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NM_000038.6(APC):c.1458T>C (p.Tyr486=) AND Carcinoma of colon

Germline classification:
Benign (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001353619.9

Allele description [Variation Report for NM_000038.6(APC):c.1458T>C (p.Tyr486=)]

NM_000038.6(APC):c.1458T>C (p.Tyr486=)

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.1458T>C (p.Tyr486=)
Other names:
NM_000038.6(APC):c.1458T>C; p.Tyr486=
HGVS:
  • NC_000005.10:g.112827157T>C
  • NG_008481.4:g.139637T>C
  • NM_000038.6:c.1458T>CMANE SELECT
  • NM_001127510.3:c.1458T>C
  • NM_001127511.3:c.1404T>C
  • NM_001354895.2:c.1458T>C
  • NM_001354896.2:c.1512T>C
  • NM_001354897.2:c.1488T>C
  • NM_001354898.2:c.1383T>C
  • NM_001354899.2:c.1374T>C
  • NM_001354900.2:c.1335T>C
  • NM_001354901.2:c.1281T>C
  • NM_001354902.2:c.1185T>C
  • NM_001354903.2:c.1155T>C
  • NM_001354904.2:c.1080T>C
  • NM_001354905.2:c.978T>C
  • NM_001354906.2:c.609T>C
  • NP_000029.2:p.Tyr486=
  • NP_001120982.1:p.Tyr486=
  • NP_001120983.2:p.Tyr468=
  • NP_001341824.1:p.Tyr486=
  • NP_001341825.1:p.Tyr504=
  • NP_001341826.1:p.Tyr496=
  • NP_001341827.1:p.Tyr461=
  • NP_001341828.1:p.Tyr458=
  • NP_001341829.1:p.Tyr445=
  • NP_001341830.1:p.Tyr427=
  • NP_001341831.1:p.Tyr395=
  • NP_001341832.1:p.Tyr385=
  • NP_001341833.1:p.Tyr360=
  • NP_001341834.1:p.Tyr326=
  • NP_001341835.1:p.Tyr203=
  • LRG_130t1:c.1458T>C
  • LRG_130:g.139637T>C
  • NC_000005.8:g.112190753T>C
  • NC_000005.9:g.112162854T>C
  • NM_000038.4:c.1458T>C
  • NM_000038.5:c.1458T>C
  • NM_001127510.2:c.1458T>C
  • NP_000029.2:p.(=)
  • c.1458T>C
  • p.Y486Y
Links:
dbSNP: rs2229992
NCBI 1000 Genomes Browser:
rs2229992
Molecular consequence:
  • NM_000038.6:c.1458T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127510.3:c.1458T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127511.3:c.1404T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354895.2:c.1458T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354896.2:c.1512T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354897.2:c.1488T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354898.2:c.1383T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354899.2:c.1374T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354900.2:c.1335T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354901.2:c.1281T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354902.2:c.1185T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354903.2:c.1155T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354904.2:c.1080T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354905.2:c.978T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354906.2:c.609T>C - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Name:
Carcinoma of colon (CRC)
Synonyms:
Colonic carcinoma; Colon carcinoma
Identifiers:
MONDO: MONDO:0002032; MedGen: C0699790

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000591074Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Benignunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV000591074.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The c.1458T>C, p.Tyr486Tyr silent variant, located in exon 12 of APC, is not expected to have clinical significance because it does not alter an amino acid residue, is not located near a splice junction, is listed in dbSNP (rs_id:rs2229992) with a minor allele frequency of 0.46. Based on the above information, this is a likely benign variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 24, 2024