Name: rs10422590
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.

rs10422590

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:588516 (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: A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.336216 (88993/264690, TOPMED)
G=0.22094 (13242/59936, ALFA)
G=0.06115 (1728/28258, 14KJPN) (+ 17 more)
G=0.06128 (1027/16760, 8.3KJPN)
G=0.3207 (2054/6404, 1000G_30x)
G=0.3045 (1525/5008, 1000G)
G=0.2286 (1024/4480, Estonian)
G=0.2161 (833/3854, ALSPAC)
G=0.2050 (760/3708, TWINSUK)
G=0.0654 (191/2922, KOREAN)
G=0.0722 (130/1800, Korea1K)
G=0.2839 (452/1592, HapMap)
G=0.216 (216/998, GoNL)
G=0.245 (147/600, NorthernSweden)
A=0.395 (87/220, SGDP_PRJ)
G=0.255 (55/216, Qatari)
G=0.065 (14/216, Vietnamese)
G=0.17 (7/40, GENOME_DK)
A=0.50 (7/14, Siberian)
G=0.50 (7/14, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: HCN2 : 2KB Upstream 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	59936	A=0.77906	G=0.22094, T=0.00000
European	Sub	47356	A=0.80520	G=0.19480, T=0.00000
African	Sub	3750	A=0.5040	G=0.4960, T=0.0000
African Others	Sub	116	A=0.448	G=0.552, T=0.000
African American	Sub	3634	A=0.5058	G=0.4942, T=0.0000
Asian	Sub	422	A=0.941	G=0.059, T=0.000
East Asian	Sub	358	A=0.936	G=0.064, T=0.000
Other Asian	Sub	64	A=0.97	G=0.03, T=0.00
Latin American 1	Sub	500	A=0.652	G=0.348, T=0.000
Latin American 2	Sub	4570	A=0.7339	G=0.2661, T=0.0000
South Asian	Sub	118	A=0.924	G=0.076, T=0.000
Other	Sub	3220	A=0.7724	G=0.2276, T=0.0000

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	A=0.663784	G=0.336216
Allele Frequency Aggregator	Total	Global	59936	A=0.77906	G=0.22094, T=0.00000
Allele Frequency Aggregator	European	Sub	47356	A=0.80520	G=0.19480, T=0.00000
Allele Frequency Aggregator	Latin American 2	Sub	4570	A=0.7339	G=0.2661, T=0.0000
Allele Frequency Aggregator	African	Sub	3750	A=0.5040	G=0.4960, T=0.0000
Allele Frequency Aggregator	Other	Sub	3220	A=0.7724	G=0.2276, T=0.0000
Allele Frequency Aggregator	Latin American 1	Sub	500	A=0.652	G=0.348, T=0.000
Allele Frequency Aggregator	Asian	Sub	422	A=0.941	G=0.059, T=0.000
Allele Frequency Aggregator	South Asian	Sub	118	A=0.924	G=0.076, T=0.000
14KJPN	JAPANESE	Study-wide	28258	A=0.93885	G=0.06115
8.3KJPN	JAPANESE	Study-wide	16760	A=0.93872	G=0.06128
1000Genomes_30x	Global	Study-wide	6404	A=0.6793	G=0.3207
1000Genomes_30x	African	Sub	1786	A=0.3656	G=0.6344
1000Genomes_30x	Europe	Sub	1266	A=0.8033	G=0.1967
1000Genomes_30x	South Asian	Sub	1202	A=0.7754	G=0.2246
1000Genomes_30x	East Asian	Sub	1170	A=0.9359	G=0.0641
1000Genomes_30x	American	Sub	980	A=0.666	G=0.334
1000Genomes	Global	Study-wide	5008	A=0.6955	G=0.3045
1000Genomes	African	Sub	1322	A=0.3759	G=0.6241
1000Genomes	East Asian	Sub	1008	A=0.9405	G=0.0595
1000Genomes	Europe	Sub	1006	A=0.8012	G=0.1988
1000Genomes	South Asian	Sub	978	A=0.784	G=0.216
1000Genomes	American	Sub	694	A=0.670	G=0.330
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7714	G=0.2286
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7839	G=0.2161
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7950	G=0.2050
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.9346	G=0.0654
Korean Genome Project	KOREAN	Study-wide	1800	A=0.9278	G=0.0722
HapMap	Global	Study-wide	1592	A=0.7161	G=0.2839
HapMap	American	Sub	764	A=0.802	G=0.198
HapMap	African	Sub	398	A=0.374	G=0.626
HapMap	Asian	Sub	254	A=0.945	G=0.055
HapMap	Europe	Sub	176	A=0.784	G=0.216
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.784	G=0.216
Northern Sweden	ACPOP	Study-wide	600	A=0.755	G=0.245
SGDP_PRJ	Global	Study-wide	220	A=0.395	G=0.605
Qatari	Global	Study-wide	216	A=0.745	G=0.255
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.935	G=0.065
The Danish reference pan genome	Danish	Study-wide	40	A=0.82	G=0.17
Siberian	Global	Study-wide	14	A=0.50	G=0.50

