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NM_000038.6(APC):c.6354TGC[5] (p.Ala2122dup)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(3);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Mar 31, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000140994.10
Variation ID:
140994
Description:
3bp microsatellite
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NM_000038.6(APC):c.6354TGC[5] (p.Ala2122dup)

Allele ID
150708
Variant type
Microsatellite
Variant length
3 bp
Cytogenetic location
5q22.2
Genomic location
5: 112841945-112841946 (GRCh38) GRCh38 UCSC
5: 112177642-112177643 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.112841948TGC[5]
NC_000005.9:g.112177645TGC[5]
NM_000038.6:c.6354TGC[5] MANE Select NP_000029.2:p.Ala2122dup
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000005.10:112841945:GCTGCTGCTGCTGC:GCTGCTGCTGCTGCTGC
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA011093
dbSNP: rs587780602
Varsome
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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 Feb 5, 2020 RCV000129306.8
Uncertain significance 1 criteria provided, single submitter Mar 29, 2017 RCV000237032.3
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Aug 24, 2017 RCV000588527.3
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Dec 7, 2020 RCV001080265.4
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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
8955 8989

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Mar 29, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000292463.3
Submitted: (Jul 13, 2017)
Evidence details
Comment:
This duplication of three nucleotides in APC is denoted c.6363_6365dupTGC at the cDNA level and p.Ala2122dup at the protein level. The normal sequence, with the … (more)
Uncertain significance
(Aug 24, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000805452.1
Submitted: (Jan 29, 2018)
Evidence details
Likely benign
(Feb 05, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000681795.3
Submitted: (May 19, 2020)
Evidence details
Likely benign
(Aug 13, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000184068.7
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Co-occurence with a mutation in another gene that clearly explains a proband's phenotype;Other data supporting benign classification
Uncertain significance
(Apr 30, 2019)
criteria provided, single submitter
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: paternal
Baylor Genetics
Study: CSER-TexasKidsCanSeq
Accession: SCV001482688.1
Submitted: (Feb 10, 2021)
Evidence details
Comment:
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Likely benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: germline
Invitae
Accession: SCV000166048.12
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Benign
(Sep 30, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000694090.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: The APC c.6363_6365dupTGC (p.Ala2121dup) variant involves the insertion of three nucleotides in a 5 alanine repeat region, resulting in an in-frame duplication of … (more)
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV000591198.2
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The p.Ala2122dup variant was identified in 1 of 342 proband chromosomes (frequency: 0.003) from individuals or families with FAP, but was classified as a VUS … (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
Germline multi-gene hereditary cancer panel testing in an unselected endometrial cancer cohort. Ring KL Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2016 PMID: 27443514
Identification of a Variety of Mutations in Cancer Predisposition Genes in Patients With Suspected Lynch Syndrome. Yurgelun MB Gastroenterology 2015 PMID: 25980754

Text-mined citations for rs587780602...

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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 Jun 23, 2021