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NM_001164508.2(NEB):c.12018+1G>A

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Sep 24, 2021)
Last evaluated:
Dec 24, 2019
Accession:
VCV000265494.6
Variation ID:
265494
Description:
single nucleotide variant
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NM_001164508.2(NEB):c.12018+1G>A

Allele ID
259697
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q23.3
Genomic location
2: 151610515 (GRCh38) GRCh38 UCSC
2: 152467029 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_202:g.128973G>A
LRG_202t1:c.12018+1G>A
NC_000002.12:g.151610515C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:151610514:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
ClinGen: CA1908612
dbSNP: rs762278237
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Dec 24, 2019 RCV000254952.3
Pathogenic/Likely pathogenic 4 criteria provided, multiple submitters, no conflicts Dec 3, 2018 RCV000593350.6
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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
3747 4669

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Dec 24, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000322455.7
Submitted: (Sep 24, 2021)
Evidence details
Comment:
Canonical splice site variant predicted to result in an in-frame deletion of a critical region; Not observed at a significant frequency in large population cohorts … (more)
Pathogenic
(Nov 15, 2017)
criteria provided, single submitter
Method: clinical testing
Nemaline myopathy 2
Allele origin: germline
Invitae
Accession: SCV000832679.1
Submitted: (Aug 29, 2018)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change affects a donor splice site in intron 80 of the NEB gene. It is expected to disrupt RNA splicing and likely results … (more)
Pathogenic
(Dec 21, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000704802.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely pathogenic
(Dec 03, 2018)
criteria provided, single submitter
Method: research
Nemaline myopathy 2
(Autosomal recessive inheritance)
Allele origin: germline
Broad Institute Rare Disease Group, Broad Institute
Accession: SCV001164420.1
Submitted: (Oct 03, 2019)
Evidence details
Publications
PubMed (1)
Comment:
The heterozygous c.12018+1G>A variant in NEB was identified by our study in the compound heterozygous state, with a pathogenic variant, in one individual with nemaline … (more)
Pathogenic
(Dec 28, 2016)
no assertion criteria provided
Method: clinical testing
Nemaline myopathy 2
Allele origin: unknown
Counsyl
Accession: SCV001132440.1
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (1)
Pathogenic
(-)
no assertion criteria provided
Method: clinical testing
Nemaline myopathy 2
Allele origin: germline
Genomics England Pilot Project,Genomics England
Accession: SCV001760060.1
Submitted: (Jul 15, 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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Mutation update: the spectra of nebulin variants and associated myopathies. Lehtokari VL Human mutation 2014 PMID: 25205138
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=NEB - - - -

Text-mined citations for rs762278237...

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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