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 19	NC_000019.10:g.588516A>G
GRCh38.p14 chr 19	NC_000019.10:g.588516A>T
GRCh37.p13 chr 19	NC_000019.9:g.588516A>G
GRCh37.p13 chr 19	NC_000019.9:g.588516A>T
HCN2 RefSeqGene	NG_052810.1:g.3624A>G
HCN2 RefSeqGene	NG_052810.1:g.3624A>T

Gene: HCN2, hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
HCN2 transcript	NM_001194.4:c.	N/A	Upstream 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	A=	G	T
GRCh38.p14 chr 19	NC_000019.10:g.588516=	NC_000019.10:g.588516A>G	NC_000019.10:g.588516A>T
GRCh37.p13 chr 19	NC_000019.9:g.588516=	NC_000019.9:g.588516A>G	NC_000019.9:g.588516A>T
HCN2 RefSeqGene	NG_052810.1:g.3624=	NG_052810.1:g.3624A>G	NG_052810.1:g.3624A>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#.

75 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss14723130	Dec 05, 2003 (119)
2	ABI	ss44190435	Mar 15, 2006 (126)
3	ILLUMINA	ss75266444	Dec 07, 2007 (129)
4	HGSV	ss84268790	Dec 15, 2007 (130)
5	HGSV	ss85593541	Dec 15, 2007 (130)
6	HUMANGENOME_JCVI	ss96284586	Feb 06, 2009 (130)
7	1000GENOMES	ss114725817	Jan 25, 2009 (130)
8	KRIBB_YJKIM	ss119621626	Dec 01, 2009 (131)
9	ENSEMBL	ss143814672	Dec 01, 2009 (131)
10	GMI	ss155512090	Dec 01, 2009 (131)
11	ILLUMINA	ss159892103	Dec 01, 2009 (131)
12	ILLUMINA	ss170057857	Jul 04, 2010 (132)
13	BUSHMAN	ss203572072	Jul 04, 2010 (132)
14	1000GENOMES	ss228003033	Jul 14, 2010 (132)
15	1000GENOMES	ss237574191	Jul 15, 2010 (132)
16	1000GENOMES	ss243802110	Jul 15, 2010 (132)
17	BL	ss255423243	May 09, 2011 (134)
18	GMI	ss283093809	May 04, 2012 (137)
19	PJP	ss292171734	May 09, 2011 (134)
20	ILLUMINA	ss479262898	May 04, 2012 (137)
21	ILLUMINA	ss479265831	May 04, 2012 (137)
22	ILLUMINA	ss479634246	Sep 08, 2015 (146)
23	ILLUMINA	ss484432128	May 04, 2012 (137)
24	TISHKOFF	ss565801103	Apr 25, 2013 (138)
25	ILLUMINA	ss782662530	Aug 21, 2014 (142)
26	EVA-GONL	ss993999699	Aug 21, 2014 (142)
27	1000GENOMES	ss1362014164	Aug 21, 2014 (142)
28	DDI	ss1428307701	Apr 01, 2015 (144)
29	EVA_GENOME_DK	ss1578520637	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1637410723	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1680404756	Apr 01, 2015 (144)
32	EVA_DECODE	ss1698062651	Apr 01, 2015 (144)
33	EVA_SVP	ss1713646110	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1809167653	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1937474966	Feb 12, 2016 (147)
36	JJLAB	ss2029513428	Sep 14, 2016 (149)
37	USC_VALOUEV	ss2158023135	Dec 20, 2016 (150)
38	HUMAN_LONGEVITY	ss2223604672	Dec 20, 2016 (150)
