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NM_182961.4(SYNE1):c.13863G>A (p.Thr4621=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Sep 30, 2021)
Last evaluated:
Jan 6, 2021
Accession:
VCV000283313.13
Variation ID:
283313
Description:
single nucleotide variant
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NM_182961.4(SYNE1):c.13863G>A (p.Thr4621=)

Allele ID
267550
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6q25.2
Genomic location
6: 152330822 (GRCh38) GRCh38 UCSC
6: 152651957 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_427:g.311578G>A
LRG_427t2:c.13650G>A LRG_427p2:p.Thr4550=
LRG_427t1:c.13863G>A LRG_427p1:p.Thr4621=
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000006.12:152330821:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00519 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00233
The Genome Aggregation Database (gnomAD), exomes 0.00139
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00269
Trans-Omics for Precision Medicine (TOPMed) 0.00300
1000 Genomes Project 0.00519
Exome Aggregation Consortium (ExAC) 0.00171
Links
ClinGen: CA4056110
dbSNP: rs112266645
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 Jul 2, 2020 RCV000281347.3
Likely benign 2 criteria provided, multiple submitters, no conflicts Jan 6, 2021 RCV001092458.3
Likely benign 1 criteria provided, single submitter Jan 12, 2018 RCV000317886.2
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000388662.2
Benign 1 criteria provided, single submitter Oct 12, 2020 RCV000532177.5
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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
3453 3592

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Sep 15, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000335327.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
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: SCV000461190.3
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
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Spinocerebellar ataxia, autosomal recessive 8
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000461189.3
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
(Jul 02, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV001476186.1
Submitted: (Dec 30, 2020)
Evidence details
Benign
(Oct 12, 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: SCV000649036.5
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 06, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000714502.2
Submitted: (Sep 30, 2021)
Evidence details
Likely benign
(Dec 01, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001248978.6
Submitted: (Jul 04, 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 rs112266645...

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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 Oct 24, 2021