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NM_000455.5(STK11):c.816C>T (p.Tyr272=) AND Malignant tumor of breast

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:
RCV001355314.3

Allele description

NM_000455.5(STK11):c.816C>T (p.Tyr272=)

Gene:
STK11:serine/threonine kinase 11 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.3
Genomic location:
Preferred name:
NM_000455.5(STK11):c.816C>T (p.Tyr272=)
HGVS:
  • NC_000019.10:g.1221294C>T
  • NG_007460.2:g.36888C>T
  • NM_000455.5:c.816C>TMANE SELECT
  • NP_000446.1:p.Tyr272=
  • NP_000446.1:p.Tyr272=
  • LRG_319t1:c.816C>T
  • LRG_319:g.36888C>T
  • LRG_319p1:p.Tyr272=
  • NC_000019.9:g.1221293C>T
  • NM_000455.4:c.816C>T
  • p.Tyr272Tyr
  • p.Y272Y
Links:
dbSNP: rs9282859
NCBI 1000 Genomes Browser:
rs9282859
Molecular consequence:
  • NM_000455.5:c.816C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Malignant tumor of breast
Synonyms:
Malignant breast neoplasm; Cancer breast
Identifiers:
MONDO: MONDO:0007254; MedGen: C0006142

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001550171Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Benignunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot 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), SCV001550171.1

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

Description

The STK11 p.Tyr272Tyr variant was not identified in the literature nor was it identified in the MutDB, LOVD 3.0, Zhejiang Colon Cancer Database, and Insight Hereditary Tumors Database databases. The variant was identified in dbSNP (ID: rs9282859) as “Other”, ClinVar (classified benign by Ambry Genetics and Prevention Genetics, and likely benign by Illumina), and in Cosmic (3X all in lung carcinomas). The variant was also identified in control databases in 2204 (84 homozygous) of 273338 chromosomes at a frequency of 0.008 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017), identified in the following populations at a frequency greater than 1%: African in 1993 of 23530 chromosomes (freq: 0.085). The p.Tyr272Tyr variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.

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

Last Updated: May 1, 2024