.3
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
(Nov 26, 2020)
criteria provided, single submitter
Method: clinical testing
Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B1
Walker-Warburg congenital muscular dystrophy
Limb-girdle muscular dystrophy-dystroglycanopathy, type C1
Allele origin: germline
Invitae
Accession: SCV000649863.4
Submitted: (Jan 07, 2021)
Evidence details

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=POMT1 - - - -

Text-mined citations for rs202095070...

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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 Jun 23, 2021