ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.4568_4572del (p.Arg1523fs)
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.4568_4572del (p.Arg1523fs)
Variation ID: 2583903 Accession: VCV002583903.2
- Type and length
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Deletion, 5 bp
- Location
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Cytogenetic: 5q22.2 5: 112840161-112840165 (GRCh38) [ NCBI UCSC ] 5: 112175858-112175862 (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 11, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000038.6:c.4568_4572del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Arg1523fs frameshift NM_001127510.3:c.4568_4572del NP_001120982.1:p.Arg1523fs frameshift NM_001127511.3:c.4514_4518del NP_001120983.2:p.Arg1505fs frameshift NM_001354895.2:c.4568_4572del NP_001341824.1:p.Arg1523fs frameshift NM_001354896.2:c.4622_4626del NP_001341825.1:p.Arg1541fs frameshift NM_001354897.2:c.4598_4602del NP_001341826.1:p.Arg1533fs frameshift NM_001354898.2:c.4493_4497del NP_001341827.1:p.Arg1498fs frameshift NM_001354899.2:c.4484_4488del NP_001341828.1:p.Arg1495fs frameshift NM_001354900.2:c.4445_4449del NP_001341829.1:p.Arg1482fs frameshift NM_001354901.2:c.4391_4395del NP_001341830.1:p.Arg1464fs frameshift NM_001354902.2:c.4295_4299del NP_001341831.1:p.Arg1432fs frameshift NM_001354903.2:c.4265_4269del NP_001341832.1:p.Arg1422fs frameshift NM_001354904.2:c.4190_4194del NP_001341833.1:p.Arg1397fs frameshift NM_001354905.2:c.4088_4092del NP_001341834.1:p.Arg1363fs frameshift NM_001354906.2:c.3719_3723del NP_001341835.1:p.Arg1240fs frameshift NM_001407446.1:c.4652_4656del NP_001394375.1:p.Arg1551fs frameshift NM_001407447.1:c.4622_4626del NP_001394376.1:p.Arg1541fs frameshift NM_001407448.1:c.4622_4626del NP_001394377.1:p.Arg1541fs frameshift NM_001407449.1:c.4622_4626del NP_001394378.1:p.Arg1541fs frameshift NM_001407450.1:c.4568_4572del NP_001394379.1:p.Arg1523fs frameshift NM_001407451.1:c.4547_4551del NP_001394380.1:p.Arg1516fs frameshift NM_001407452.1:c.4538_4542del NP_001394381.1:p.Arg1513fs frameshift NM_001407453.1:c.4391_4395del NP_001394382.1:p.Arg1464fs frameshift NM_001407454.1:c.4319_4323del NP_001394383.1:p.Arg1440fs frameshift NM_001407455.1:c.4319_4323del NP_001394384.1:p.Arg1440fs frameshift NM_001407456.1:c.4319_4323del NP_001394385.1:p.Arg1440fs frameshift NM_001407457.1:c.4319_4323del NP_001394386.1:p.Arg1440fs frameshift NM_001407458.1:c.4265_4269del NP_001394387.1:p.Arg1422fs frameshift NM_001407459.1:c.4265_4269del NP_001394388.1:p.Arg1422fs frameshift NM_001407460.1:c.4265_4269del NP_001394389.1:p.Arg1422fs frameshift NM_001407467.1:c.4181_4185del NP_001394396.1:p.Arg1394fs frameshift NM_001407469.1:c.4181_4185del NP_001394398.1:p.Arg1394fs frameshift NM_001407470.1:c.3719_3723del NP_001394399.1:p.Arg1240fs frameshift NM_001407471.1:c.3416_3420del NP_001394400.1:p.Arg1139fs frameshift NM_001407472.1:c.3416_3420del NP_001394401.1:p.Arg1139fs frameshift NR_176365.1:n.4403_4407del non-coding transcript variant NR_176366.1:n.4822_4826del non-coding transcript variant NC_000005.10:g.112840162_112840166del NC_000005.9:g.112175859_112175863del NG_008481.4:g.152642_152646del LRG_130:g.152642_152646del LRG_130t1:c.4568_4572del LRG_130p1:p.Arg1523Asnfs LRG_130t2:c.4568_4572del LRG_130p2:p.Arg1523Asnfs LRG_130t3:c.4568_4572del LRG_130p3:p.Arg1523Asnfs - Protein change
- R1139fs, R1240fs, R1363fs, R1394fs, R1397fs, R1422fs, R1432fs, R1440fs, R1464fs, R1482fs, R1495fs, R1498fs, R1505fs, R1513fs, R1516fs, R1523fs, R1533fs, R1541fs, R1551fs
- Other names
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- Canonical SPDI
- NC_000005.10:112840160:AGAATA: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
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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
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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
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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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 11, 2023 | RCV004566228.1 |
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
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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 11, 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: SCV004044762.2
First in ClinVar: Oct 21, 2023 Last updated: Oct 28, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a frameshift 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 13, 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.