SEC31A: BP4, BS2
ClinVar Genomic variation as it relates to human health
NM_001077207.4(SEC31A):c.2868C>T (p.Gly956=)
Germline
Classification
Help
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.
(1)
Help
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.
Likely benign
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001077207.4(SEC31A):c.2868C>T (p.Gly956=)
Variation ID: 2654848 Accession: VCV002654848.10
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 4q21.22 4: 82842240 (GRCh38) [ NCBI UCSC ] 4: 83763393 (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 Nov 20, 2023 Oct 20, 2024 Nov 1, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001077207.4:c.2868C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001070675.1:p.Gly956= synonymous NM_001077206.4:c.2626+2146C>T intron variant NM_001077208.4:c.2868C>T NP_001070676.1:p.Gly956= synonymous NM_001191049.2:c.2853C>T NP_001177978.1:p.Gly951= synonymous NM_001300744.3:c.2509+2146C>T intron variant NM_001300745.3:c.2751C>T NP_001287674.1:p.Gly917= synonymous NM_001318119.2:c.2868C>T NP_001305048.1:p.Gly956= synonymous NM_001318120.2:c.2868C>T NP_001305049.1:p.Gly956= synonymous NM_001400154.1:c.2961C>T NP_001387083.1:p.Gly987= synonymous NM_001400155.1:c.2961C>T NP_001387084.1:p.Gly987= synonymous NM_001400156.1:c.2961C>T NP_001387085.1:p.Gly987= synonymous NM_001400157.1:c.2868C>T NP_001387086.1:p.Gly956= synonymous NM_001400158.1:c.2868C>T NP_001387087.1:p.Gly956= synonymous NM_001400159.1:c.2868C>T NP_001387088.1:p.Gly956= synonymous NM_001400160.1:c.2883C>T NP_001387089.1:p.Gly961= synonymous NM_001400161.1:c.2844C>T NP_001387090.1:p.Gly948= synonymous NM_001400162.1:c.2922C>T NP_001387091.1:p.Gly974= synonymous NM_001400164.1:c.2868C>T NP_001387093.1:p.Gly956= synonymous NM_001400165.1:c.2829C>T NP_001387094.1:p.Gly943= synonymous NM_001400166.1:c.2868C>T NP_001387095.1:p.Gly956= synonymous NM_001400167.1:c.2844C>T NP_001387096.1:p.Gly948= synonymous NM_001400168.1:c.2844C>T NP_001387097.1:p.Gly948= synonymous NM_001400180.1:c.2790C>T NP_001387109.1:p.Gly930= synonymous NM_001400184.1:c.2829C>T NP_001387113.1:p.Gly943= synonymous NM_001400186.1:c.2829C>T NP_001387115.1:p.Gly943= synonymous NM_001400188.1:c.2790C>T NP_001387117.1:p.Gly930= synonymous NM_001400190.1:c.2868C>T NP_001387119.1:p.Gly956= synonymous NM_001400191.1:c.2868C>T NP_001387120.1:p.Gly956= synonymous NM_001400193.1:c.2868C>T NP_001387122.1:p.Gly956= synonymous NM_001400194.1:c.2868C>T NP_001387123.1:p.Gly956= synonymous NM_001400197.1:c.2790C>T NP_001387126.1:p.Gly930= synonymous NM_001400198.1:c.2751C>T NP_001387127.1:p.Gly917= synonymous NM_001400200.1:c.2790C>T NP_001387129.1:p.Gly930= synonymous NM_001400202.1:c.2751C>T NP_001387131.1:p.Gly917= synonymous NM_001400203.1:c.2790C>T NP_001387132.1:p.Gly930= synonymous NM_001400204.1:c.2829C>T NP_001387133.1:p.Gly943= synonymous NM_001400205.1:c.2829C>T NP_001387134.1:p.Gly943= synonymous NM_001400206.1:c.2829C>T NP_001387135.1:p.Gly943= synonymous NM_001400207.1:c.2751C>T NP_001387136.1:p.Gly917= synonymous NM_001400208.1:c.2868C>T NP_001387137.1:p.Gly956= synonymous NM_001400209.1:c.2751C>T NP_001387138.1:p.Gly917= synonymous NM_001400210.1:c.2790C>T NP_001387139.1:p.Gly930= synonymous NM_001400211.1:c.2790C>T NP_001387140.1:p.Gly930= synonymous NM_001400212.1:c.2853C>T NP_001387141.1:p.Gly951= synonymous NM_001400213.1:c.2751C>T NP_001387142.1:p.Gly917= synonymous NM_001400214.1:c.2853C>T NP_001387143.1:p.Gly951= synonymous NM_001400215.1:c.2589C>T NP_001387144.1:p.Gly863= synonymous NM_001400216.1:c.2829C>T NP_001387145.1:p.Gly943= synonymous NM_001400217.1:c.2626+2146C>T intron variant NM_001400218.1:c.2602+2146C>T intron variant NM_001400219.1:c.2626+2146C>T intron variant NM_001400220.1:c.2626+2146C>T intron variant NM_001400221.1:c.2548+2146C>T intron variant NM_001400222.1:c.2548+2146C>T intron variant NM_001400223.1:c.2509+2146C>T intron variant NM_001400224.1:c.2394C>T NP_001387153.1:p.Gly798= synonymous NM_016211.5:c.2751C>T NP_057295.2:p.Gly917= synonymous NC_000004.12:g.82842240G>A NC_000004.11:g.83763393G>A NG_029569.3:g.63332C>T - Protein change
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- Other names
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- Canonical SPDI
- NC_000004.12:82842239:G:A
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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.
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- Links
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 | ||
|---|---|---|---|---|---|---|
| HI score
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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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| SEC31A | - | - |
GRCh38 GRCh37 |
92 | 131 | |
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
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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. |
|---|---|---|---|---|
| Likely benign (1) |
criteria provided, single submitter
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Nov 1, 2023 | RCV003439366.10 |
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
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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
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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
(Nov 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV004152833.10
First in ClinVar: Nov 20, 2023 Last updated: Oct 20, 2024 |
Comment:
SEC31A: BP4, BS2
Number of individuals with the variant: 2
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Comment:
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. |
Comment:
SEC31A: BP4, BS2
Citations for germline classification of this variant
Help| There 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 this variant ...
HelpRecord last updated Oct 20, 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.