NM_000455.5(STK11):c.-2G>T AND not provided

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jul 28, 2017
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:: RCV000586834.6

Allele description [Variation Report for NM_000455.5(STK11):c.-2G>T]

NM_000455.5(STK11):c.-2G>T

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.-2G>T

HGVS:

NC_000019.10:g.1206912G>T
NG_007460.2:g.22506G>T
NM_000455.5:c.-2G>TMANE SELECT
NM_001407255.1:c.-2G>T
LRG_319t1:c.-2G>T
LRG_319:g.22506G>T
NC_000019.9:g.1206911G>T
NM_000455.4:c.-2G>T
NR_176325.1:n.1135G>T

Links:

dbSNP: rs774072752

NCBI 1000 Genomes Browser:

rs774072752

Molecular consequence:

NM_000455.5:c.-2G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407255.1:c.-2G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NR_176325.1:n.1135G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000696714	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Jun 27, 2016)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV000806066	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jul 28, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000696714

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Jun 27, 2016)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV000806066

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jul 28, 2017)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696714.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Variant summary: The STK11 c.-2G>T variant is located in the 5'UTR involving a conserved nucleotide with 5/5 splice prediction tools predicting no significant impact on splicing and alterations to ESE binding, although these predictions have yet to be functionally assesed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 6/24392 (1/4065), predominantly in the Latino cohort, 6/916 (1/152), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic STK11 variant of 1/158730. Therefore, suggesting the variant of interest is a common polymorphism found in population(s) of Latino origin. The variant of interest was has not been, to our knowledge, reported in affected individuals via publications and/or reputable databases/clinical laboratories. However, an internal LCA specimen reports the variant to co-occur with another potentially pathogenic MLH1 variant, c.1731+1G>T (scored "likely pathogenic"). Therefore, taking all available lines of evidence into consideration, the variant of interest has been classified as Benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000806066.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

ClinVar

Relating variation to medicine