Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000038.6(APC):c.4669A>G (p.Ile1557Val)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 25, 2020
Accession:
VCV000245712.8
Variation ID:
245712
Description:
single nucleotide variant
Help

NM_000038.6(APC):c.4669A>G (p.Ile1557Val)

Allele ID
244435
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q22.2
Genomic location
5: 112840263 (GRCh38) GRCh38 UCSC
5: 112175960 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.9:g.112175960A>G
NC_000005.10:g.112840263A>G
NM_000038.6:c.4669A>G MANE Select NP_000029.2:p.Ile1557Val missense
... more HGVS
Protein change
I1539V, I1557V, I1456V, I1466V, I1567V, I1575V, I1431V, I1529V, I1532V, I1274V, I1397V, I1498V, I1516V
Other names
-
Canonical SPDI
NC_000005.10:112840262:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00010
Exome Aggregation Consortium (ExAC) 0.00012
The Genome Aggregation Database (gnomAD), exomes 0.00008
The Genome Aggregation Database (gnomAD) 0.00010
Links
ClinGen: CA039538
dbSNP: rs763578917
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Mar 19, 2019 RCV000491300.3
Likely benign 1 criteria provided, single submitter Nov 25, 2020 RCV000469610.7
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Nov 23, 2018 RCV000589170.2
Help
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
8938 8972

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jul 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000694056.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: The APC c.4669A>G (p.Ile1557Val) variant involves the alteration of a non-conserved nucleotide, which is not located in any known domain (InterPro). 4/4 in … (more)
Uncertain significance
(Nov 23, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000292773.10
Submitted: (Jan 29, 2019)
Evidence details
Comment:
This variant is denoted APC c.4669A>G at the cDNA level, p.Ile1557Val (I1557V) at the protein level, and results in the change of an Isoleucine to … (more)
Likely benign
(Mar 19, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000579816.4
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Co-occurence with a mutation in another gene that clearly explains a proband's phenotype;In silico models in agreement (benign);Other strong data supporting benign classification
Likely benign
(Nov 25, 2020)
criteria provided, single submitter
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: germline
Invitae
Accession: SCV000552671.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Likely benign
(Jan 04, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000910831.1
Submitted: (Nov 06, 2018)
Evidence details

Functional evidence

Help
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

Help
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
Variant Profiling of Candidate Genes in Pancreatic Ductal Adenocarcinoma. Huang J Clinical chemistry 2015 PMID: 26378065

Text-mined citations for rs763578917...

Help
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 Jun 14, 2021