Name: rs17778577
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.

rs17778577

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:167985135 (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: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.335113 (88701/264690, TOPMED)
C=0.357402 (50057/140058, GnomAD)
C=0.08335 (2355/28256, 14KJPN) (+ 18 more)
C=0.38801 (7061/18198, ALFA)
C=0.08288 (1389/16760, 8.3KJPN)
C=0.2545 (1630/6404, 1000G_30x)
C=0.2454 (1229/5008, 1000G)
T=0.5000 (2240/4480, Estonian)
C=0.5000 (2240/4480, Estonian)
C=0.4050 (1561/3854, ALSPAC)
C=0.3908 (1449/3708, TWINSUK)
C=0.0329 (96/2922, KOREAN)
C=0.0278 (51/1832, Korea1K)
C=0.393 (392/998, GoNL)
C=0.380 (228/600, NorthernSweden)
C=0.285 (94/330, HapMap)
C=0.324 (70/216, Qatari)
C=0.046 (10/216, Vietnamese)
T=0.426 (87/204, SGDP_PRJ)
C=0.45 (18/40, GENOME_DK)
T=0.44 (8/18, 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	18198	T=0.61199	A=0.00000, C=0.38801
European	Sub	13844	T=0.57852	A=0.00000, C=0.42148
African	Sub	2700	T=0.7278	A=0.0000, C=0.2722
African Others	Sub	108	T=0.833	A=0.000, C=0.167
African American	Sub	2592	T=0.7234	A=0.0000, C=0.2766
Asian	Sub	112	T=0.973	A=0.000, C=0.027
East Asian	Sub	86	T=0.97	A=0.00, C=0.03
Other Asian	Sub	26	T=1.00	A=0.00, C=0.00
Latin American 1	Sub	146	T=0.671	A=0.000, C=0.329
Latin American 2	Sub	610	T=0.661	A=0.000, C=0.339
South Asian	Sub	98	T=0.81	A=0.00, C=0.19
Other	Sub	688	T=0.689	A=0.000, C=0.311

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	T=0.664887	C=0.335113
gnomAD - Genomes	Global	Study-wide	140058	T=0.642598	C=0.357402
gnomAD - Genomes	European	Sub	75860	T=0.58845	C=0.41155
gnomAD - Genomes	African	Sub	41952	T=0.69768	C=0.30232
gnomAD - Genomes	American	Sub	13644	T=0.67737	C=0.32263
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.6933	C=0.3067
gnomAD - Genomes	East Asian	Sub	3128	T=0.9706	C=0.0294
gnomAD - Genomes	Other	Sub	2152	T=0.7021	C=0.2979
14KJPN	JAPANESE	Study-wide	28256	T=0.91665	C=0.08335
Allele Frequency Aggregator	Total	Global	18198	T=0.61199	A=0.00000, C=0.38801
Allele Frequency Aggregator	European	Sub	13844	T=0.57852	A=0.00000, C=0.42148
Allele Frequency Aggregator	African	Sub	2700	T=0.7278	A=0.0000, C=0.2722
Allele Frequency Aggregator	Other	Sub	688	T=0.689	A=0.000, C=0.311
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.661	A=0.000, C=0.339
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.671	A=0.000, C=0.329
Allele Frequency Aggregator	Asian	Sub	112	T=0.973	A=0.000, C=0.027
Allele Frequency Aggregator	South Asian	Sub	98	T=0.81	A=0.00, C=0.19
8.3KJPN	JAPANESE	Study-wide	16760	T=0.91712	C=0.08288
1000Genomes_30x	Global	Study-wide	6404	T=0.7455	C=0.2545
1000Genomes_30x	African	Sub	1786	T=0.7066	C=0.2934
1000Genomes_30x	Europe	Sub	1266	T=0.6122	C=0.3878
1000Genomes_30x	South Asian	Sub	1202	T=0.7845	C=0.2155
1000Genomes_30x	East Asian	Sub	1170	T=0.9718	C=0.0282
1000Genomes_30x	American	Sub	980	T=0.670	C=0.330
1000Genomes	Global	Study-wide	5008	T=0.7546	C=0.2454
1000Genomes	African	Sub	1322	T=0.7088	C=0.2912
1000Genomes	East Asian	Sub	1008	T=0.9702	C=0.0298
1000Genomes	Europe	Sub	1006	T=0.6262	C=0.3738
1000Genomes	South Asian	Sub	978	T=0.784	C=0.216
1000Genomes	American	Sub	694	T=0.673	C=0.327
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5000	C=0.5000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5950	C=0.4050
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.6092	C=0.3908
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9671	C=0.0329
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9722	C=0.0278
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.607	C=0.393
Northern Sweden	ACPOP	Study-wide	600	T=0.620	C=0.380
HapMap	Global	Study-wide	330	T=0.715	C=0.285
HapMap	African	Sub	120	T=0.683	C=0.317
HapMap	American	Sub	120	T=0.575	C=0.425
HapMap	Asian	Sub	90	T=0.94	C=0.06
Qatari	Global	Study-wide	216	T=0.676	C=0.324
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.954	C=0.046
SGDP_PRJ	Global	Study-wide	204	T=0.426	C=0.574
The Danish reference pan genome	Danish	Study-wide	40	T=0.55	C=0.45
Siberian	Global	Study-wide	18	T=0.44	C=0.56

