This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.6474del (p.Phe2159fs)
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.
(2)
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.
Pathogenic
2
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_000038.6(APC):c.6474del (p.Phe2159fs)
Variation ID: 2574116 Accession: VCV002574116.4
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 5q22.2 5: 112842066 (GRCh38) [ NCBI UCSC ] 5: 112177763 (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 Feb 4, 2024 May 15, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000038.6:c.6474del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Phe2159fs frameshift NM_001127510.3:c.6474del NP_001120982.1:p.Phe2159fs frameshift NM_001127511.3:c.6420del NP_001120983.2:p.Phe2141fs frameshift NM_001354895.2:c.6474del NP_001341824.1:p.Phe2159fs frameshift NM_001354896.2:c.6528del NP_001341825.1:p.Phe2177fs frameshift NM_001354897.2:c.6504del NP_001341826.1:p.Phe2169fs frameshift NM_001354898.2:c.6399del NP_001341827.1:p.Phe2134fs frameshift NM_001354899.2:c.6390del NP_001341828.1:p.Phe2131fs frameshift NM_001354900.2:c.6351del NP_001341829.1:p.Phe2118fs frameshift NM_001354901.2:c.6297del NP_001341830.1:p.Phe2100fs frameshift NM_001354902.2:c.6201del NP_001341831.1:p.Phe2068fs frameshift NM_001354903.2:c.6171del NP_001341832.1:p.Phe2058fs frameshift NM_001354904.2:c.6096del NP_001341833.1:p.Phe2033fs frameshift NM_001354905.2:c.5994del NP_001341834.1:p.Phe1999fs frameshift NM_001354906.2:c.5625del NP_001341835.1:p.Phe1876fs frameshift NM_001407446.1:c.6558del NP_001394375.1:p.Phe2187fs frameshift NM_001407447.1:c.6528del NP_001394376.1:p.Phe2177fs frameshift NM_001407448.1:c.6528del NP_001394377.1:p.Phe2177fs frameshift NM_001407449.1:c.6528del NP_001394378.1:p.Phe2177fs frameshift NM_001407450.1:c.6474del NP_001394379.1:p.Phe2159fs frameshift NM_001407451.1:c.6453del NP_001394380.1:p.Phe2152fs frameshift NM_001407452.1:c.6444del NP_001394381.1:p.Phe2149fs frameshift NM_001407453.1:c.6297del NP_001394382.1:p.Phe2100fs frameshift NM_001407454.1:c.6225del NP_001394383.1:p.Phe2076fs frameshift NM_001407455.1:c.6225del NP_001394384.1:p.Phe2076fs frameshift NM_001407456.1:c.6225del NP_001394385.1:p.Phe2076fs frameshift NM_001407457.1:c.6225del NP_001394386.1:p.Phe2076fs frameshift NM_001407458.1:c.6171del NP_001394387.1:p.Phe2058fs frameshift NM_001407459.1:c.6171del NP_001394388.1:p.Phe2058fs frameshift NM_001407460.1:c.6171del NP_001394389.1:p.Phe2058fs frameshift NM_001407467.1:c.6087del NP_001394396.1:p.Phe2030fs frameshift NM_001407469.1:c.6087del NP_001394398.1:p.Phe2030fs frameshift NM_001407470.1:c.5625del NP_001394399.1:p.Phe1876fs frameshift NM_001407471.1:c.5322del NP_001394400.1:p.Phe1775fs frameshift NM_001407472.1:c.5322del NP_001394401.1:p.Phe1775fs frameshift NR_176365.1:n.6309del non-coding transcript variant NR_176366.1:n.6728del non-coding transcript variant NC_000005.10:g.112842068del NC_000005.9:g.112177765del NG_008481.4:g.154548del LRG_130:g.154548del LRG_130t1:c.6474del LRG_130p1:p.Phe2159Leufs LRG_130t2:c.6474del LRG_130p2:p.Phe2159Leufs LRG_130t3:c.6474del LRG_130p3:p.Phe2159Leufs - Protein change
- F1775fs, F1876fs, F1999fs, F2030fs, F2033fs, F2058fs, F2068fs, F2076fs, F2100fs, F2118fs, F2131fs, F2134fs, F2141fs, F2149fs, F2152fs, F2159fs, F2169fs, F2177fs, F2187fs
- Other names
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- Canonical SPDI
- NC_000005.10:112842065:CCC:CC
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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
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 |
14981 | 15119 | |
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 (2) |
criteria provided, single submitter
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May 15, 2023 | RCV003485929.2 |
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 15, 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: SCV004042983.2
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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Likely pathogenic
(Jul 21, 2023)
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no assertion criteria provided
Method: research
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Familial adenomatous polyposis 1
Affected status: yes
Allele origin:
germline
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deCODE genetics, Amgen
Accession: SCV004022246.1
First in ClinVar: Feb 04, 2024 Last updated: Feb 04, 2024 |
Comment:
The variant NM_000038.6:c.6474del (chr5:112842065) in APC was detected in 2 heterozygotes out of 58K WGS Icelanders (MAF= 0,002%). This variant has not been reported in … (more)
The variant NM_000038.6:c.6474del (chr5:112842065) in APC was detected in 2 heterozygotes out of 58K WGS Icelanders (MAF= 0,002%). This variant has not been reported in ClinVar previously. Based on ACMG criteria (PVS1, PM2) this variant classifies as likely pathogenic. (less)
Number of individuals with the variant: 6
Ethnicity/Population group: Icelandic
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Comment:
Comment:
The variant NM_000038.6:c.6474del (chr5:112842065) in APC was detected in 2 heterozygotes out of 58K WGS Icelanders (MAF= 0,002%). This variant has not been reported in ClinVar previously. Based on ACMG criteria (PVS1, PM2) this variant classifies as likely pathogenic.
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:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
Comment:
The variant NM_000038.6:c.6474del (chr5:112842065) in APC was detected in 2 heterozygotes out of 58K WGS Icelanders (MAF= 0,002%). This variant has not been reported in ClinVar previously. Based on ACMG criteria (PVS1, PM2) this variant classifies as likely pathogenic.
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 Nov 25, 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.