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NM_000455.4(STK11):c.1109-4C>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(4);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jun 11, 2021)
Last evaluated:
Nov 15, 2020
Accession:
VCV000458012.9
Variation ID:
458012
Description:
single nucleotide variant
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NM_000455.4(STK11):c.1109-4C>T

Allele ID
470419
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.3
Genomic location
19: 1226450 (GRCh38) GRCh38 UCSC
19: 1226449 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.10:g.1226450C>T
NC_000019.9:g.1226449C>T
NM_000455.4:c.1109-4C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000019.10:1226449:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00001
Links
ClinGen: CA631033964
dbSNP: rs1407794756
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Nov 15, 2020 RCV001088020.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Nov 8, 2020 RCV000572712.4
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Oct 3, 2017 RCV000589586.3
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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
1733 1801

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 19, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000696701.1
Submitted: (Jan 25, 2018)
Evidence details
Comment:
Variant summary: The STK11 c.1109-4C>T variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant. … (more)
Likely benign
(Sep 14, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000806069.1
Submitted: (Jan 29, 2018)
Evidence details
Likely benign
(Oct 03, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000888635.1
Submitted: (Aug 31, 2018)
Evidence details
Likely benign
(Jun 06, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000676284.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);RNA Studies
Likely benign
(Nov 15, 2020)
criteria provided, single submitter
Method: clinical testing
Peutz-Jeghers syndrome
Allele origin: germline
Invitae
Accession: SCV000629060.4
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Nov 08, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000912998.3
Submitted: (Jun 11, 2021)
Evidence details
Comment:
This variant causes a C to T nucleotide substitution at the -4 position of intron 8 of the STK11 gene. To our knowledge, functional studies … (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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs1407794756...

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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 Jun 23, 2021