NM_000455.5(STK11):c.723T>C (p.Ala241=) AND not specified

Clinical significance:Benign (Last evaluated: May 21, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000418469.3

Allele description [Variation Report for NM_000455.5(STK11):c.723T>C (p.Ala241=)]

NM_000455.5(STK11):c.723T>C (p.Ala241=)

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.723T>C (p.Ala241=)
HGVS:
  • NC_000019.10:g.1220706T>C
  • NG_007460.2:g.36300T>C
  • NM_000455.4:c.723T>C
  • NM_000455.5:c.723T>CMANE SELECT
  • NP_000446.1:p.Ala241=
  • NP_000446.1:p.Ala241=
  • LRG_319t1:c.723T>C
  • LRG_319:g.36300T>C
  • LRG_319p1:p.Ala241=
  • NC_000019.9:g.1220705T>C
  • p.A241A
Links:
dbSNP: rs533550278
NCBI 1000 Genomes Browser:
rs533550278
Molecular consequence:
  • NM_000455.4:c.723T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_000455.5:c.723T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000918287Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(May 21, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000918287.1

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

Description

Variant summary: STK11 c.723T>C alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 368 fold above the estimated maximal expected allele frequency for a pathogenic variant in STK11 causing Peutz-Jeghers Syndrome phenotype (6.3e-06), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. To our knowledge, no occurrence of c.723T>C in individuals affected with Peutz-Jeghers Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.

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

Last Updated: Oct 30, 2021

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