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.167985135T>A
GRCh38.p14 chr 2	NC_000002.12:g.167985135T>C
GRCh37.p13 chr 2	NC_000002.11:g.168841645T>A
GRCh37.p13 chr 2	NC_000002.11:g.168841645T>C
STK39 RefSeqGene	NG_052783.1:g.267461A>T
STK39 RefSeqGene	NG_052783.1:g.267461A>G

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

Molecule type	Change	Amino acid[Codon]	SO Term
STK39 transcript variant 1	NM_013233.3:c.1499-20409A… NM_013233.3:c.1499-20409A>T	N/A	Intron Variant
STK39 transcript variant X2	XM_005246465.3:c.1436-204… XM_005246465.3:c.1436-20409A>T	N/A	Intron Variant
STK39 transcript variant X1	XM_017003813.3:c.1499-204… XM_017003813.3:c.1499-20409A>T	N/A	Intron Variant
STK39 transcript variant X6	XM_017003817.3:c.1007-204… XM_017003817.3:c.1007-20409A>T	N/A	Intron Variant
STK39 transcript variant X2	XM_047443941.1:c.1436-204… XM_047443941.1:c.1436-20409A>T	N/A	Intron Variant
STK39 transcript variant X4	XM_047443944.1:c.1193-204… XM_047443944.1:c.1193-20409A>T	N/A	Intron Variant
STK39 transcript variant X3	XM_017003814.3:c.	N/A	Genic Downstream Transcript Variant
STK39 transcript variant X5	XM_017003816.3:c.	N/A	Genic Downstream Transcript 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	T=	A	C
GRCh38.p14 chr 2	NC_000002.12:g.167985135=	NC_000002.12:g.167985135T>A	NC_000002.12:g.167985135T>C
GRCh37.p13 chr 2	NC_000002.11:g.168841645=	NC_000002.11:g.168841645T>A	NC_000002.11:g.168841645T>C
STK39 RefSeqGene	NG_052783.1:g.267461=	NG_052783.1:g.267461A>T	NG_052783.1:g.267461A>G
STK39 transcript	NM_013233.2:c.1499-20409=	NM_013233.2:c.1499-20409A>T	NM_013233.2:c.1499-20409A>G
STK39 transcript variant 1	NM_013233.3:c.1499-20409=	NM_013233.3:c.1499-20409A>T	NM_013233.3:c.1499-20409A>G
STK39 transcript variant X1	XM_005246465.1:c.1436-20409=	XM_005246465.1:c.1436-20409A>T	XM_005246465.1:c.1436-20409A>G
STK39 transcript variant X2	XM_005246465.3:c.1436-20409=	XM_005246465.3:c.1436-20409A>T	XM_005246465.3:c.1436-20409A>G
STK39 transcript variant X2	XM_005246466.1:c.1007-20409=	XM_005246466.1:c.1007-20409A>T	XM_005246466.1:c.1007-20409A>G
STK39 transcript variant X1	XM_017003813.3:c.1499-20409=	XM_017003813.3:c.1499-20409A>T	XM_017003813.3:c.1499-20409A>G
STK39 transcript variant X6	XM_017003817.3:c.1007-20409=	XM_017003817.3:c.1007-20409A>T	XM_017003817.3:c.1007-20409A>G
STK39 transcript variant X2	XM_047443941.1:c.1436-20409=	XM_047443941.1:c.1436-20409A>T	XM_047443941.1:c.1436-20409A>G
STK39 transcript variant X4	XM_047443944.1:c.1193-20409=	XM_047443944.1:c.1193-20409A>T	XM_047443944.1:c.1193-20409A>G

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#.

