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NM_001164508.2(NEB):c.2944-9G>A

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Jul 25, 2021)
Last evaluated:
Jul 10, 2021
Accession:
VCV000129738.8
Variation ID:
129738
Description:
single nucleotide variant
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NM_001164508.2(NEB):c.2944-9G>A

Allele ID
135184
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q23.3
Genomic location
2: 151680837 (GRCh38) GRCh38 UCSC
2: 152537351 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.152537351C>T
NM_004543.5:c.2944-9G>A
LRG_202:g.58651G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:151680836:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.09505 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.07423
The Genome Aggregation Database (gnomAD) 0.10205
The Genome Aggregation Database (gnomAD), exomes 0.07063
Trans-Omics for Precision Medicine (TOPMed) 0.10353
Trans-Omics for Precision Medicine (TOPMed) 0.10489
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.10851
The Genome Aggregation Database (gnomAD) 0.09409
1000 Genomes Project 0.09505
Links
ClinGen: CA153980
dbSNP: rs13427102
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 4 criteria provided, multiple submitters, no conflicts Jan 5, 2016 RCV000117753.7
Benign 4 criteria provided, multiple submitters, no conflicts Jul 10, 2021 RCV000362012.5
Benign 1 criteria provided, single submitter Feb 27, 2017 RCV000586159.1
Benign 1 criteria provided, single submitter Jul 10, 2021 RCV001543001.1
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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
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000307338.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Nemaline myopathy 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000417025.3
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
(Feb 27, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000697827.1
Submitted: (Jan 25, 2018)
Evidence details
Comment:
Variant summary: The NEB c.2944-9G>A variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant. … (more)
Benign
(Jan 05, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000519851.4
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 13, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000711691.2
Submitted: (Mar 21, 2019)
Evidence details
Comment:
c.2944-9G>A in intron 29 of NEB: This variant is not expected to have clinical s ignificance because it has been identified in 16.9% (626/3704) of … (more)
Benign
(Nov 25, 2020)
criteria provided, single submitter
Method: clinical testing
Nemaline myopathy 2
Allele origin: germline
Invitae
Accession: SCV001722775.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 10, 2021)
criteria provided, single submitter
Method: clinical testing
Arthrogryposis multiplex congenita 6
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001761445.1
Submitted: (Jul 25, 2021)
Evidence details
Benign
(Jul 10, 2021)
criteria provided, single submitter
Method: clinical testing
Nemaline myopathy 2
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001761590.1
Submitted: (Jul 25, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000152008.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Nemaline myopathy type 2
Allele origin: germline
Natera, Inc.
Accession: SCV001455514.1
Submitted: (Dec 28, 2020)
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 rs13427102...

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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