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NM_000455.5(STK11):c.96C>G (p.Thr32=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Mar 31, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000135930.10
Variation ID:
135930
Description:
single nucleotide variant
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NM_000455.5(STK11):c.96C>G (p.Thr32=)

Allele ID
139642
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.3
Genomic location
19: 1207009 (GRCh38) GRCh38 UCSC
19: 1207008 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.9:g.1207008C>G
NM_000455.4:c.96C>G NP_000446.1:p.Thr32= synonymous
NC_000019.10:g.1207009C>G
... more HGVS
Protein change
-
Other names
p.T32T:ACC>ACG
Canonical SPDI
NC_000019.10:1207008:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00015
Exome Aggregation Consortium (ExAC) 0.00039
Trans-Omics for Precision Medicine (TOPMed) 0.00010
1000 Genomes Project 0.00100
Links
ClinGen: CA023379
dbSNP: rs79175212
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 8, 2020 RCV000123069.9
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts May 2, 2016 RCV000160981.7
Benign 3 criteria provided, multiple submitters, no conflicts Mar 28, 2018 RCV000213009.2
Benign 1 criteria provided, single submitter Nov 23, 2016 RCV000759363.4
Likely benign 1 no assertion criteria provided - RCV001357485.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
STK11 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1748 1819

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Nov 23, 2015)
criteria provided, single submitter
Method: clinical testing
Peutz-Jeghers syndrome
Allele origin: unknown
Counsyl
Accession: SCV000487860.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (1)
Benign
(Sep 08, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000211691.10
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Mar 15, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000213653.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Peutz-Jeghers syndrome
Allele origin: germline
Invitae
Accession: SCV000166364.9
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Nov 23, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000602246.1
Submitted: (Aug 01, 2017)
Evidence details
Publications
PubMed (1)
Benign
(May 02, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000686710.1
Submitted: (Oct 26, 2017)
Evidence details
Benign
(Nov 23, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000888652.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Mar 28, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000918279.1
Submitted: (Apr 24, 2019)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: STK11 c.96C>G alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Peutz-Jeghers syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001287377.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
Malignant tumor of breast
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001552969.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The STK11 p.Thr32= variant was identified in the literature as a somatic variant in adenocarcinoma of the small intestine or uterine cervix in 2 Japanese … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Evaluation of a novel approach to circulating tumor cell isolation for cancer gene panel analysis in patients with breast cancer. Lee SJ Oncology letters 2017 PMID: 28521409
Mutations in the STK11 gene characterize minimal deviation adenocarcinoma of the uterine cervix. Kuragaki C Laboratory investigation; a journal of technical methods and pathology 2003 PMID: 12533684
Frameshift mutation of the STK11 gene in a sporadic gastrointestinal cancer with microsatellite instability. Nakagawa H Japanese journal of cancer research : Gann 1999 PMID: 10429655

Text-mined citations for rs79175212...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021