61 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss24306203	Sep 20, 2004 (123)
2	HGSV	ss77610039	Dec 07, 2007 (129)
3	HGSV	ss85753444	Dec 14, 2007 (130)
4	1000GENOMES	ss110222430	Jan 24, 2009 (130)
5	ILLUMINA-UK	ss117961081	Feb 14, 2009 (130)
6	COMPLETE_GENOMICS	ss165575641	Jul 04, 2010 (132)
7	COMPLETE_GENOMICS	ss167391718	Jul 04, 2010 (132)
8	BUSHMAN	ss201341114	Jul 04, 2010 (132)
9	BCM-HGSC-SUB	ss205661695	Jul 04, 2010 (132)
10	1000GENOMES	ss211038617	Jul 14, 2010 (132)
11	1000GENOMES	ss219640922	Jul 14, 2010 (132)
12	1000GENOMES	ss231458748	Jul 14, 2010 (132)
13	1000GENOMES	ss238949236	Jul 15, 2010 (132)
14	GMI	ss276777114	May 04, 2012 (137)
15	GMI	ss284480977	Apr 25, 2013 (138)
16	TISHKOFF	ss556020607	Apr 25, 2013 (138)
17	SSMP	ss649672009	Apr 25, 2013 (138)
18	EVA-GONL	ss977618312	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1069686181	Aug 21, 2014 (142)
20	1000GENOMES	ss1300331811	Aug 21, 2014 (142)
21	DDI	ss1428813078	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1579187713	Apr 01, 2015 (144)
23	EVA_DECODE	ss1587055617	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1605095531	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1648089564	Apr 01, 2015 (144)
26	WEILL_CORNELL_DGM	ss1920870461	Feb 12, 2016 (147)
27	GENOMED	ss1968946858	Jul 19, 2016 (147)
28	JJLAB	ss2020968895	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2149033712	Dec 20, 2016 (150)
30	HUMAN_LONGEVITY	ss2236380095	Dec 20, 2016 (150)
31	GRF	ss2703670759	Nov 08, 2017 (151)
32	GNOMAD	ss2782546232	Nov 08, 2017 (151)
33	SWEGEN	ss2990825117	Nov 08, 2017 (151)
34	BIOINF_KMB_FNS_UNIBA	ss3024244841	Nov 08, 2017 (151)
35	CSHL	ss3344593919	Nov 08, 2017 (151)
36	EGCUT_WGS	ss3658694765	Jul 13, 2019 (153)
37	EVA_DECODE	ss3705375110	Jul 13, 2019 (153)
38	ACPOP	ss3729084456	Jul 13, 2019 (153)
39	EVA	ss3757690613	Jul 13, 2019 (153)
40	PACBIO	ss3784060012	Jul 13, 2019 (153)
41	PACBIO	ss3789613020	Jul 13, 2019 (153)
42	PACBIO	ss3794486015	Jul 13, 2019 (153)
43	KHV_HUMAN_GENOMES	ss3802049198	Jul 13, 2019 (153)
44	EVA	ss3827340875	Apr 25, 2020 (154)
45	EVA	ss3837088174	Apr 25, 2020 (154)
46	EVA	ss3842507940	Apr 25, 2020 (154)
47	SGDP_PRJ	ss3853923997	Apr 25, 2020 (154)
48	KRGDB	ss3899552096	Apr 25, 2020 (154)
49	KOGIC	ss3949452194	Apr 25, 2020 (154)
50	TOPMED	ss4532917076	Apr 26, 2021 (155)
51	TOMMO_GENOMICS	ss5155008422	Apr 26, 2021 (155)
52	1000G_HIGH_COVERAGE	ss5250884828	Oct 12, 2022 (156)
53	HUGCELL_USP	ss5450610921	Oct 12, 2022 (156)
54	EVA	ss5506680162	Oct 12, 2022 (156)
55	1000G_HIGH_COVERAGE	ss5527630561	Oct 12, 2022 (156)
56	SANFORD_IMAGENETICS	ss5630307887	Oct 12, 2022 (156)
57	TOMMO_GENOMICS	ss5685460246	Oct 12, 2022 (156)
58	YY_MCH	ss5802943337	Oct 12, 2022 (156)
59	EVA	ss5821144104	Oct 12, 2022 (156)
60	EVA	ss5933382452	Oct 12, 2022 (156)
61	EVA	ss5956529869	Oct 12, 2022 (156)
62	1000Genomes	NC_000002.11 - 168841645	Oct 11, 2018 (152)
