NM_001127511.3(APC):c.-109_-108delinsTG AND Familial adenomatous polyposis 1

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Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 22, 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:: RCV003744794.1

Allele description

NM_001127511.3(APC):c.-109_-108delinsTG

Gene:

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

Variant type:

Indel

Cytogenetic location:

5q22.2

Genomic location:

Preferred name:

NM_001127511.3(APC):c.-109_-108delinsTG

HGVS:

NC_000005.10:g.112707609_112707610delinsTG
NG_008481.4:g.20089_20090delinsTG
NG_173817.1:g.232_233delinsTG
NM_001127511.3:c.-109_-108delinsTG
NM_001354895.2:c.-292_-291delinsTG
NM_001354897.2:c.-109_-108delinsTG
NM_001354902.2:c.-109_-108delinsTG
NM_001407446.1:c.-109_-108delinsTG
NM_001407447.1:c.-292_-291delinsTG
NM_001407448.1:c.-59_-58delinsTG
NM_001407450.1:c.-59_-58delinsTG
NM_001407452.1:c.-292_-291delinsTG
NM_001407453.1:c.-83_-82delinsTG
NM_001407456.1:c.-292_-291delinsTG
NM_001407457.1:c.-59_-58delinsTG
NM_001407458.1:c.-59_-58delinsTG
NM_001407460.1:c.-292_-291delinsTG
NM_001407469.1:c.-292_-291delinsTG
NM_001407470.1:c.-1327_-1326delinsTG
NM_001407472.1:c.-1327_-1326delinsTG
LRG_130t3:c.-292_-291delCCinsTG
LRG_130:g.20089_20090delinsTG
NC_000005.9:g.112043306_112043307delinsTG
NM_001127511.1:c.-292_-291delCCinsTG
NR_176365.1:n.112_113delinsTG
NR_176366.1:n.112_113delinsTG

Links:

dbSNP: rs1750588164

NCBI 1000 Genomes Browser:

rs1750588164

Molecular consequence:

NM_001127511.3:c.-109_-108delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354895.2:c.-292_-291delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354897.2:c.-109_-108delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354902.2:c.-109_-108delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407446.1:c.-109_-108delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407447.1:c.-292_-291delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407448.1:c.-59_-58delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407450.1:c.-59_-58delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407452.1:c.-292_-291delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407453.1:c.-83_-82delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407456.1:c.-292_-291delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407457.1:c.-59_-58delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407458.1:c.-59_-58delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407460.1:c.-292_-291delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407469.1:c.-292_-291delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407470.1:c.-1327_-1326delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407472.1:c.-1327_-1326delinsTG - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NR_176365.1:n.112_113delinsTG - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176366.1:n.112_113delinsTG - 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
SCV001486615	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 22, 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

SCV001486615

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 22, 2022)

germline

clinical testing

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

Help

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, SCV001486615.3

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

Description

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. This variant has not been reported in the literature in individuals affected with APC-related conditions. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. 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.

#	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 9, 2024

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