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NM_182961.4(SYNE1):c.22452A>G (p.Ser7484=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Sep 30, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000130420.9
Variation ID:
130420
Description:
single nucleotide variant
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NM_182961.4(SYNE1):c.22452A>G (p.Ser7484=)

Allele ID
135866
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6q25.2
Genomic location
6: 152213654 (GRCh38) GRCh38 UCSC
6: 152534789 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_427:g.428746A>G
LRG_427t2:c.22239A>G LRG_427p2:p.Ser7413=
LRG_427t1:c.22452A>G LRG_427p1:p.Ser7484=
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000006.12:152213653:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.01358 (C)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.01755
The Genome Aggregation Database (gnomAD) 0.02562
The Genome Aggregation Database (gnomAD) 0.03465
Trans-Omics for Precision Medicine (TOPMed) 0.01841
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.02176
1000 Genomes Project 0.01358
Exome Aggregation Consortium (ExAC) 0.02601
The Genome Aggregation Database (gnomAD), exomes 0.02597
Links
ClinGen: CA155407
dbSNP: rs36044575
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 6 criteria provided, multiple submitters, no conflicts Mar 7, 2016 RCV000118460.9
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000264676.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000355566.2
Benign 1 criteria provided, single submitter Dec 8, 2020 RCV000531886.3
Benign 1 criteria provided, single submitter Apr 23, 2019 RCV000993154.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SYNE1 - - GRCh38
GRCh37
3489 3628

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000315132.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Mar 07, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000524609.4
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
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Emery-Dreifuss muscular dystrophy 4, autosomal dominant
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000460976.3
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 13, 2018)
criteria provided, single submitter
Method: clinical testing
Spinocerebellar ataxia, autosomal recessive 8
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000460975.3
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
(Apr 23, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001145929.1
Submitted: (Sep 25, 2019)
Evidence details
Benign
(Dec 08, 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: SCV000649119.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000152866.2
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: SCV001920596.1
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: SCV001959390.1
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: SCV001974837.1
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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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 rs36044575...

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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