NM_001127511.3(APC):c.-133dup AND Familial adenomatous polyposis 1

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Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 25, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003538738.1

Allele description

NM_001127511.3(APC):c.-133dup

Gene:

APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

5q22.2

Genomic location:

Preferred name:

NM_001127511.3(APC):c.-133dup

HGVS:

NC_000005.10:g.112707585dup
NG_008481.4:g.20065dup
NG_173817.1:g.208dup
NM_001127511.3:c.-133dup
NM_001354895.2:c.-316dup
NM_001354897.2:c.-133dup
NM_001354902.2:c.-133dup
NM_001407446.1:c.-133dup
NM_001407447.1:c.-316dup
NM_001407448.1:c.-83dup
NM_001407450.1:c.-83dup
NM_001407452.1:c.-316dup
NM_001407453.1:c.-107dup
NM_001407456.1:c.-316dup
NM_001407457.1:c.-83dup
NM_001407458.1:c.-83dup
NM_001407460.1:c.-316dup
NM_001407469.1:c.-316dup
NM_001407470.1:c.-1351dup
NM_001407472.1:c.-1351dup
LRG_130t3:c.-316dup
LRG_130:g.20065dup
NC_000005.9:g.112043281_112043282insC
NC_000005.9:g.112043282dup
NM_001127511.1:c.-316dup
NR_176365.1:n.88dup
NR_176366.1:n.88dup

Links:

dbSNP: rs1554060212

NCBI 1000 Genomes Browser:

rs1554060212

Molecular consequence:

NM_001127511.3:c.-133dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354895.2:c.-316dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354897.2:c.-133dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354902.2:c.-133dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407446.1:c.-133dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407447.1:c.-316dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407448.1:c.-83dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407450.1:c.-83dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407452.1:c.-316dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407453.1:c.-107dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407456.1:c.-316dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407457.1:c.-83dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407458.1:c.-83dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407460.1:c.-316dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407469.1:c.-316dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407470.1:c.-1351dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407472.1:c.-1351dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NR_176365.1:n.88dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176366.1:n.88dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Familial adenomatous polyposis 1 (FAP1)
Synonyms:: POLYPOSIS, ADENOMATOUS INTESTINAL; FAMILIAL ADENOMATOUS POLYPOSIS 1, ATTENUATED; APC-Associated Polyposis Conditions
Identifiers:: MONDO: MONDO:0021056; MedGen: C2713442; OMIM: 175100

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001557940	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 25, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001557940

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 25, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001557940.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant has not been reported in the literature in individuals affected with APC-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant occurs in a non-coding region of the APC gene. It does not change the encoded amino acid sequence of the APC protein. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 2, 2024

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