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NM_000038.6(APC):c.6639G>A (p.Met2213Ile)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(5)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 24, 2021)
Last evaluated:
Dec 15, 2020
Accession:
VCV000141618.10
Variation ID:
141618
Description:
single nucleotide variant
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NM_000038.6(APC):c.6639G>A (p.Met2213Ile)

Allele ID
151332
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q22.2
Genomic location
5: 112842233 (GRCh38) GRCh38 UCSC
5: 112177930 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_130:g.154713G>A
NC_000005.10:g.112842233G>A
NC_000005.9:g.112177930G>A
... more HGVS
Protein change
M2195I, M2213I, M1930I, M2188I, M2231I, M2053I, M2172I, M2185I, M2087I, M2112I, M2223I, M2122I, M2154I
Other names
-
Canonical SPDI
NC_000005.10:112842232:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
Links
ClinGen: CA012330
dbSNP: rs35540155
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Dec 15, 2020 RCV000484737.3
Uncertain significance 1 criteria provided, single submitter Oct 31, 2018 RCV000765788.1
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV001157265.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Jan 29, 2019 RCV000130211.5
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 4, 2020 RCV000409211.7
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
APC Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
9015 9049

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jul 18, 2016)
criteria provided, single submitter
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: unknown
Counsyl
Accession: SCV000488876.1
Submitted: (Nov 23, 2016)
Evidence details
Uncertain significance
(Jan 29, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000185049.6
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (2)
Comment:
The p.M2213I variant (also known as c.6639G>A), located in coding exon 15 of the APC gene, results from a G to A substitution at nucleotide … (more)
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: germline
Invitae
Accession: SCV000552646.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Likely benign
(Dec 15, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000566001.5
Submitted: (Sep 24, 2021)
Evidence details
Comment:
Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports … (more)
Uncertain significance
(Aug 01, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
GeneKor MSA
Accession: SCV000821822.1
Submitted: (Aug 08, 2018)
Evidence details
Uncertain significance
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Colorectal cancer
Hepatocellular carcinoma
Desmoid disease, hereditary
Familial adenomatous polyposis 1
Familial adenomatous polyposis 1
Stomach cancer
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000897177.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000910766.1
Submitted: (Nov 06, 2018)
Evidence details
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
APC-Associated Polyposis Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001318816.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Identification of a Variety of Mutations in Cancer Predisposition Genes in Patients With Suspected Lynch Syndrome. Yurgelun MB Gastroenterology 2015 PMID: 25980754
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 Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
Exome sequencing identifies potential risk variants for Mendelian disorders at high prevalence in Qatar. Rodriguez-Flores JL Human mutation 2014 PMID: 24123366

Text-mined citations for rs35540155...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 20, 2021