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NM_001164508.2(NEB):c.4206T>A (p.Asn1402Lys)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 23, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000257814.6
Variation ID:
257814
Description:
single nucleotide variant
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NM_001164508.2(NEB):c.4206T>A (p.Asn1402Lys)

Allele ID
250283
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q23.3
Genomic location
2: 151672462 (GRCh38) GRCh38 UCSC
2: 152528976 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_202:g.67026T>A
LRG_202t1:c.4206T>A
NC_000002.11:g.152528976A>T
... more HGVS
Protein change
N1402K
Other names
-
Canonical SPDI
NC_000002.12:151672461:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00046
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00127
The Genome Aggregation Database (gnomAD), exomes 0.00037
1000 Genomes Project 0.00100
The Genome Aggregation Database (gnomAD) 0.00147
Trans-Omics for Precision Medicine (TOPMed) 0.00193
Links
ClinGen: CA1910700
dbSNP: rs201169452
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 Dec 28, 2015 RCV000247985.5
Likely benign 1 criteria provided, single submitter Dec 4, 2020 RCV001084411.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jan 15, 2019 RCV000514092.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NEB - - GRCh38
GRCh37
3723 4645

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: SCV000307352.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Dec 28, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000331866.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(May 08, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000610437.1
Submitted: (Oct 05, 2017)
Evidence details
Likely benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Nemaline myopathy 2
Allele origin: germline
Invitae
Accession: SCV000640794.5
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 15, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000724987.2
Submitted: (Sep 23, 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=NEB - - - -

Text-mined citations for rs201169452...

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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 30, 2021