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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs587778695

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr19:1223152 (GRCh38.p13) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000030 (8/264690, TOPMED)
T=0.000036 (5/140302, GnomAD)
T=0.00000 (0/14050, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
STK11 : Missense Variant
Publications
3 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p13 chr 19 NC_000019.10:g.1223152C>A
GRCh38.p13 chr 19 NC_000019.10:g.1223152C>G
GRCh38.p13 chr 19 NC_000019.10:g.1223152C>T
GRCh37.p13 chr 19 NC_000019.9:g.1223151C>A
GRCh37.p13 chr 19 NC_000019.9:g.1223151C>G
GRCh37.p13 chr 19 NC_000019.9:g.1223151C>T
STK11 RefSeqGene (LRG_319) NG_007460.2:g.38746C>A
STK11 RefSeqGene (LRG_319) NG_007460.2:g.38746C>G
STK11 RefSeqGene (LRG_319) NG_007460.2:g.38746C>T
Gene: STK11, serine/threonine kinase 11 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
STK11 transcript NM_000455.5:c.1088C>A T [ACT] > N [AAT] Coding Sequence Variant
serine/threonine-protein kinase STK11 NP_000446.1:p.Thr363Asn T (Thr) > N (Asn) Missense Variant
STK11 transcript NM_000455.5:c.1088C>G T [ACT] > S [AGT] Coding Sequence Variant
serine/threonine-protein kinase STK11 NP_000446.1:p.Thr363Ser T (Thr) > S (Ser) Missense Variant
STK11 transcript NM_000455.5:c.1088C>T T [ACT] > I [ATT] Coding Sequence Variant
serine/threonine-protein kinase STK11 NP_000446.1:p.Thr363Ile T (Thr) > I (Ile) Missense Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: A (allele ID: 814902 )
ClinVar Accession Disease Names Clinical Significance
RCV001009872.1 Hereditary cancer-predisposing syndrome Uncertain-Significance
Allele: G (allele ID: 928837 )
ClinVar Accession Disease Names Clinical Significance
RCV001221717.2 Peutz-Jeghers syndrome Uncertain-Significance
Allele: T (allele ID: 139016 )
ClinVar Accession Disease Names Clinical Significance
RCV000122092.2 not specified Not-Provided
RCV000206210.7 Peutz-Jeghers syndrome Conflicting-Interpretations-Of-Pathogenicity
RCV000219976.5 Hereditary cancer-predisposing syndrome Uncertain-Significance
RCV000656983.3 not provided Uncertain-Significance

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 14050 C=1.00000 T=0.00000
European Sub 9690 C=1.0000 T=0.0000
African Sub 2898 C=1.0000 T=0.0000
African Others Sub 114 C=1.000 T=0.000
African American Sub 2784 C=1.0000 T=0.0000
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 496 C=1.000 T=0.000


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.999970 T=0.000030
gnomAD - Genomes Global Study-wide 140302 C=0.999964 T=0.000036
gnomAD - Genomes European Sub 75960 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 42064 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13670 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=0.9984 T=0.0016
gnomAD - Genomes Other Sub 2150 C=1.0000 T=0.0000
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= A G T
GRCh38.p13 chr 19 NC_000019.10:g.1223152= NC_000019.10:g.1223152C>A NC_000019.10:g.1223152C>G NC_000019.10:g.1223152C>T
GRCh37.p13 chr 19 NC_000019.9:g.1223151= NC_000019.9:g.1223151C>A NC_000019.9:g.1223151C>G NC_000019.9:g.1223151C>T
STK11 RefSeqGene (LRG_319) NG_007460.2:g.38746= NG_007460.2:g.38746C>A NG_007460.2:g.38746C>G NG_007460.2:g.38746C>T
STK11 transcript NM_000455.5:c.1088= NM_000455.5:c.1088C>A NM_000455.5:c.1088C>G NM_000455.5:c.1088C>T
STK11 transcript NM_000455.4:c.1088= NM_000455.4:c.1088C>A NM_000455.4:c.1088C>G NM_000455.4:c.1088C>T
serine/threonine-protein kinase STK11 NP_000446.1:p.Thr363= NP_000446.1:p.Thr363Asn NP_000446.1:p.Thr363Ser NP_000446.1:p.Thr363Ile
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

