U.S. flag

An official website of the United States government

NM_000038.6(APC):c.7686C>T (p.Ser2562=) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Mar 31, 2022
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:
RCV002400139.10

Allele description [Variation Report for NM_000038.6(APC):c.7686C>T (p.Ser2562=)]

NM_000038.6(APC):c.7686C>T (p.Ser2562=)

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.7686C>T (p.Ser2562=)
HGVS:
  • NC_000005.10:g.112843280C>T
  • NG_008481.4:g.155760C>T
  • NM_000038.6:c.7686C>TMANE SELECT
  • NM_001127510.3:c.7686C>T
  • NM_001127511.3:c.7632C>T
  • NM_001354895.2:c.7686C>T
  • NM_001354896.2:c.7740C>T
  • NM_001354897.2:c.7716C>T
  • NM_001354898.2:c.7611C>T
  • NM_001354899.2:c.7602C>T
  • NM_001354900.2:c.7563C>T
  • NM_001354901.2:c.7509C>T
  • NM_001354902.2:c.7413C>T
  • NM_001354903.2:c.7383C>T
  • NM_001354904.2:c.7308C>T
  • NM_001354905.2:c.7206C>T
  • NM_001354906.2:c.6837C>T
  • NP_000029.2:p.Ser2562=
  • NP_001120982.1:p.Ser2562=
  • NP_001120983.2:p.Ser2544=
  • NP_001341824.1:p.Ser2562=
  • NP_001341825.1:p.Ser2580=
  • NP_001341826.1:p.Ser2572=
  • NP_001341827.1:p.Ser2537=
  • NP_001341828.1:p.Ser2534=
  • NP_001341829.1:p.Ser2521=
  • NP_001341830.1:p.Ser2503=
  • NP_001341831.1:p.Ser2471=
  • NP_001341832.1:p.Ser2461=
  • NP_001341833.1:p.Ser2436=
  • NP_001341834.1:p.Ser2402=
  • NP_001341835.1:p.Ser2279=
  • LRG_130:g.155760C>T
  • NC_000005.9:g.112178977C>T
  • NM_000038.5:c.7686C>T
Links:
dbSNP: rs1580685620
NCBI 1000 Genomes Browser:
rs1580685620
Molecular consequence:
  • NM_000038.6:c.7686C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127510.3:c.7686C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127511.3:c.7632C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354895.2:c.7686C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354896.2:c.7740C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354897.2:c.7716C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354898.2:c.7611C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354899.2:c.7602C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354900.2:c.7563C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354901.2:c.7509C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354902.2:c.7413C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354903.2:c.7383C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354904.2:c.7308C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354905.2:c.7206C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354906.2:c.6837C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002674232Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Apr 13, 2021) 		germlineclinical testing

Citation Link,

SCV004357671Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Mar 31, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Ambry Genetics, SCV002674232.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

From Color Diagnostics, LLC DBA Color Health, SCV004357671.1

#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: Oct 26, 2024