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NM_182961.4(SYNE1):c.5070C>G (p.Val1690=)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Sep 25, 2021)
Last evaluated:
Nov 4, 2020
Accession:
VCV000281953.14
Variation ID:
281953
Description:
single nucleotide variant
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NM_182961.4(SYNE1):c.5070C>G (p.Val1690=)

Allele ID
266190
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6q25.2
Genomic location
6: 152427723 (GRCh38) GRCh38 UCSC
6: 152748858 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.11:g.152748858G>C
NM_033071.3:c.5091C>G NP_149062.1:p.Val1697= synonymous
NC_000006.12:g.152427723G>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000006.12:152427722:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00046
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00046
Trans-Omics for Precision Medicine (TOPMed) 0.00054
Links
ClinGen: CA4058384
dbSNP: rs146789107
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000276411.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000371036.2
Likely benign 1 criteria provided, single submitter Nov 4, 2020 RCV001087521.2
Conflicting interpretations of pathogenicity 6 criteria provided, conflicting interpretations Dec 27, 2019 RCV000659066.8
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SYNE1 - - GRCh38
GRCh37
3503 3642

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 19, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000333023.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jul 30, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000615670.2
Submitted: (Sep 25, 2019)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Spinocerebellar ataxia, autosomal recessive 8
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000461473.3
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
Emery-Dreifuss muscular dystrophy 4, autosomal dominant
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000461474.3
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 04, 2020)
criteria provided, single submitter
Method: clinical testing
Emery-Dreifuss muscular dystrophy 4, autosomal dominant
Spinocerebellar ataxia, autosomal recessive 8
Allele origin: germline
Invitae
Accession: SCV001006450.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Dec 27, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000527031.4
Submitted: (Sep 25, 2021)
Evidence details
Likely benign
(Mar 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000780874.9
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001926877.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
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: SCV001971673.1
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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SYNE1 - - - -

Text-mined citations for rs146789107...

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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