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NM_000455.5(STK11):c.1284G>A (p.Ser428=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(5);Likely benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
10 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 1, 2020
Accession:
VCV000184031.10
Variation ID:
184031
Description:
single nucleotide variant
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NM_000455.5(STK11):c.1284G>A (p.Ser428=)

Allele ID
185561
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.3
Genomic location
19: 1226629 (GRCh38) GRCh38 UCSC
19: 1226628 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.9:g.1226628G>A
NM_000455.4:c.1284G>A NP_000446.1:p.Ser428= synonymous
NC_000019.10:g.1226629G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000019.10:1226628:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00008
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00048
Trans-Omics for Precision Medicine (TOPMed) 0.00033
The Genome Aggregation Database (gnomAD) 0.00035
Links
ClinGen: CA022604
dbSNP: rs369097329
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Jul 17, 2015 RCV000163145.2
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Aug 29, 2018 RCV000437311.4
Benign 1 criteria provided, single submitter Sep 25, 2017 RCV000760077.4
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Dec 1, 2020 RCV000205545.8
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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
(Jun 09, 2016)
criteria provided, single submitter
Method: clinical testing
Peutz-Jeghers syndrome
Allele origin: unknown
Counsyl
Accession: SCV000488765.1
Submitted: (Nov 23, 2016)
Evidence details
Benign
(Jun 22, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000515486.4
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
(Jul 15, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000213662.5
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 01, 2020)
criteria provided, single submitter
Method: clinical testing
Peutz-Jeghers syndrome
Allele origin: germline
Invitae
Accession: SCV000260993.8
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Sep 16, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000602215.1
Submitted: (Aug 01, 2017)
Evidence details
Likely benign
(Jul 17, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000686617.1
Submitted: (Oct 26, 2017)
Evidence details
Benign
(Feb 23, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000696711.2
Submitted: (Nov 27, 2018)
Evidence details
Comment:
Variant summary: STK11 c.1284G>A 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
(Sep 25, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000889851.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Aug 29, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001157802.1
Submitted: (Aug 05, 2019)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Peutz-Jeghers syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001287493.1
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)

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 rs369097329...

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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 11, 2021