10 SubSNP, 7 Frequency, 6 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss1457610787 Nov 23, 2014 (142)
2 EVA_EXAC ss1693223213 Apr 01, 2015 (144)
3 EVA_EXAC ss1693223214 Apr 01, 2015 (144)
4 GNOMAD ss2743408495 Nov 08, 2017 (151)
5 GNOMAD ss2749996245 Nov 08, 2017 (151)
6 GNOMAD ss2959533964 Nov 08, 2017 (151)
7 TOPMED ss3285792070 Nov 08, 2017 (151)
8 EVA ss3755716345 Jul 13, 2019 (153)
9 TOPMED ss5065409248 Apr 27, 2021 (155)
10 EVA ss5236952530 Apr 27, 2021 (155)
11 ExAC

Submission ignored due to conflicting rows:
Row 3700346 (NC_000019.9:1223150:C:C 99567/99568, NC_000019.9:1223150:C:A 1/99568)
Row 3700347 (NC_000019.9:1223150:C:C 99559/99568, NC_000019.9:1223150:C:T 9/99568)

- Oct 12, 2018 (152)
12 ExAC

Submission ignored due to conflicting rows:
Row 3700346 (NC_000019.9:1223150:C:C 99567/99568, NC_000019.9:1223150:C:A 1/99568)
Row 3700347 (NC_000019.9:1223150:C:C 99559/99568, NC_000019.9:1223150:C:T 9/99568)

- Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000019.10 - 1223152 Apr 27, 2021 (155)
14 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 12721874 (NC_000019.9:1223150:C:C 244325/244326, NC_000019.9:1223150:C:A 1/244326)
Row 12721875 (NC_000019.9:1223150:C:C 244306/244326, NC_000019.9:1223150:C:T 20/244326)

- Jul 13, 2019 (153)
15 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 12721874 (NC_000019.9:1223150:C:C 244325/244326, NC_000019.9:1223150:C:A 1/244326)
Row 12721875 (NC_000019.9:1223150:C:C 244306/244326, NC_000019.9:1223150:C:T 20/244326)

- Jul 13, 2019 (153)
16 TopMed NC_000019.10 - 1223152 Apr 27, 2021 (155)
17 ALFA NC_000019.10 - 1223152 Apr 27, 2021 (155)
18 ClinVar RCV000122092.2 Oct 12, 2018 (152)
19 ClinVar RCV000206210.7 Apr 27, 2021 (155)
20 ClinVar RCV000219976.5 Apr 27, 2021 (155)
21 ClinVar RCV000656983.3 Apr 27, 2021 (155)
22 ClinVar RCV001009872.1 Apr 27, 2020 (154)
23 ClinVar RCV001221717.2 Apr 27, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1693223214, ss2743408495 NC_000019.9:1223150:C:A NC_000019.10:1223151:C:A (self)
RCV001009872.1 NC_000019.10:1223151:C:A NC_000019.10:1223151:C:A (self)
RCV001221717.2 NC_000019.10:1223151:C:G NC_000019.10:1223151:C:G
ss1693223213, ss2743408495, ss2749996245, ss2959533964, ss3755716345 NC_000019.9:1223150:C:T NC_000019.10:1223151:C:T (self)
RCV000122092.2, RCV000206210.7, RCV000219976.5, RCV000656983.3, 531768844, 175278209, 280954912, 7483623076, ss1457610787, ss3285792070, ss5065409248, ss5236952530 NC_000019.10:1223151:C:T NC_000019.10:1223151:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

3 citations for rs587778695
PMID Title Author Year Journal
22942091 Two variants in STK11 gene in Chinese patients with Peutz-Jeghers syndrome. Liu D et al. 2012 Journal of genetics
24728327 Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. Bodian DL et al. 2014 PloS one
25186627 Frequency of mutations in individuals with breast cancer referred for BRCA1 and BRCA2 testing using next-generation sequencing with a 25-gene panel. Tung N et al. 2015 Cancer
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post596+ae089ad