39	GRF	ss2702627737	Nov 08, 2017 (151)
40	GNOMAD	ss2959453324	Nov 08, 2017 (151)
41	SWEGEN	ss3016938710	Nov 08, 2017 (151)
42	ILLUMINA	ss3021865780	Nov 08, 2017 (151)
43	BIOINF_KMB_FNS_UNIBA	ss3028589284	Nov 08, 2017 (151)
44	CSHL	ss3352154054	Nov 08, 2017 (151)
45	ILLUMINA	ss3636408522	Oct 12, 2018 (152)
46	ILLUMINA	ss3638210408	Oct 12, 2018 (152)
47	ILLUMINA	ss3641092919	Oct 12, 2018 (152)
48	ILLUMINA	ss3641388536	Oct 12, 2018 (152)
49	ILLUMINA	ss3643185155	Oct 12, 2018 (152)
50	URBANLAB	ss3650849825	Oct 12, 2018 (152)
51	ILLUMINA	ss3652289487	Oct 12, 2018 (152)
52	EGCUT_WGS	ss3683789156	Jul 13, 2019 (153)
53	EVA_DECODE	ss3702159326	Jul 13, 2019 (153)
54	ACPOP	ss3742776072	Jul 13, 2019 (153)
55	EVA	ss3755708189	Jul 13, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3820962416	Jul 13, 2019 (153)
57	EVA	ss3835304405	Apr 27, 2020 (154)
58	EVA	ss3841274942	Apr 27, 2020 (154)
59	EVA	ss3846778667	Apr 27, 2020 (154)
60	SGDP_PRJ	ss3887563037	Apr 27, 2020 (154)
61	KRGDB	ss3937481539	Apr 27, 2020 (154)
62	KOGIC	ss3980620336	Apr 27, 2020 (154)
63	TOPMED	ss5065190617	Apr 26, 2021 (155)
64	TOMMO_GENOMICS	ss5226293983	Apr 26, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5306166179	Oct 16, 2022 (156)
66	EVA	ss5433017155	Oct 16, 2022 (156)
67	HUGCELL_USP	ss5498846918	Oct 16, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5611439773	Oct 16, 2022 (156)
69	SANFORD_IMAGENETICS	ss5661801657	Oct 16, 2022 (156)
70	TOMMO_GENOMICS	ss5784413437	Oct 16, 2022 (156)
71	YY_MCH	ss5817326836	Oct 16, 2022 (156)
72	EVA	ss5840129539	Oct 16, 2022 (156)
73	EVA	ss5852169959	Oct 16, 2022 (156)
74	EVA	ss5926962140	Oct 16, 2022 (156)
75	EVA	ss5953235299	Oct 16, 2022 (156)
76	1000Genomes	NC_000019.9 - 588516	Oct 12, 2018 (152)
77	1000Genomes_30x	NC_000019.10 - 588516	Oct 16, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 588516	Oct 12, 2018 (152)
79	Genetic variation in the Estonian population	NC_000019.9 - 588516	Oct 12, 2018 (152)
80	The Danish reference pan genome	NC_000019.9 - 588516	Apr 27, 2020 (154)
81	gnomAD - Genomes Submission ignored due to conflicting rows: Row 531570258 (NC_000019.10:588515:A:G 45477/140238) Row 531570259 (NC_000019.10:588515:A:T 2/140264)	-	Apr 26, 2021 (155)
82	gnomAD - Genomes Submission ignored due to conflicting rows: Row 531570258 (NC_000019.10:588515:A:G 45477/140238) Row 531570259 (NC_000019.10:588515:A:T 2/140264)	-	Apr 26, 2021 (155)
83	Genome of the Netherlands Release 5	NC_000019.9 - 588516	Apr 27, 2020 (154)
