NM_001127511.3(APC):c.-39T>C AND Familial adenomatous polyposis 1

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Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 5, 2023
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:: RCV003538720.1

Allele description

NM_001127511.3(APC):c.-39T>C

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

5q22.2

Genomic location:

Preferred name:

NM_001127511.3(APC):c.-39T>C

HGVS:

NC_000005.10:g.112707679T>C
NG_008481.4:g.20159T>C
NM_001127511.3:c.-39T>C
NM_001354895.2:c.-222T>C
NM_001354897.2:c.-39T>C
NM_001354902.2:c.-39T>C
NM_001407446.1:c.-39T>C
NM_001407447.1:c.-222T>C
NM_001407448.1:c.-19+30T>C
NM_001407450.1:c.-19+30T>C
NM_001407452.1:c.-222T>C
NM_001407453.1:c.-43+30T>C
NM_001407456.1:c.-222T>C
NM_001407457.1:c.-19+30T>C
NM_001407458.1:c.-19+30T>C
NM_001407460.1:c.-222T>C
NM_001407469.1:c.-222T>C
NM_001407470.1:c.-1257T>C
NM_001407472.1:c.-1257T>C
LRG_130t3:c.-222T>C
LRG_130:g.20159T>C
NC_000005.9:g.112043376T>C
NM_001127511.1:c.-222T>C
NR_176366.1:n.182T>C

Links:

dbSNP: rs1466692709

NCBI 1000 Genomes Browser:

rs1466692709

Molecular consequence:

NM_001127511.3:c.-39T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354895.2:c.-222T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354897.2:c.-39T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354902.2:c.-39T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407446.1:c.-39T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407447.1:c.-222T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407452.1:c.-222T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407456.1:c.-222T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407460.1:c.-222T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407469.1:c.-222T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407470.1:c.-1257T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407472.1:c.-1257T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407448.1:c.-19+30T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407450.1:c.-19+30T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407453.1:c.-43+30T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407457.1:c.-19+30T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407458.1:c.-19+30T>C - intron variant - [Sequence Ontology: SO:0001627]
NR_176366.1:n.182T>C - 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
SCV001543607	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 5, 2023)	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

SCV001543607

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 5, 2023)

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, SCV001543607.4

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

Description

This variant occurs in a non-coding region of the APC gene. It does not change the encoded amino acid sequence of the APC protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with APC-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	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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