Name: rs755844
Published: September 21, 2022
License: Open Access

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.

rs755844

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:168116561 (GRCh38.p14) 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: G>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.233586 (61828/264690, TOPMED)
A=0.226661 (31723/139958, GnomAD)
A=0.20098 (5679/28256, 14KJPN) (+ 18 more)
A=0.20729 (4671/22534, ALFA)
A=0.20131 (3374/16760, 8.3KJPN)
A=0.2583 (1654/6404, 1000G_30x)
A=0.2580 (1292/5008, 1000G)
A=0.1705 (764/4480, Estonian)
A=0.1881 (725/3854, ALSPAC)
A=0.1837 (681/3708, TWINSUK)
A=0.2334 (684/2930, KOREAN)
A=0.2314 (424/1832, Korea1K)
A=0.1882 (213/1132, Daghestan)
A=0.205 (205/998, GoNL)
A=0.190 (114/600, NorthernSweden)
A=0.253 (83/328, HapMap)
G=0.433 (97/224, SGDP_PRJ)
A=0.227 (49/216, Qatari)
A=0.355 (76/214, Vietnamese)
A=0.12 (5/40, GENOME_DK)
G=0.42 (11/26, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: STK39 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	22534	G=0.79271	A=0.20729
European	Sub	16452	G=0.81036	A=0.18964
African	Sub	4078	G=0.7214	A=0.2786
African Others	Sub	144	G=0.639	A=0.361
African American	Sub	3934	G=0.7245	A=0.2755
Asian	Sub	116	G=0.707	A=0.293
East Asian	Sub	88	G=0.73	A=0.27
Other Asian	Sub	28	G=0.64	A=0.36
Latin American 1	Sub	154	G=0.727	A=0.273
Latin American 2	Sub	616	G=0.787	A=0.213
South Asian	Sub	98	G=0.87	A=0.13
Other	Sub	1020	G=0.8088	A=0.1912

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.766414	A=0.233586
gnomAD - Genomes	Global	Study-wide	139958	G=0.773339	A=0.226661
gnomAD - Genomes	European	Sub	75822	G=0.80614	A=0.19386
gnomAD - Genomes	African	Sub	41914	G=0.72324	A=0.27676
gnomAD - Genomes	American	Sub	13628	G=0.76475	A=0.23525
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.7470	A=0.2530
gnomAD - Genomes	East Asian	Sub	3122	G=0.7197	A=0.2803
gnomAD - Genomes	Other	Sub	2148	G=0.7663	A=0.2337
14KJPN	JAPANESE	Study-wide	28256	G=0.79902	A=0.20098
Allele Frequency Aggregator	Total	Global	22534	G=0.79271	A=0.20729
Allele Frequency Aggregator	European	Sub	16452	G=0.81036	A=0.18964
Allele Frequency Aggregator	African	Sub	4078	G=0.7214	A=0.2786
Allele Frequency Aggregator	Other	Sub	1020	G=0.8088	A=0.1912
Allele Frequency Aggregator	Latin American 2	Sub	616	G=0.787	A=0.213
Allele Frequency Aggregator	Latin American 1	Sub	154	G=0.727	A=0.273
Allele Frequency Aggregator	Asian	Sub	116	G=0.707	A=0.293
Allele Frequency Aggregator	South Asian	Sub	98	G=0.87	A=0.13
8.3KJPN	JAPANESE	Study-wide	16760	G=0.79869	A=0.20131
1000Genomes_30x	Global	Study-wide	6404	G=0.7417	A=0.2583
1000Genomes_30x	African	Sub	1786	G=0.7088	A=0.2912
1000Genomes_30x	Europe	Sub	1266	G=0.7994	A=0.2006
1000Genomes_30x	South Asian	Sub	1202	G=0.7712	A=0.2288
1000Genomes_30x	East Asian	Sub	1170	G=0.6889	A=0.3111
1000Genomes_30x	American	Sub	980	G=0.754	A=0.246
1000Genomes	Global	Study-wide	5008	G=0.7420	A=0.2580
1000Genomes	African	Sub	1322	G=0.7126	A=0.2874
1000Genomes	East Asian	Sub	1008	G=0.6954	A=0.3046
1000Genomes	Europe	Sub	1006	G=0.7922	A=0.2078
1000Genomes	South Asian	Sub	978	G=0.766	A=0.234
1000Genomes	American	Sub	694	G=0.759	A=0.241
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8295	A=0.1705
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.8119	A=0.1881
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.8163	A=0.1837
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.7666	A=0.2334
Korean Genome Project	KOREAN	Study-wide	1832	G=0.7686	A=0.2314
Genome-wide autozygosity in Daghestan	Global	Study-wide	1132	G=0.8118	A=0.1882
Genome-wide autozygosity in Daghestan	Daghestan	Sub	626	G=0.823	A=0.177
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	G=0.785	A=0.215
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	G=0.811	A=0.189
Genome-wide autozygosity in Daghestan	Europe	Sub	108	G=0.833	A=0.167
Genome-wide autozygosity in Daghestan	South Asian	Sub	96	G=0.76	A=0.24
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	G=0.81	A=0.19
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.795	A=0.205
Northern Sweden	ACPOP	Study-wide	600	G=0.810	A=0.190
HapMap	Global	Study-wide	328	G=0.747	A=0.253
HapMap	African	Sub	120	G=0.642	A=0.358
HapMap	American	Sub	120	G=0.800	A=0.200
HapMap	Asian	Sub	88	G=0.82	A=0.18
SGDP_PRJ	Global	Study-wide	224	G=0.433	A=0.567
Qatari	Global	Study-wide	216	G=0.773	A=0.227
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.645	A=0.355
The Danish reference pan genome	Danish	Study-wide	40	G=0.88	A=0.12
Siberian	Global	Study-wide	26	G=0.42	A=0.58

