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NM_000038.6(APC):c.7821C>T (p.Ser2607=) AND not provided

Germline classification:
Benign/Likely benign (2 submissions)
Last evaluated:
Nov 1, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000589014.35

Allele description [Variation Report for NM_000038.6(APC):c.7821C>T (p.Ser2607=)]

NM_000038.6(APC):c.7821C>T (p.Ser2607=)

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.7821C>T (p.Ser2607=)
HGVS:
  • NC_000005.10:g.112843415C>T
  • NG_008481.4:g.155895C>T
  • NM_000038.6:c.7821C>TMANE SELECT
  • NM_001127510.3:c.7821C>T
  • NM_001127511.3:c.7767C>T
  • NM_001354895.2:c.7821C>T
  • NM_001354896.2:c.7875C>T
  • NM_001354897.2:c.7851C>T
  • NM_001354898.2:c.7746C>T
  • NM_001354899.2:c.7737C>T
  • NM_001354900.2:c.7698C>T
  • NM_001354901.2:c.7644C>T
  • NM_001354902.2:c.7548C>T
  • NM_001354903.2:c.7518C>T
  • NM_001354904.2:c.7443C>T
  • NM_001354905.2:c.7341C>T
  • NM_001354906.2:c.6972C>T
  • NP_000029.2:p.Ser2607=
  • NP_001120982.1:p.Ser2607=
  • NP_001120983.2:p.Ser2589=
  • NP_001341824.1:p.Ser2607=
  • NP_001341825.1:p.Ser2625=
  • NP_001341826.1:p.Ser2617=
  • NP_001341827.1:p.Ser2582=
  • NP_001341828.1:p.Ser2579=
  • NP_001341829.1:p.Ser2566=
  • NP_001341830.1:p.Ser2548=
  • NP_001341831.1:p.Ser2516=
  • NP_001341832.1:p.Ser2506=
  • NP_001341833.1:p.Ser2481=
  • NP_001341834.1:p.Ser2447=
  • NP_001341835.1:p.Ser2324=
  • LRG_130t1:c.7821C>T
  • LRG_130:g.155895C>T
  • NC_000005.9:g.112179112C>T
  • NM_000038.4:c.7821C>T
  • NM_000038.5:c.7821C>T
  • p.S2607S
  • p.Ser2607Ser
Links:
dbSNP: rs532235331
Molecular consequence:
  • NM_000038.6:c.7821C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127510.3:c.7821C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127511.3:c.7767C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354895.2:c.7821C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354896.2:c.7875C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354897.2:c.7851C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354898.2:c.7746C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354899.2:c.7737C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354900.2:c.7698C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354901.2:c.7644C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354902.2:c.7548C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354903.2:c.7518C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354904.2:c.7443C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354905.2:c.7341C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354906.2:c.6972C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
2

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000694125Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Jul 1, 2016) 		germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV004011613CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)		Likely benign
(Nov 1, 2024) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not 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, SCV000694125.1

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

Description

Variant summary: The APC c.7821C>T (p.Ser2607Ser) causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools predicting no significant impact on 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 110/120952 (3 homozygotes, 1/1111), predominantly observed in the South Asian, 107/16502 (3 homozygotes, 1/154), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic APC variant of 1/14,0005 (0.0000714). Therefore, suggesting this variant is a common polymorphism found in population(s) of South Asian orign. The variant of interest, to our knowledge, has not been reported in affected individuals via publications, although multiple reputable clinical laboratories cite the variant as "likely benign/benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.

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

From CeGaT Center for Human Genetics Tuebingen, SCV004011613.24

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided

Description

APC: BP4, BP7

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

Last Updated: Jun 20, 2026

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