NM_000038.6(APC):c.-43A>C AND Familial adenomatous polyposis 1

Germline classification:: Likely benign (1 submission)
Last evaluated:: Apr 9, 2024
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:: RCV000708948.3

Allele description [Variation Report for NM_000038.6(APC):c.-43A>C]

NM_000038.6(APC):c.-43A>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_000038.6(APC):c.-43A>C

HGVS:

NC_000005.10:g.112737901A>C
NG_008481.4:g.50381A>C
NM_000038.6:c.-43A>CMANE SELECT
NM_001127510.3:c.-151A>C
NM_001127511.3:c.166-28425A>C
NM_001354895.2:c.-18-16972A>C
NM_001354896.2:c.-43A>C
NM_001354897.1:c.166-28425A>C
NM_001354897.2:c.166-28425A>C
NM_001354898.2:c.-73A>C
NM_001354899.2:c.-43A>C
NM_001354900.2:c.-67A>C
NM_001354901.2:c.-67A>C
NM_001354902.2:c.166-28425A>C
NM_001354903.2:c.-43A>C
NM_001354904.2:c.-73A>C
NM_001354905.2:c.-67A>C
NM_001354906.2:c.-1078A>C
LRG_130:g.50381A>C
NC_000005.9:g.112073598A>C
NM_000038.5:c.-43A>C

Links:

dbSNP: rs879254014

NCBI 1000 Genomes Browser:

rs879254014

Molecular consequence:

NM_000038.6:c.-43A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001127510.3:c.-151A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354896.2:c.-43A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354898.2:c.-73A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354899.2:c.-43A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354900.2:c.-67A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354901.2:c.-67A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354903.2:c.-43A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354904.2:c.-73A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354905.2:c.-67A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354906.2:c.-1078A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001127511.3:c.166-28425A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354895.2:c.-18-16972A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354897.2:c.166-28425A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354902.2:c.166-28425A>C - intron variant - [Sequence Ontology: SO:0001627]

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

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Cupriavidus sp. DL-D2 contig26, whole genome shotgun sequence
Cupriavidus sp. DL-D2 contig26, whole genome shotgun sequence
gi|2735532256|ref|NZ_JBDKXK01000002 gnl|WGS:NZ_JBDKXK01|contig26

Nucleotide
PREDICTED: Apis mellifera sodium/potassium-transporting ATPase subunit alpha (LO...
PREDICTED: Apis mellifera sodium/potassium-transporting ATPase subunit alpha (LOC411083), transcript variant X4, mRNA
gi|1477750402|ref|XM_026441029.1|

Nucleotide
sodium/potassium-transporting ATPase subunit alpha isoform X6 [Apis mellifera]
sodium/potassium-transporting ATPase subunit alpha isoform X6 [Apis mellifera]
gi|1477750407|ref|XP_026296816.1|

Protein
PREDICTED: Homo sapiens methyltransferase 3, N6-adenosine-methyltransferase comp...
PREDICTED: Homo sapiens methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit (METTL3), transcript variant X2, mRNA
gi|2217298038|ref|XM_047431594.1|

Nucleotide
Tssr41969 AND (alive[prop]) (0)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000838057	Mendelics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 9, 2024)	unknown	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

SCV000838057

Mendelics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Apr 9, 2024)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Mendelics, SCV000838057.3

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

#	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

Last Updated: Oct 13, 2024

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