84	HapMap	NC_000019.10 - 588516	Apr 27, 2020 (154)
85	KOREAN population from KRGDB	NC_000019.9 - 588516	Apr 27, 2020 (154)
86	Korean Genome Project	NC_000019.10 - 588516	Apr 27, 2020 (154)
87	Northern Sweden	NC_000019.9 - 588516	Jul 13, 2019 (153)
88	Qatari	NC_000019.9 - 588516	Apr 27, 2020 (154)
89	SGDP_PRJ	NC_000019.9 - 588516	Apr 27, 2020 (154)
90	Siberian	NC_000019.9 - 588516	Apr 27, 2020 (154)
91	8.3KJPN	NC_000019.9 - 588516	Apr 26, 2021 (155)
92	14KJPN	NC_000019.10 - 588516	Oct 16, 2022 (156)
93	TopMed	NC_000019.10 - 588516	Apr 26, 2021 (155)
94	UK 10K study - Twins	NC_000019.9 - 588516	Oct 12, 2018 (152)
95	A Vietnamese Genetic Variation Database	NC_000019.9 - 588516	Jul 13, 2019 (153)
96	ALFA	NC_000019.10 - 588516	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)
rs60887429	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss84268790, ss85593541, ss114725817, ss159892103, ss203572072, ss255423243, ss283093809, ss292171734, ss479262898, ss1698062651, ss1713646110, ss3643185155	NC_000019.8:539515:A:G	NC_000019.10:588515:A:G	(self)
75378842, 41787331, 29527404, 4707964, 18619181, 44658933, 16060937, 19516888, 39580017, 10539489, 84263290, 41787331, 9241650, ss228003033, ss237574191, ss243802110, ss479265831, ss479634246, ss484432128, ss565801103, ss782662530, ss993999699, ss1362014164, ss1428307701, ss1578520637, ss1637410723, ss1680404756, ss1809167653, ss1937474966, ss2029513428, ss2158023135, ss2702627737, ss2959453324, ss3016938710, ss3021865780, ss3352154054, ss3636408522, ss3638210408, ss3641092919, ss3641388536, ss3652289487, ss3683789156, ss3742776072, ss3755708189, ss3835304405, ss3841274942, ss3887563037, ss3937481539, ss5226293983, ss5433017155, ss5661801657, ss5840129539, ss5953235299	NC_000019.9:588515:A:G	NC_000019.10:588515:A:G	(self)
98965708, 1657638, 36998337, 118250541, 280736281, 4137330245, ss2223604672, ss3028589284, ss3650849825, ss3702159326, ss3820962416, ss3846778667, ss3980620336, ss5065190617, ss5306166179, ss5498846918, ss5611439773, ss5784413437, ss5817326836, ss5852169959, ss5926962140	NC_000019.10:588515:A:G	NC_000019.10:588515:A:G	(self)
ss14723130, ss44190435, ss75266444, ss96284586, ss119621626, ss143814672, ss155512090, ss170057857	NT_011255.14:528515:A:G	NC_000019.10:588515:A:G	(self)
ss2959453324	NC_000019.9:588515:A:T	NC_000019.10:588515:A:T	(self)
4137330245	NC_000019.10:588515:A:T	NC_000019.10:588515:A:T	(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 rs10422590

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

rs10422590