ClinVar Genomic variation as it relates to human health
NM_198252.3(GSN):c.123C>T (p.Gly41=)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_198252.3(GSN):c.123C>T (p.Gly41=)
Variation ID: 364797 Accession: VCV000364797.9
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 9q33.2 9: 121302094 (GRCh38) [ NCBI UCSC ] 9: 124064372 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Dec 6, 2016 Mar 16, 2024 Jun 5, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_198252.3:c.123C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_937895.1:p.Gly41= synonymous NM_000177.5:c.276C>T NP_000168.1:p.Gly92= synonymous NM_001127662.2:c.123C>T NP_001121134.1:p.Gly41= synonymous NM_001127663.2:c.231C>T NP_001121135.2:p.Gly77= synonymous NM_001127664.2:c.123C>T NP_001121136.1:p.Gly41= synonymous NM_001127665.2:c.123C>T NP_001121137.1:p.Gly41= synonymous NM_001127666.2:c.156C>T NP_001121138.1:p.Gly52= synonymous NM_001127667.2:c.156C>T NP_001121139.1:p.Gly52= synonymous NM_001258029.2:c.174C>T NP_001244958.1:p.Gly58= synonymous NM_001258030.2:c.147C>T NP_001244959.1:p.Gly49= synonymous NM_001353053.1:c.123C>T NP_001339982.1:p.Gly41= synonymous NM_001353054.1:c.123C>T NP_001339983.1:p.Gly41= synonymous NM_001353055.2:c.123C>T NP_001339984.1:p.Gly41= synonymous NM_001353056.2:c.123C>T NP_001339985.1:p.Gly41= synonymous NM_001353057.2:c.123C>T NP_001339986.1:p.Gly41= synonymous NM_001353058.2:c.123C>T NP_001339987.1:p.Gly41= synonymous NM_001353059.2:c.123C>T NP_001339988.1:p.Gly41= synonymous NM_001353060.2:c.123C>T NP_001339989.1:p.Gly41= synonymous NM_001353061.2:c.123C>T NP_001339990.1:p.Gly41= synonymous NM_001353062.1:c.123C>T NP_001339991.1:p.Gly41= synonymous NM_001353063.2:c.156C>T NP_001339992.1:p.Gly52= synonymous NM_001353064.2:c.156C>T NP_001339993.1:p.Gly52= synonymous NM_001353065.2:c.156C>T NP_001339994.1:p.Gly52= synonymous NM_001353066.2:c.156C>T NP_001339995.1:p.Gly52= synonymous NM_001353067.2:c.156C>T NP_001339996.1:p.Gly52= synonymous NM_001353068.2:c.156C>T NP_001339997.1:p.Gly52= synonymous NM_001353069.2:c.156C>T NP_001339998.1:p.Gly52= synonymous NM_001353070.2:c.156C>T NP_001339999.1:p.Gly52= synonymous NM_001353071.2:c.156C>T NP_001340000.1:p.Gly52= synonymous NM_001353072.2:c.156C>T NP_001340001.1:p.Gly52= synonymous NM_001353073.2:c.156C>T NP_001340002.1:p.Gly52= synonymous NM_001353074.2:c.156C>T NP_001340003.1:p.Gly52= synonymous NM_001353075.1:c.156C>T NP_001340004.1:p.Gly52= synonymous NM_001353076.2:c.195C>T NP_001340005.1:p.Gly65= synonymous NM_001353077.1:c.156C>T NP_001340006.1:p.Gly52= synonymous NM_001353078.2:c.-458-817C>T intron variant NC_000009.12:g.121302094C>T NC_000009.11:g.124064372C>T NG_012872.2:g.106013C>T - Protein change
- Other names
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- Canonical SPDI
- NC_000009.12:121302093:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
Trans-Omics for Precision Medicine (TOPMed) 0.00000
The Genome Aggregation Database (gnomAD) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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GSN | - | - |
GRCh38 GRCh37 |
709 | 744 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Likely benign (1) |
criteria provided, single submitter
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Jan 13, 2018 | RCV000275412.5 | |
Likely benign (1) |
criteria provided, single submitter
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Jul 11, 2019 | RCV002436223.1 | |
Likely benign (1) |
criteria provided, single submitter
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Jun 5, 2023 | RCV002523730.2 | |
Likely benign (1) |
criteria provided, single submitter
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Apr 29, 2022 | RCV003972537.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Likely benign
(Jan 13, 2018)
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criteria provided, single submitter
Method: clinical testing
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Meretoja syndrome
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000476980.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
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)
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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. (less)
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Likely benign
(Jul 11, 2019)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002746162.1
First in ClinVar: Nov 29, 2022 Last updated: Nov 29, 2022 |
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
Number of individuals with the variant: 1
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Likely benign
(Jun 05, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV003511873.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
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Likely benign
(Apr 29, 2022)
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criteria provided, single submitter
Method: clinical testing
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GSN-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004798186.1
First in ClinVar: Mar 16, 2024 Last updated: Mar 16, 2024 |
Comment:
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
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Germline Functional Evidence
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 germline classification of this variant
HelpThere are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for rs774617795 ...
HelpRecord last updated Mar 17, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.