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.p14 chr 2	NC_000002.12:g.168116561G>A
GRCh37.p13 chr 2	NC_000002.11:g.168973071G>A
STK39 RefSeqGene	NG_052783.1:g.136035C>T

Gene: STK39, serine/threonine kinase 39 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
STK39 transcript variant 1	NM_013233.3:c.1089+12980C… NM_013233.3:c.1089+12980C>T	N/A	Intron Variant
STK39 transcript variant X2	XM_005246465.3:c.1089+129… XM_005246465.3:c.1089+12980C>T	N/A	Intron Variant
STK39 transcript variant X1	XM_017003813.3:c.1089+129… XM_017003813.3:c.1089+12980C>T	N/A	Intron Variant
STK39 transcript variant X3	XM_017003814.3:c.1089+129… XM_017003814.3:c.1089+12980C>T	N/A	Intron Variant
STK39 transcript variant X5	XM_017003816.3:c.1090-496… XM_017003816.3:c.1090-4965C>T	N/A	Intron Variant
STK39 transcript variant X6	XM_017003817.3:c.597+1298… XM_017003817.3:c.597+12980C>T	N/A	Intron Variant
STK39 transcript variant X2	XM_047443941.1:c.1089+129… XM_047443941.1:c.1089+12980C>T	N/A	Intron Variant
STK39 transcript variant X4	XM_047443944.1:c.783+1298… XM_047443944.1:c.783+12980C>T	N/A	Intron Variant

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.

Not Reported in ClinVar

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	G=	A
GRCh38.p14 chr 2	NC_000002.12:g.168116561=	NC_000002.12:g.168116561G>A
GRCh37.p13 chr 2	NC_000002.11:g.168973071=	NC_000002.11:g.168973071G>A
STK39 RefSeqGene	NG_052783.1:g.136035=	NG_052783.1:g.136035C>T
STK39 transcript	NM_013233.2:c.1089+12980=	NM_013233.2:c.1089+12980C>T
STK39 transcript variant 1	NM_013233.3:c.1089+12980=	NM_013233.3:c.1089+12980C>T
STK39 transcript variant X1	XM_005246465.1:c.1089+12980=	XM_005246465.1:c.1089+12980C>T
STK39 transcript variant X2	XM_005246465.3:c.1089+12980=	XM_005246465.3:c.1089+12980C>T
STK39 transcript variant X2	XM_005246466.1:c.597+12980=	XM_005246466.1:c.597+12980C>T
STK39 transcript variant X1	XM_017003813.3:c.1089+12980=	XM_017003813.3:c.1089+12980C>T
STK39 transcript variant X3	XM_017003814.3:c.1089+12980=	XM_017003814.3:c.1089+12980C>T
STK39 transcript variant X5	XM_017003816.3:c.1090-4965=	XM_017003816.3:c.1090-4965C>T
STK39 transcript variant X6	XM_017003817.3:c.597+12980=	XM_017003817.3:c.597+12980C>T
STK39 transcript variant X2	XM_047443941.1:c.1089+12980=	XM_047443941.1:c.1089+12980C>T
STK39 transcript variant X4	XM_047443944.1:c.783+12980=	XM_047443944.1:c.783+12980C>T

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#.

