ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.5047_5051del (p.Gly1682_Glu1683insTer)
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_000038.6(APC):c.5047_5051del (p.Gly1682_Glu1683insTer)
Variation ID: 2584071 Accession: VCV002584071.2
- Type and length
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Deletion, 5 bp
- Location
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Cytogenetic: 5q22.2 5: 112840640-112840644 (GRCh38) [ NCBI UCSC ] 5: 112176337-112176341 (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 Oct 21, 2023 Oct 28, 2023 May 12, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000038.6:c.5047_5051del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Gly1682_Glu1683insTer nonsense NM_001127510.3:c.5047_5051del NP_001120982.1:p.Gly1682_Glu1683insTer nonsense NM_001127511.3:c.4993_4997del NP_001120983.2:p.Gly1664_Glu1665insTer nonsense NM_001354895.2:c.5047_5051del NP_001341824.1:p.Gly1682_Glu1683insTer nonsense NM_001354896.2:c.5101_5105del NP_001341825.1:p.Gly1700_Glu1701insTer nonsense NM_001354897.2:c.5077_5081del NP_001341826.1:p.Gly1692_Glu1693insTer nonsense NM_001354898.2:c.4972_4976del NP_001341827.1:p.Gly1657_Glu1658insTer nonsense NM_001354899.2:c.4963_4967del NP_001341828.1:p.Gly1654_Glu1655insTer nonsense NM_001354900.2:c.4924_4928del NP_001341829.1:p.Gly1641_Glu1642insTer nonsense NM_001354901.2:c.4870_4874del NP_001341830.1:p.Gly1623_Glu1624insTer nonsense NM_001354902.2:c.4774_4778del NP_001341831.1:p.Gly1591_Glu1592insTer nonsense NM_001354903.2:c.4744_4748del NP_001341832.1:p.Gly1581_Glu1582insTer nonsense NM_001354904.2:c.4669_4673del NP_001341833.1:p.Gly1556_Glu1557insTer nonsense NM_001354905.2:c.4567_4571del NP_001341834.1:p.Gly1522_Glu1523insTer nonsense NM_001354906.2:c.4198_4202del NP_001341835.1:p.Gly1399_Glu1400insTer nonsense NM_001407446.1:c.5131_5135del NP_001394375.1:p.Gly1710_Glu1711insTer nonsense NM_001407447.1:c.5101_5105del NP_001394376.1:p.Gly1700_Glu1701insTer nonsense NM_001407448.1:c.5101_5105del NP_001394377.1:p.Gly1700_Glu1701insTer nonsense NM_001407449.1:c.5101_5105del NP_001394378.1:p.Gly1700_Glu1701insTer nonsense NM_001407450.1:c.5047_5051del NP_001394379.1:p.Gly1682_Glu1683insTer nonsense NM_001407451.1:c.5026_5030del NP_001394380.1:p.Gly1675_Glu1676insTer nonsense NM_001407452.1:c.5017_5021del NP_001394381.1:p.Gly1672_Glu1673insTer nonsense NM_001407453.1:c.4870_4874del NP_001394382.1:p.Gly1623_Glu1624insTer nonsense NM_001407454.1:c.4798_4802del NP_001394383.1:p.Gly1599_Glu1600insTer nonsense NM_001407455.1:c.4798_4802del NP_001394384.1:p.Gly1599_Glu1600insTer nonsense NM_001407456.1:c.4798_4802del NP_001394385.1:p.Gly1599_Glu1600insTer nonsense NM_001407457.1:c.4798_4802del NP_001394386.1:p.Gly1599_Glu1600insTer nonsense NM_001407458.1:c.4744_4748del NP_001394387.1:p.Gly1581_Glu1582insTer nonsense NM_001407459.1:c.4744_4748del NP_001394388.1:p.Gly1581_Glu1582insTer nonsense NM_001407460.1:c.4744_4748del NP_001394389.1:p.Gly1581_Glu1582insTer nonsense NM_001407467.1:c.4660_4664del NP_001394396.1:p.Gly1553_Glu1554insTer nonsense NM_001407469.1:c.4660_4664del NP_001394398.1:p.Gly1553_Glu1554insTer nonsense NM_001407470.1:c.4198_4202del NP_001394399.1:p.Gly1399_Glu1400insTer nonsense NM_001407471.1:c.3895_3899del NP_001394400.1:p.Gly1298_Glu1299insTer nonsense NM_001407472.1:c.3895_3899del NP_001394401.1:p.Gly1298_Glu1299insTer nonsense NR_176365.1:n.4882_4886del non-coding transcript variant NR_176366.1:n.5301_5305del non-coding transcript variant NC_000005.10:g.112840641_112840645del NC_000005.9:g.112176338_112176342del NG_008481.4:g.153121_153125del LRG_130:g.153121_153125del LRG_130t1:c.5047_5051del LRG_130p1:p.Glu1683Terfs LRG_130t2:c.5047_5051del LRG_130p2:p.Glu1683Terfs LRG_130t3:c.5047_5051del LRG_130p3:p.Glu1683Terfs - Protein change
- Other names
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- Canonical SPDI
- NC_000005.10:112840639:TGAATT: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.
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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 | ||
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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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APC | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
14956 | 15094 |
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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Pathogenic (1) |
criteria provided, single submitter
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May 12, 2023 | RCV003334993.2 |
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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Pathogenic
(May 12, 2023)
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criteria provided, single submitter
Method: clinical testing
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Familial adenomatous polyposis 1
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV004045750.2
First in ClinVar: Oct 21, 2023 Last updated: Oct 28, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
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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 this variant ...
HelpRecord last updated Oct 28, 2023
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.