NM_000038.6(APC):c.6387G>A (p.Ser2129=) AND not provided

Clinical significance:Benign (Last evaluated: Jan 26, 2017)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000589653.6

Allele description [Variation Report for NM_000038.6(APC):c.6387G>A (p.Ser2129=)]

NM_000038.6(APC):c.6387G>A (p.Ser2129=)

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.6387G>A (p.Ser2129=)
HGVS:
  • NC_000005.10:g.112841981G>A
  • NG_008481.4:g.154461G>A
  • NM_000038.6:c.6387G>AMANE SELECT
  • NM_001127510.3:c.6387G>A
  • NM_001127511.3:c.6333G>A
  • NM_001354895.2:c.6387G>A
  • NM_001354896.2:c.6441G>A
  • NM_001354897.2:c.6417G>A
  • NM_001354898.2:c.6312G>A
  • NM_001354899.2:c.6303G>A
  • NM_001354900.2:c.6264G>A
  • NM_001354901.2:c.6210G>A
  • NM_001354902.2:c.6114G>A
  • NM_001354903.2:c.6084G>A
  • NM_001354904.2:c.6009G>A
  • NM_001354905.2:c.5907G>A
  • NM_001354906.2:c.5538G>A
  • NP_000029.2:p.Ser2129=
  • NP_001120982.1:p.Ser2129=
  • NP_001120983.2:p.Ser2111=
  • NP_001341824.1:p.Ser2129=
  • NP_001341825.1:p.Ser2147=
  • NP_001341826.1:p.Ser2139=
  • NP_001341827.1:p.Ser2104=
  • NP_001341828.1:p.Ser2101=
  • NP_001341829.1:p.Ser2088=
  • NP_001341830.1:p.Ser2070=
  • NP_001341831.1:p.Ser2038=
  • NP_001341832.1:p.Ser2028=
  • NP_001341833.1:p.Ser2003=
  • NP_001341834.1:p.Ser1969=
  • NP_001341835.1:p.Ser1846=
  • LRG_130:g.154461G>A
  • NC_000005.9:g.112177678G>A
  • NM_000038.5:c.6387G>A
  • p.S2129S
  • p.Ser2129Ser
Links:
dbSNP: rs374310157
NCBI 1000 Genomes Browser:
rs374310157
Molecular consequence:
  • NM_000038.6:c.6387G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127510.3:c.6387G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127511.3:c.6333G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354895.2:c.6387G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354896.2:c.6441G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354897.2:c.6417G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354898.2:c.6312G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354899.2:c.6303G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354900.2:c.6264G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354901.2:c.6210G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354902.2:c.6114G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354903.2:c.6084G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354904.2:c.6009G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354905.2:c.5907G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354906.2:c.5538G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000694091Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Jan 26, 2017)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001838322GeneDxcriteria provided, single submitter
Benign
(Mar 3, 2015)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000694091.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: The APC c.6387G>A (p.Ser2129Ser) variant causes a synonymous change involving a non-conserved nucleotide, 4/5 splice prediction tools predict no significant impact on normal splicing, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 34/121086 (1/3561), predominantly in the Latino cohort, 30/11544 (1/384), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic APC variant of 1/14005. Therefore, suggesting this is likely a benign polymorphism found primarily in population(s) of Latino origin. The variant of interest has not been, to our knowledge, reported in affected individuals via publications, although multiple clinical diagnostic laboratories cite the variant with a classification of "likely benign/benign." Therefore, the variant of interest has been classified as Benign.

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

From GeneDx, SCV001838322.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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