69 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss110220	Oct 05, 2000 (86)
2	PERLEGEN	ss23249847	Sep 20, 2004 (123)
3	AFFY	ss66005080	Dec 01, 2006 (127)
4	HGSV	ss77353047	Dec 07, 2007 (129)
5	HGSV	ss82422535	Dec 15, 2007 (130)
6	BCMHGSC_JDW	ss91431166	Mar 24, 2008 (129)
7	HUMANGENOME_JCVI	ss97097540	Feb 05, 2009 (130)
8	1000GENOMES	ss110224096	Jan 24, 2009 (130)
9	ENSEMBL	ss138573101	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss167392697	Jul 04, 2010 (132)
11	ILLUMINA	ss174417249	Jul 04, 2010 (132)
12	1000GENOMES	ss211038880	Jul 14, 2010 (132)
13	1000GENOMES	ss219641597	Jul 14, 2010 (132)
14	1000GENOMES	ss231459109	Jul 14, 2010 (132)
15	1000GENOMES	ss238949566	Jul 15, 2010 (132)
16	BL	ss253659740	May 09, 2011 (134)
17	GMI	ss276777480	May 04, 2012 (137)
18	PJP	ss292420315	May 09, 2011 (134)
19	ILLUMINA	ss537482372	Sep 08, 2015 (146)
20	TISHKOFF	ss556021380	Apr 25, 2013 (138)
21	SSMP	ss649672594	Apr 25, 2013 (138)
22	EVA-GONL	ss977619237	Aug 21, 2014 (142)
23	JMKIDD_LAB	ss1069686984	Aug 21, 2014 (142)
24	1000GENOMES	ss1300335764	Aug 21, 2014 (142)
25	HAMMER_LAB	ss1397311257	Sep 08, 2015 (146)
26	DDI	ss1428813419	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1579188092	Apr 01, 2015 (144)
28	EVA_DECODE	ss1587056614	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1605097614	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1648091647	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1797879078	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1920871477	Feb 12, 2016 (147)
33	GENOMED	ss1968947109	Jul 19, 2016 (147)
34	JJLAB	ss2020969436	Sep 14, 2016 (149)
35	USC_VALOUEV	ss2149034209	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2236388056	Dec 20, 2016 (150)
37	SYSTEMSBIOZJU	ss2624988673	Nov 08, 2017 (151)
38	GRF	ss2703671271	Nov 08, 2017 (151)
39	GNOMAD	ss2782556540	Nov 08, 2017 (151)
40	SWEGEN	ss2990826424	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3024245090	Nov 08, 2017 (151)
42	CSHL	ss3344594252	Nov 08, 2017 (151)
43	ILLUMINA	ss3628216189	Oct 11, 2018 (152)
44	ILLUMINA	ss3638300524	Oct 11, 2018 (152)
45	URBANLAB	ss3647200613	Oct 11, 2018 (152)
46	EGCUT_WGS	ss3658696227	Jul 13, 2019 (153)
47	EVA_DECODE	ss3705376917	Jul 13, 2019 (153)
48	ACPOP	ss3729085178	Jul 13, 2019 (153)
49	EVA	ss3757691764	Jul 13, 2019 (153)
50	KHV_HUMAN_GENOMES	ss3802050425	Jul 13, 2019 (153)
51	EVA	ss3827341373	Apr 25, 2020 (154)
52	SGDP_PRJ	ss3853925857	Apr 25, 2020 (154)
53	KRGDB	ss3899554000	Apr 25, 2020 (154)
54	KOGIC	ss3949453984	Apr 25, 2020 (154)
55	EVA	ss4017032891	Apr 26, 2021 (155)
56	TOPMED	ss4532949087	Apr 26, 2021 (155)
57	TOMMO_GENOMICS	ss5155012225	Apr 26, 2021 (155)
58	1000G_HIGH_COVERAGE	ss5250888104	Oct 12, 2022 (156)
59	EVA	ss5333952683	Oct 12, 2022 (156)
60	HUGCELL_USP	ss5450614024	Oct 12, 2022 (156)
61	EVA	ss5506680603	Oct 12, 2022 (156)
62	1000G_HIGH_COVERAGE	ss5527635465	Oct 12, 2022 (156)
63	SANFORD_IMAGENETICS	ss5630309837	Oct 12, 2022 (156)
64	TOMMO_GENOMICS	ss5685465090	Oct 12, 2022 (156)
65	YY_MCH	ss5802944011	Oct 12, 2022 (156)
66	EVA	ss5821145252	Oct 12, 2022 (156)
67	EVA	ss5852820649	Oct 12, 2022 (156)
68	EVA	ss5933386541	Oct 12, 2022 (156)
69	EVA	ss5956532063	Oct 12, 2022 (156)
70	1000Genomes	NC_000002.11 - 168973071	Oct 11, 2018 (152)
71	1000Genomes_30x	NC_000002.12 - 168116561	Oct 12, 2022 (156)
72	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 168973071	Oct 11, 2018 (152)
73	Genome-wide autozygosity in Daghestan	NC_000002.10 - 168681317	Apr 25, 2020 (154)
74	Genetic variation in the Estonian population	NC_000002.11 - 168973071	Oct 11, 2018 (152)
75	The Danish reference pan genome	NC_000002.11 - 168973071	Apr 25, 2020 (154)
76	gnomAD - Genomes	NC_000002.12 - 168116561	Apr 26, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000002.11 - 168973071	Apr 25, 2020 (154)
78	HapMap	NC_000002.12 - 168116561	Apr 25, 2020 (154)
79	KOREAN population from KRGDB	NC_000002.11 - 168973071	Apr 25, 2020 (154)
80	Korean Genome Project	NC_000002.12 - 168116561	Apr 25, 2020 (154)
81	Northern Sweden	NC_000002.11 - 168973071	Jul 13, 2019 (153)
82	Qatari	NC_000002.11 - 168973071	Apr 25, 2020 (154)
83	SGDP_PRJ	NC_000002.11 - 168973071	Apr 25, 2020 (154)
84	Siberian	NC_000002.11 - 168973071	Apr 25, 2020 (154)
85	8.3KJPN	NC_000002.11 - 168973071	Apr 26, 2021 (155)
86	14KJPN	NC_000002.12 - 168116561	Oct 12, 2022 (156)
87	TopMed	NC_000002.12 - 168116561	Apr 26, 2021 (155)
88	UK 10K study - Twins	NC_000002.11 - 168973071	Oct 11, 2018 (152)
89	A Vietnamese Genetic Variation Database	NC_000002.11 - 168973071	Jul 13, 2019 (153)
90	ALFA	NC_000002.12 - 168116561	Apr 26, 2021 (155)

