NM_001127511.3(APC):c.146del (p.His49fs) AND Familial adenomatous polyposis 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 29, 2020
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:: RCV002543536.10

Allele description [Variation Report for NM_001127511.3(APC):c.146del (p.His49fs)]

NM_001127511.3(APC):c.146del (p.His49fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

5q22.2

Genomic location:

Preferred name:

NM_001127511.3(APC):c.146del (p.His49fs)

HGVS:

NC_000005.10:g.112707863del
NG_008481.4:g.20343del
NM_001127511.3:c.146del
NM_001354895.2:c.-38del
NM_001354897.2:c.146del
NM_001354902.2:c.146del
NM_001407446.1:c.146del
NM_001407447.1:c.-38del
NM_001407448.1:c.-19+214del
NM_001407450.1:c.-19+214del
NM_001407452.1:c.-38del
NM_001407453.1:c.-43+214del
NM_001407456.1:c.-38del
NM_001407457.1:c.-19+214del
NM_001407458.1:c.-19+214del
NM_001407460.1:c.-38del
NM_001407469.1:c.-38del
NM_001407470.1:c.-1073del
NM_001407472.1:c.-1073del
NP_001120983.2:p.His49fs
NP_001341826.1:p.His49fs
NP_001341831.1:p.His49fs
NP_001394375.1:p.His49fs
LRG_130t3:c.-38del
LRG_130:g.20343del
NC_000005.9:g.112043560del
NM_001127511.1:c.-38delA
NR_176366.1:n.366del

Protein change:

H49fs

Links:

dbSNP: rs1750616412

NCBI 1000 Genomes Browser:

rs1750616412

Molecular consequence:

NM_001354895.2:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407447.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407452.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407456.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407460.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407469.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407470.1:c.-1073del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407472.1:c.-1073del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001127511.3:c.146del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354897.2:c.146del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354902.2:c.146del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407446.1:c.146del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407448.1:c.-19+214del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407450.1:c.-19+214del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407453.1:c.-43+214del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407457.1:c.-19+214del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407458.1:c.-19+214del - intron variant - [Sequence Ontology: SO:0001627]
NR_176366.1:n.366del - 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
SCV001499422	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 29, 2020)	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

SCV001499422

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 29, 2020)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001499422.4

#	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 for this variant, and the functional significance of this non-coding change is currently unknown. This variant has not been reported in the literature in individuals with APC-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC 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: Nov 10, 2024

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