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NM_001256545.2(MEGF10):c.1002C>T (p.His334=)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000350644.5
Variation ID:
350644
Description:
single nucleotide variant
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NM_001256545.2(MEGF10):c.1002C>T (p.His334=)

Allele ID
295138
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q23.2
Genomic location
5: 127410473 (GRCh38) GRCh38 UCSC
5: 126746165 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.9:g.126746165C>T
NC_000005.10:g.127410473C>T
NG_032072.2:g.124710C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000005.10:127410472:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00047
Exome Aggregation Consortium (ExAC) 0.00054
Trans-Omics for Precision Medicine (TOPMed) 0.00270
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00208
The Genome Aggregation Database (gnomAD) 0.00254
1000 Genomes Project 0.00100
The Genome Aggregation Database (gnomAD) 0.00236
Trans-Omics for Precision Medicine (TOPMed) 0.00264
Links
ClinGen: CA3391453
dbSNP: rs142947482
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 Oct 27, 2017 RCV000439607.3
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 3, 2020 RCV000397639.7
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MEGF10 - - GRCh38
GRCh37
626 646

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Myopathy, areflexia, respiratory distress, and dysphagia, early-onset
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000452397.3
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
(May 25, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000614076.1
Submitted: (Aug 17, 2017)
Evidence details
Likely benign
(Oct 27, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000530915.4
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)
Benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Myopathy, areflexia, respiratory distress, and dysphagia, early-onset
Allele origin: germline
Invitae
Accession: SCV000651919.5
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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs142947482...

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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