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).

Associated ID	History Updated (Build)
rs16854741	Oct 07, 2004 (123)
rs59583693	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77353047, ss82422535	NC_000002.9:168798577:G:A	NC_000002.12:168116560:G:A	(self)
261135, ss91431166, ss110224096, ss167392697, ss211038880, ss253659740, ss276777480, ss292420315, ss1397311257, ss1587056614	NC_000002.10:168681316:G:A	NC_000002.12:168116560:G:A	(self)
11389612, 6283312, 4434475, 5353031, 2760257, 6731394, 2370043, 2913407, 5942837, 1550563, 12981532, 6283312, 1365261, ss219641597, ss231459109, ss238949566, ss537482372, ss556021380, ss649672594, ss977619237, ss1069686984, ss1300335764, ss1428813419, ss1579188092, ss1605097614, ss1648091647, ss1797879078, ss1920871477, ss1968947109, ss2020969436, ss2149034209, ss2624988673, ss2703671271, ss2782556540, ss2990826424, ss3344594252, ss3628216189, ss3638300524, ss3658696227, ss3729085178, ss3757691764, ss3827341373, ss3853925857, ss3899554000, ss4017032891, ss5155012225, ss5333952683, ss5506680603, ss5630309837, ss5821145252, ss5956532063	NC_000002.11:168973070:G:A	NC_000002.12:168116560:G:A	(self)
15161400, 81201954, 1944034, 5831985, 19302194, 336771966, 5816633658, ss2236388056, ss3024245090, ss3647200613, ss3705376917, ss3802050425, ss3949453984, ss4532949087, ss5250888104, ss5450614024, ss5527635465, ss5685465090, ss5802944011, ss5852820649, ss5933386541	NC_000002.12:168116560:G:A	NC_000002.12:168116560:G:A	(self)
ss110220, ss23249847, ss66005080, ss97097540, ss138573101, ss174417249	NT_005403.17:19182488:G:A	NC_000002.12:168116560:G:A	(self)

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

No publications for rs755844

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs755844