VCV002442316.1 - ClinVar

Single allele

Germline

Top reviewed classifications are shown here.

Submission summary:

1 submission

1 submitter

1 condition

Reviewed by expert panel

Likely pathogenic

Feb 2023 by ClinGen InSiGH… FDA Recognized Database

for Familial adenomatous polyposis 1

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

Single allele

Variation ID: 2442316 Accession: VCV002442316.1

Type and length

Deletion, -

Location

Timeline in ClinVar

	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	Mar 11, 2023	Mar 11, 2023	Feb 26, 2023

HGVS

Protein change

Other names

NC_000005.10:g.(?_112775619)_(112801393_?)del

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

Genes

No affected genes found.

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.
Familial adenomatous polyposis 1	Likely pathogenic (1)	reviewed by expert panel	Feb 26, 2023	RCV003149089.1

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 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.
Likely pathogenic (Feb 26, 2023)	reviewed by expert panel (ClinGen InSiGHT HCCP VCEP ACMG Specifications APC V1) Method: curation	Familial adenomatous polyposis 1 (Autosomal dominant inheritance) Affected status: unknown Allele origin: germline	ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel FDA Recognized Database Accession: SCV003836618.1 First in ClinVar: Mar 11, 2023 Last updated: Mar 11, 2023	Other databases https://erepo.clinicalgenome.org… https://erepo.clinicalgenome.org/evrepo/ui/interpretation/5bee178f-c9b5-4102-8807-f297a0daa4ec Comment: The NC_000005.10:g.(?_112775619)_(112801393_?)del variant in APC is a deletion predicted to result in an out-of-frame deletion of exons 5-8 in a gene in which loss-of-function is … (more) The NC_000005.10:g.(?_112775619)_(112801393_?)del variant in APC is a deletion predicted to result in an out-of-frame deletion of exons 5-8 in a gene in which loss-of-function is an established disease (PVS1). This variant is absent from gnomAD SVs v2.1 (PM2_Supporting). In summary, this variant meets the criteria to be classified as of Likely Pathogenic for FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel: PVS1, PM2_Supporting (VCEP specifications version 1; date of approval: 12/12/2022). (less)

Comment:

The NC_000005.10:g.(?_112775619)_(112801393_?)del variant in APC is a deletion predicted to result in an out-of-frame deletion of exons 5-8 in a gene in which loss-of-function is an established disease (PVS1). This variant is absent from gnomAD SVs v2.1 (PM2_Supporting). In summary, this variant meets the criteria to be classified as of Likely Pathogenic for FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel: PVS1, PM2_Supporting (VCEP specifications version 1; date of approval: 12/12/2022).

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:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/5bee178f-c9b5-4102-8807-f297a0daa4ec	-	-	-	-

Text-mined citations for this variant ...

Record last updated Mar 11, 2023

ClinVar Genomic variation as it relates to human health

Single allele

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...