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NM_182961.4(SYNE1):c.15313G>A (p.Asp5105Asn)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 10, 2020
Accession:
VCV000355867.8
Variation ID:
355867
Description:
single nucleotide variant
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NM_182961.4(SYNE1):c.15313G>A (p.Asp5105Asn)

Allele ID
301925
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6q25.2
Genomic location
6: 152326083 (GRCh38) GRCh38 UCSC
6: 152647218 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.11:g.152647218C>T
NM_033071.3:c.15100G>A NP_149062.1:p.Asp5034Asn missense
LRG_427:g.316317G>A
... more HGVS
Protein change
D5034N, D5105N
Other names
-
Canonical SPDI
NC_000006.12:152326082:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00639 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00462
Trans-Omics for Precision Medicine (TOPMed) 0.00595
Trans-Omics for Precision Medicine (TOPMed) 0.00605
The Genome Aggregation Database (gnomAD), exomes 0.00153
The Genome Aggregation Database (gnomAD) 0.00602
1000 Genomes Project 0.00639
Exome Aggregation Consortium (ExAC) 0.00189
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00630
Links
ClinGen: CA4055822
dbSNP: rs35493783
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 23, 2018 RCV000517257.6
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000285970.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000342677.2
Benign 1 criteria provided, single submitter Dec 21, 2017 RCV000710242.4
Benign 1 criteria provided, single submitter Nov 10, 2020 RCV001080179.2
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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
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: SCV000461151.3
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: SCV000461152.3
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
(Aug 23, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000730044.1
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 21, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000615566.2
Submitted: (Aug 31, 2018)
Evidence details
Likely benign
(Oct 23, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001158150.1
Submitted: (Aug 05, 2019)
Evidence details
Benign
(Nov 10, 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: SCV000649047.5
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 rs35493783...

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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