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NM_182961.4(SYNE1):c.10786G>A (p.Val3596Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 15, 2020
Accession:
VCV000289756.6
Variation ID:
289756
Description:
single nucleotide variant
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NM_182961.4(SYNE1):c.10786G>A (p.Val3596Met)

Allele ID
273993
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6q25.2
Genomic location
6: 152354799 (GRCh38) GRCh38 UCSC
6: 152675934 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.11:g.152675934C>T
NC_000006.12:g.152354799C>T
NG_012855.2:g.287601G>A
... more HGVS
Protein change
V3596M, V3603M
Other names
-
Canonical SPDI
NC_000006.12:152354798:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00019
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00025
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00069
Links
ClinGen: CA4056875
dbSNP: rs143034104
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 3 criteria provided, multiple submitters, no conflicts Jan 7, 2020 RCV000261699.3
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000266205.2
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000321203.2
Likely benign 1 criteria provided, single submitter Sep 15, 2020 RCV000647618.4
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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
Likely benign
(Jun 20, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000344166.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
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: SCV000461291.3
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)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Spinocerebellar ataxia, autosomal recessive 8
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000461292.3
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
(Jun 27, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000714130.1
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
(Jan 07, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV001475586.1
Submitted: (Dec 30, 2020)
Evidence details
Likely benign
(Sep 15, 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: SCV000769416.4
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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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SYNE1 - - - -

Text-mined citations for rs143034104...

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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 Dec 04, 2021