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NM_001164508.2(NEB):c.8734T>C (p.Ser2912Pro)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
11 (Most recent: Jul 25, 2021)
Last evaluated:
Jul 10, 2021
Accession:
VCV000129761.9
Variation ID:
129761
Description:
single nucleotide variant
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NM_001164508.2(NEB):c.8734T>C (p.Ser2912Pro)

Allele ID
135207
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q23.3
Genomic location
2: 151640012 (GRCh38) GRCh38 UCSC
2: 152496526 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P20929:p.Ser2912Pro
LRG_202:g.99476T>C
LRG_202t1:c.8734T>C
... more HGVS
Protein change
S2912P
Other names
-
Canonical SPDI
NC_000002.12:151640011:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.44529 (G)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.25401
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.30102
The Genome Aggregation Database (gnomAD), exomes 0.24306
The Genome Aggregation Database (gnomAD) 0.31097
Trans-Omics for Precision Medicine (TOPMed) 0.33693
1000 Genomes Project 0.44529
Links
ClinGen: CA154047
UniProtKB: P20929#VAR_047702
dbSNP: rs6713162
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 RCV000117776.7
Benign 4 criteria provided, multiple submitters, no conflicts Jul 10, 2021 RCV000383498.5
Benign 2 criteria provided, multiple submitters, no conflicts Mar 4, 2019 RCV000587395.2
Benign 1 criteria provided, single submitter Jul 10, 2021 RCV001543083.1
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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
3723 4645

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: SCV000307399.1
Submitted: (Apr 28, 2016)
Evidence details
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: SCV000697842.1
Submitted: (Jan 25, 2018)
Evidence details
Comment:
Variant summary: The NEB c.8734T>C (p.Ser2912Pro) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict 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: SCV000518387.4
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
(Nov 26, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000269441.3
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Ser2912Pro in exon 62 of NEB: This variant is not expected to have clinical si gnificance because it has been identified in 60% (2256/3774) of … (more)
Benign
(Mar 04, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001144731.1
Submitted: (Sep 25, 2019)
Evidence details
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Nemaline myopathy 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000416951.3
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
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
Nemaline myopathy 2
Allele origin: germline
Invitae
Accession: SCV001716707.1
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: SCV001761585.1
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: SCV001761586.1
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: SCV000152036.2
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: SCV001463524.1
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 rs6713162...

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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 05, 2021