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NM_013296.5(GPSM2):c.1370C>T (p.Thr457Met)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Feb 20, 2020)
Last evaluated:
Oct 12, 2018
Accession:
VCV000045564.3
Variation ID:
45564
Description:
single nucleotide variant
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NM_013296.5(GPSM2):c.1370C>T (p.Thr457Met)

Allele ID
54730
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p13.3
Genomic location
1: 108918719 (GRCh38) GRCh38 UCSC
1: 109461341 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.11:g.108918719C>T
NG_028108.2:g.48370C>T
NM_001321038.2:c.1370C>T NP_001307967.1:p.Thr457Met missense
... more HGVS
Protein change
T457M
Other names
-
Canonical SPDI
NC_000001.11:108918718:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.04034 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.02092
The Genome Aggregation Database (gnomAD) 0.02745
1000 Genomes Project 0.04034
Exome Aggregation Consortium (ExAC) 0.02258
Trans-Omics for Precision Medicine (TOPMed) 0.03159
Trans-Omics for Precision Medicine (TOPMed) 0.03354
The Genome Aggregation Database (gnomAD) 0.03137
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.03175
Links
ClinGen: CA136662
dbSNP: rs35089879
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Mar 14, 2016 RCV000038780.4
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV000333660.2
Benign 1 criteria provided, single submitter Oct 12, 2018 RCV000992088.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GPSM2 - - GRCh38
GRCh37
155 202

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(May 07, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000062458.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Thr457Met in Exon 12 of GPSM2: This variant is not expected to have clinical sig nificance because it has been identified in 7.2% (270/3738) of … (more)
Benign
(Mar 14, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000519413.4
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
(Oct 12, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001144077.1
Submitted: (Sep 25, 2019)
Evidence details
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Chudley-McCullough syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000347061.3
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
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000311960.1
Submitted: (Apr 28, 2016)
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 rs35089879...

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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