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NM_013382.7(POMT2):c.1654-6A>G

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
11 (Most recent: Sep 30, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000095537.8
Variation ID:
95537
Description:
single nucleotide variant
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NM_013382.7(POMT2):c.1654-6A>G

Allele ID
101436
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
14q24.3
Genomic location
14: 77280469 (GRCh38) GRCh38 UCSC
14: 77746812 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000014.8:g.77746812T>C
NC_000014.9:g.77280469T>C
NG_008897.1:g.45414A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000014.9:77280468:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.15755 (C)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.14351
The Genome Aggregation Database (gnomAD) 0.14937
The Genome Aggregation Database (gnomAD) 0.14330
1000 Genomes Project 0.15755
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.14563
Trans-Omics for Precision Medicine (TOPMed) 0.14730
Links
ClinGen: CA148609
dbSNP: rs4540995
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 7 criteria provided, multiple submitters, no conflicts Nov 26, 2014 RCV000081567.14
Benign 2 criteria provided, multiple submitters, no conflicts May 1, 2017 RCV000576561.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000270588.2
Benign 1 criteria provided, single submitter Dec 3, 2020 RCV001510199.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
POMT2 - - GRCh38
GRCh37
582 604

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000311987.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(May 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000677422.2
Submitted: (Aug 31, 2018)
Evidence details
Publications
PubMed (1)
Benign
(Jul 18, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000113498.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Nov 26, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000269716.3
Submitted: (Mar 21, 2019)
Evidence details
Comment:
c.1654-6A>G in intron 15 of POMT2: This variant is not expected to have clinical significance because it has been identified in 23% (1034/4406) of African … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Limb-girdle muscular dystrophy-dystroglycanopathy, type C2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000388976.3
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B2
Congenital muscular dystrophy-dystroglycanopathy with brain and eye anomalies, type A2
Limb-girdle muscular dystrophy-dystroglycanopathy, type C2
Allele origin: germline
Invitae
Accession: SCV001717180.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001910212.1
Submitted: (Sep 21, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000152367.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001923352.1
Submitted: (Sep 23, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001953286.1
Submitted: (Sep 30, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001974714.1
Submitted: (Sep 21, 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
Congenital muscular dystrophies with defective glycosylation of dystroglycan: a population study. Mercuri E Neurology 2009 PMID: 19299310
POMT1 and POMT2 mutations in CMD patients: a multicentric Italian study. Messina S Neuromuscular disorders : NMD 2008 PMID: 18513969
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=POMT2 - - - -

Text-mined citations for rs4540995...

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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 Nov 27, 2021