NM_001127511.3(APC):c.-5C>A AND Familial adenomatous polyposis 1

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 26, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000662776.11

Allele description [Variation Report for NM_001127511.3(APC):c.-5C>A]

NM_001127511.3(APC):c.-5C>A

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.-5C>A

HGVS:

NC_000005.10:g.112707713C>A
NG_008481.4:g.20193C>A
NM_001127511.3:c.-5C>A
NM_001354895.2:c.-188C>A
NM_001354897.2:c.-5C>A
NM_001354902.2:c.-5C>A
NM_001407446.1:c.-5C>A
NM_001407447.1:c.-188C>A
NM_001407448.1:c.-19+64C>A
NM_001407450.1:c.-19+64C>A
NM_001407452.1:c.-188C>A
NM_001407453.1:c.-43+64C>A
NM_001407456.1:c.-188C>A
NM_001407457.1:c.-19+64C>A
NM_001407458.1:c.-19+64C>A
NM_001407460.1:c.-188C>A
NM_001407469.1:c.-188C>A
NM_001407470.1:c.-1223C>A
NM_001407472.1:c.-1223C>A
LRG_130t3:c.-188C>A
LRG_130:g.20193C>A
NC_000005.9:g.112043410C>A
NM_001127511.1:c.-188C>A
NM_001127511.2:c.-5C>A
NR_176366.1:n.216C>A

Links:

dbSNP: rs972010514

NCBI 1000 Genomes Browser:

rs972010514

Molecular consequence:

NM_001127511.3:c.-5C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354895.2:c.-188C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354897.2:c.-5C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354902.2:c.-5C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407446.1:c.-5C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407447.1:c.-188C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407452.1:c.-188C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407456.1:c.-188C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407460.1:c.-188C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407469.1:c.-188C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407470.1:c.-1223C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407472.1:c.-1223C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407448.1:c.-19+64C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407450.1:c.-19+64C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407453.1:c.-43+64C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407457.1:c.-19+64C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407458.1:c.-19+64C>A - intron variant - [Sequence Ontology: SO:0001627]
NR_176366.1:n.216C>A - 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

Recent activity

Clear Turn Off Turn On

cytochrome oxidase subunit 1, partial (mitochondrion) [Arenocaris reducta]
cytochrome oxidase subunit 1, partial (mitochondrion) [Arenocaris reducta]
gi|1698162407|gb|QDH82391.1|

Protein
Cyth3 [Nannospalax galili]
Cyth3 [Nannospalax galili]
Gene ID:103726442

Gene
CYTH3 [Microcaecilia unicolor]
CYTH3 [Microcaecilia unicolor]
Gene ID:115475818

Gene

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000785583	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Uncertain significance (Oct 9, 2017)	unknown	clinical testing	Counsyl_Autosomal_Dominant_Disease_Classification_criteria_(2015)_v1.pdf, Citation Link,
SCV002273690	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 26, 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

SCV000785583

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Uncertain significance
(Oct 9, 2017)

unknown

clinical testing

Counsyl_Autosomal_Dominant_Disease_Classification_criteria_(2015)_v1.pdf,

Citation Link,

SCV002273690

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 26, 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
not provided	unknown	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 Counsyl, SCV000785583.2

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

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002273690.3

#	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. 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.

#	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: Oct 26, 2024

ClinVar

Relating variation to medicine