63	1000Genomes_30x	NC_000002.12 - 167985135	Oct 12, 2022 (156)
64	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 168841645	Oct 11, 2018 (152)
65	Genetic variation in the Estonian population	NC_000002.11 - 168841645	Oct 11, 2018 (152)
66	The Danish reference pan genome	NC_000002.11 - 168841645	Apr 25, 2020 (154)
67	gnomAD - Genomes	NC_000002.12 - 167985135	Apr 26, 2021 (155)
68	Genome of the Netherlands Release 5	NC_000002.11 - 168841645	Apr 25, 2020 (154)
69	HapMap	NC_000002.12 - 167985135	Apr 25, 2020 (154)
70	KOREAN population from KRGDB	NC_000002.11 - 168841645	Apr 25, 2020 (154)
71	Korean Genome Project	NC_000002.12 - 167985135	Apr 25, 2020 (154)
72	Northern Sweden	NC_000002.11 - 168841645	Jul 13, 2019 (153)
73	Qatari	NC_000002.11 - 168841645	Apr 25, 2020 (154)
74	SGDP_PRJ	NC_000002.11 - 168841645	Apr 25, 2020 (154)
75	Siberian	NC_000002.11 - 168841645	Apr 25, 2020 (154)
76	8.3KJPN	NC_000002.11 - 168841645	Apr 26, 2021 (155)
77	14KJPN	NC_000002.12 - 167985135	Oct 12, 2022 (156)
78	TopMed	NC_000002.12 - 167985135	Apr 26, 2021 (155)
79	UK 10K study - Twins	NC_000002.11 - 168841645	Oct 11, 2018 (152)
80	A Vietnamese Genetic Variation Database	NC_000002.11 - 168841645	Jul 13, 2019 (153)
81	ALFA	NC_000002.12 - 167985135	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)
rs57753758	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
9151285847	NC_000002.12:167985134:T:A	NC_000002.12:167985134:T:A	(self)
ss77610039, ss85753444	NC_000002.9:168667151:T:C	NC_000002.12:167985134:T:C	(self)
ss110222430, ss117961081, ss165575641, ss167391718, ss201341114, ss205661695, ss211038617, ss276777114, ss284480977, ss1587055617	NC_000002.10:168549890:T:C	NC_000002.12:167985134:T:C	(self)
11385540, 6281038, 4433013, 5352652, 2759341, 6729490, 2369321, 2912391, 5940977, 1550066, 12977729, 6281038, 1364771, ss219640922, ss231458748, ss238949236, ss556020607, ss649672009, ss977618312, ss1069686181, ss1300331811, ss1428813078, ss1579187713, ss1605095531, ss1648089564, ss1920870461, ss1968946858, ss2020968895, ss2149033712, ss2703670759, ss2782546232, ss2990825117, ss3344593919, ss3658694765, ss3729084456, ss3757690613, ss3784060012, ss3789613020, ss3794486015, ss3827340875, ss3837088174, ss3853923997, ss3899552096, ss5155008422, ss5506680162, ss5630307887, ss5821144104, ss5956529869	NC_000002.11:168841644:T:C	NC_000002.12:167985134:T:C	(self)
15156496, 81176281, 1943785, 5830195, 19297350, 336739955, 9151285847, ss2236380095, ss3024244841, ss3705375110, ss3802049198, ss3842507940, ss3949452194, ss4532917076, ss5250884828, ss5450610921, ss5527630561, ss5685460246, ss5802943337, ss5933382452	NC_000002.12:167985134:T:C	NC_000002.12:167985134:T:C	(self)
ss24306203	NT_005403.17:19051062:T:C	NC_000002.12:167985134:T:C	(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 rs17778577

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

rs17778577