This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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.
ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.7383A>G (p.Ser2461=)
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.
(3)
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.
Benign/Likely benign
3
criteria provided, multiple submitters, no conflicts
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.7383A>G (p.Ser2461=)
Variation ID: 1758622 Accession: VCV001758622.6
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 5q22.2 5: 112842977 (GRCh38) [ NCBI UCSC ] 5: 112178674 (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 29, 2022 Jul 23, 2024 Apr 9, 2024 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000038.6:c.7383A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Ser2461= synonymous NM_001127510.3:c.7383A>G NP_001120982.1:p.Ser2461= synonymous NM_001127511.3:c.7329A>G NP_001120983.2:p.Ser2443= synonymous NM_001354895.2:c.7383A>G NP_001341824.1:p.Ser2461= synonymous NM_001354896.2:c.7437A>G NP_001341825.1:p.Ser2479= synonymous NM_001354897.2:c.7413A>G NP_001341826.1:p.Ser2471= synonymous NM_001354898.2:c.7308A>G NP_001341827.1:p.Ser2436= synonymous NM_001354899.2:c.7299A>G NP_001341828.1:p.Ser2433= synonymous NM_001354900.2:c.7260A>G NP_001341829.1:p.Ser2420= synonymous NM_001354901.2:c.7206A>G NP_001341830.1:p.Ser2402= synonymous NM_001354902.2:c.7110A>G NP_001341831.1:p.Ser2370= synonymous NM_001354903.2:c.7080A>G NP_001341832.1:p.Ser2360= synonymous NM_001354904.2:c.7005A>G NP_001341833.1:p.Ser2335= synonymous NM_001354905.2:c.6903A>G NP_001341834.1:p.Ser2301= synonymous NM_001354906.2:c.6534A>G NP_001341835.1:p.Ser2178= synonymous NM_001407446.1:c.7467A>G NP_001394375.1:p.Ser2489= synonymous NM_001407447.1:c.7437A>G NP_001394376.1:p.Ser2479= synonymous NM_001407448.1:c.7437A>G NP_001394377.1:p.Ser2479= synonymous NM_001407449.1:c.7437A>G NP_001394378.1:p.Ser2479= synonymous NM_001407450.1:c.7383A>G NP_001394379.1:p.Ser2461= synonymous NM_001407451.1:c.7362A>G NP_001394380.1:p.Ser2454= synonymous NM_001407452.1:c.7353A>G NP_001394381.1:p.Ser2451= synonymous NM_001407453.1:c.7206A>G NP_001394382.1:p.Ser2402= synonymous NM_001407454.1:c.7134A>G NP_001394383.1:p.Ser2378= synonymous NM_001407455.1:c.7134A>G NP_001394384.1:p.Ser2378= synonymous NM_001407456.1:c.7134A>G NP_001394385.1:p.Ser2378= synonymous NM_001407457.1:c.7134A>G NP_001394386.1:p.Ser2378= synonymous NM_001407458.1:c.7080A>G NP_001394387.1:p.Ser2360= synonymous NM_001407459.1:c.7080A>G NP_001394388.1:p.Ser2360= synonymous NM_001407460.1:c.7080A>G NP_001394389.1:p.Ser2360= synonymous NM_001407467.1:c.6996A>G NP_001394396.1:p.Ser2332= synonymous NM_001407469.1:c.6996A>G NP_001394398.1:p.Ser2332= synonymous NM_001407470.1:c.6534A>G NP_001394399.1:p.Ser2178= synonymous NM_001407471.1:c.6231A>G NP_001394400.1:p.Ser2077= synonymous NM_001407472.1:c.6231A>G NP_001394401.1:p.Ser2077= synonymous NR_176365.1:n.7218A>G non-coding transcript variant NR_176366.1:n.7637A>G non-coding transcript variant NC_000005.10:g.112842977A>G NC_000005.9:g.112178674A>G NG_008481.4:g.155457A>G LRG_130:g.155457A>G LRG_130t1:c.7383A>G LRG_130p1:p.Ser2461= LRG_130t2:c.7383A>G LRG_130p2:p.Ser2461= LRG_130t3:c.7383A>G LRG_130p3:p.Ser2461= - Protein change
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- Other names
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- Canonical SPDI
- NC_000005.10:112842976:A:G
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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 |
14969 | 15107 | |
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. |
|---|---|---|---|---|
| Likely benign (1) |
criteria provided, single submitter
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Mar 8, 2022 | RCV002380418.2 | |
| Benign/Likely benign (2) |
criteria provided, multiple submitters, no conflicts
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Apr 9, 2024 | RCV004572351.3 |
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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|---|---|---|---|---|---|
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Likely benign
(May 04, 2022)
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criteria provided, single submitter
Method: clinical testing
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Familial adenomatous polyposis 1
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV003476399.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
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Likely benign
(Mar 08, 2022)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002675053.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more)
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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)
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Benign
(Apr 09, 2024)
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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: SCV005083279.1
First in ClinVar: Jul 23, 2024 Last updated: Jul 23, 2024 |
Comment:
This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing.
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Comment:
Comment:
This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing.
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 alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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.
Comment:
This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing.
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 10, 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.