NM_000038.6(APC):c.6354TGC[5] (p.Ala2122dup) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Uncertain significance(1) (Last evaluated: Aug 24, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000588527.3

Allele description [Variation Report for NM_000038.6(APC):c.6354TGC[5] (p.Ala2122dup)]

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

Gene:
APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
5q22.2
Genomic location:
Preferred name:
NM_000038.6(APC):c.6354TGC[5] (p.Ala2122dup)
HGVS:
  • NC_000005.10:g.112841948TGC[5]
  • NG_008481.4:g.154428TGC[5]
  • NM_000038.6:c.6354TGC[5]MANE SELECT
  • NM_001127510.3:c.6354TGC[5]
  • NM_001127511.3:c.6300TGC[5]
  • NM_001354895.2:c.6354TGC[5]
  • NM_001354896.2:c.6408TGC[5]
  • NM_001354897.2:c.6384TGC[5]
  • NM_001354898.2:c.6279TGC[5]
  • NM_001354899.2:c.6270TGC[5]
  • NM_001354900.2:c.6231TGC[5]
  • NM_001354901.2:c.6177TGC[5]
  • NM_001354902.2:c.6081TGC[5]
  • NM_001354903.2:c.6051TGC[5]
  • NM_001354904.2:c.5976TGC[5]
  • NM_001354905.2:c.5874TGC[5]
  • NM_001354906.2:c.5505TGC[5]
  • NP_000029.2:p.Ala2122dup
  • NP_001120982.1:p.Ala2122dup
  • NP_001120983.2:p.Ala2104dup
  • NP_001341824.1:p.Ala2122dup
  • NP_001341825.1:p.Ala2140dup
  • NP_001341826.1:p.Ala2132dup
  • NP_001341827.1:p.Ala2097dup
  • NP_001341828.1:p.Ala2094dup
  • NP_001341829.1:p.Ala2081dup
  • NP_001341830.1:p.Ala2063dup
  • NP_001341831.1:p.Ala2031dup
  • NP_001341832.1:p.Ala2021dup
  • NP_001341833.1:p.Ala1996dup
  • NP_001341834.1:p.Ala1962dup
  • NP_001341835.1:p.Ala1839dup
  • LRG_130:g.154428TGC[5]
  • NC_000005.9:g.112177642_112177643insGCT
  • NC_000005.9:g.112177645TGC[5]
  • NM_000038.5:c.6363_6365dup
  • NM_000038.5:c.6363_6365dupTGC
  • p.Q2117_A2118INSC
Links:
dbSNP: rs587780602
NCBI 1000 Genomes Browser:
rs587780602
Molecular consequence:
  • NM_000038.6:c.6354TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001127510.3:c.6354TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001127511.3:c.6300TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001354895.2:c.6354TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001354896.2:c.6408TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001354897.2:c.6384TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001354898.2:c.6279TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001354899.2:c.6270TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001354900.2:c.6231TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001354901.2:c.6177TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001354902.2:c.6081TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001354903.2:c.6051TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001354904.2:c.5976TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001354905.2:c.5874TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001354906.2:c.5505TGC[5] - inframe_insertion - [Sequence Ontology: SO:0001821]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000694090Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Sep 30, 2016)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV000805452PreventionGenetics,PreventionGeneticscriteria provided, single submitter
Uncertain significance
(Aug 24, 2017)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Identification of a Variety of Mutations in Cancer Predisposition Genes in Patients With Suspected Lynch Syndrome.

Yurgelun MB, Allen B, Kaldate RR, Bowles KR, Judkins T, Kaushik P, Roa BB, Wenstrup RJ, Hartman AR, Syngal S.

Gastroenterology. 2015 Sep;149(3):604-13.e20. doi: 10.1053/j.gastro.2015.05.006. Epub 2015 May 14.

PubMed [citation]
PMID:
25980754
PMCID:
PMC4550537

Germline multi-gene hereditary cancer panel testing in an unselected endometrial cancer cohort.

Ring KL, Bruegl AS, Allen BA, Elkin EP, Singh N, Hartman AR, Daniels MS, Broaddus RR.

Mod Pathol. 2016 Nov;29(11):1381-1389. doi: 10.1038/modpathol.2016.135. Epub 2016 Jul 22.

PubMed [citation]
PMID:
27443514
PMCID:
PMC5541389
See all PubMed Citations (3)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000694090.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

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 single Alanine. One in silico tool predicts a benign outcome for this variant. This variant was found in 36/121200 control chromosomes, predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.0004797 (32/66714). This frequency is about 7 times the estimated maximal expected allele frequency of a pathogenic APC variant (0.0000714), suggesting this is likely a benign polymorphism found primarily in the populations of European (Non-Finnish) origin. This variant has been reported in affected individuals without strong evidence of causality. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as uncertain significance/likely benign, all without evidence to independently evaluate. Taken together, this variant is classified as benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From PreventionGenetics,PreventionGenetics, SCV000805452.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 23, 2021

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