Name: rs2426337
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.

rs2426337

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:51644097 (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=0.455276 (120507/264690, TOPMED)
C=0.450470 (62936/139712, GnomAD)
T=0.26973 (7622/28258, 14KJPN) (+ 16 more)
C=0.46474 (8779/18890, ALFA)
T=0.26874 (4504/16760, 8.3KJPN)
C=0.4966 (3180/6404, 1000G_30x)
T=0.4932 (2470/5008, 1000G)
C=0.4435 (1987/4480, Estonian)
T=0.4702 (1812/3854, ALSPAC)
T=0.4711 (1747/3708, TWINSUK)
T=0.2085 (611/2930, KOREAN)
T=0.2183 (400/1832, Korea1K)
T=0.470 (469/998, GoNL)
T=0.427 (256/600, NorthernSweden)
T=0.271 (110/406, SGDP_PRJ)
C=0.486 (105/216, Qatari)
T=0.203 (43/212, Vietnamese)
T=0.31 (13/42, Siberian)
C=0.45 (18/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP9A : 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	18890	T=0.53526	C=0.46474
European	Sub	14286	T=0.49748	C=0.50252
African	Sub	2946	T=0.7488	C=0.2512
African Others	Sub	114	T=0.763	C=0.237
African American	Sub	2832	T=0.7482	C=0.2518
Asian	Sub	112	T=0.214	C=0.786
East Asian	Sub	86	T=0.19	C=0.81
Other Asian	Sub	26	T=0.31	C=0.69
Latin American 1	Sub	146	T=0.507	C=0.493
Latin American 2	Sub	610	T=0.507	C=0.493
South Asian	Sub	98	T=0.42	C=0.58
Other	Sub	692	T=0.506	C=0.494

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	T=0.544724	C=0.455276
gnomAD - Genomes	Global	Study-wide	139712	T=0.549530	C=0.450470
gnomAD - Genomes	European	Sub	75712	T=0.48206	C=0.51794
gnomAD - Genomes	African	Sub	41838	T=0.74310	C=0.25690
gnomAD - Genomes	American	Sub	13584	T=0.45436	C=0.54564
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=0.4054	C=0.5946
gnomAD - Genomes	East Asian	Sub	3122	T=0.1938	C=0.8062
gnomAD - Genomes	Other	Sub	2138	T=0.4986	C=0.5014
14KJPN	JAPANESE	Study-wide	28258	T=0.26973	C=0.73027
Allele Frequency Aggregator	Total	Global	18890	T=0.53526	C=0.46474
Allele Frequency Aggregator	European	Sub	14286	T=0.49748	C=0.50252
Allele Frequency Aggregator	African	Sub	2946	T=0.7488	C=0.2512
Allele Frequency Aggregator	Other	Sub	692	T=0.506	C=0.494
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.507	C=0.493
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.507	C=0.493
Allele Frequency Aggregator	Asian	Sub	112	T=0.214	C=0.786
Allele Frequency Aggregator	South Asian	Sub	98	T=0.42	C=0.58
8.3KJPN	JAPANESE	Study-wide	16760	T=0.26874	C=0.73126
1000Genomes_30x	Global	Study-wide	6404	T=0.5034	C=0.4966
1000Genomes_30x	African	Sub	1786	T=0.8236	C=0.1764
1000Genomes_30x	Europe	Sub	1266	T=0.4613	C=0.5387
1000Genomes_30x	South Asian	Sub	1202	T=0.3860	C=0.6140
1000Genomes_30x	East Asian	Sub	1170	T=0.1872	C=0.8128
1000Genomes_30x	American	Sub	980	T=0.496	C=0.504
1000Genomes	Global	Study-wide	5008	T=0.4932	C=0.5068
1000Genomes	African	Sub	1322	T=0.8298	C=0.1702
1000Genomes	East Asian	Sub	1008	T=0.1885	C=0.8115
1000Genomes	Europe	Sub	1006	T=0.4642	C=0.5358
1000Genomes	South Asian	Sub	978	T=0.389	C=0.611
1000Genomes	American	Sub	694	T=0.484	C=0.516
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5565	C=0.4435
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.4702	C=0.5298
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.4711	C=0.5289
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.2085	A=0.0000, C=0.7915
Korean Genome Project	KOREAN	Study-wide	1832	T=0.2183	C=0.7817
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.470	C=0.530
Northern Sweden	ACPOP	Study-wide	600	T=0.427	C=0.573
SGDP_PRJ	Global	Study-wide	406	T=0.271	C=0.729
Qatari	Global	Study-wide	216	T=0.514	C=0.486
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.203	C=0.797
Siberian	Global	Study-wide	42	T=0.31	C=0.69
The Danish reference pan genome	Danish	Study-wide	40	T=0.55	C=0.45

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 20	NC_000020.11:g.51644097T>A
GRCh38.p14 chr 20	NC_000020.11:g.51644097T>C
GRCh37.p13 chr 20	NC_000020.10:g.50260636T>A
GRCh37.p13 chr 20	NC_000020.10:g.50260636T>C

Gene: ATP9A, ATPase phospholipid transporting 9A (putative) (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP9A transcript	NM_006045.3:c.1507-4593A>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	T=	A	C
GRCh38.p14 chr 20	NC_000020.11:g.51644097=	NC_000020.11:g.51644097T>A	NC_000020.11:g.51644097T>C
GRCh37.p13 chr 20	NC_000020.10:g.50260636=	NC_000020.10:g.50260636T>A	NC_000020.10:g.50260636T>C
ATP9A transcript	NM_006045.1:c.1507-4593=	NM_006045.1:c.1507-4593A>T	NM_006045.1:c.1507-4593A>G
ATP9A transcript	NM_006045.3:c.1507-4593=	NM_006045.3:c.1507-4593A>T	NM_006045.3:c.1507-4593A>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#.

71 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3398766	Sep 28, 2001 (100)
2	SC_SNP	ss8379769	Apr 21, 2003 (114)
3	CSHL-HAPMAP	ss17698473	Feb 27, 2004 (120)
4	ABI	ss41400806	Mar 13, 2006 (126)
5	HGSV	ss78980262	Dec 07, 2007 (129)
6	BCMHGSC_JDW	ss91723249	Mar 24, 2008 (129)
7	1000GENOMES	ss112088198	Jan 25, 2009 (130)
8	ILLUMINA-UK	ss117573256	Dec 01, 2009 (131)
9	ENSEMBL	ss138256212	Dec 01, 2009 (131)
10	GMI	ss156510771	Dec 01, 2009 (131)
11	ENSEMBL	ss161329840	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss168264443	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss172143107	Jul 04, 2010 (132)
14	BUSHMAN	ss203914239	Jul 04, 2010 (132)
15	1000GENOMES	ss228395954	Jul 14, 2010 (132)
16	1000GENOMES	ss237861782	Jul 15, 2010 (132)
17	1000GENOMES	ss244027861	Jul 15, 2010 (132)
18	BL	ss255701618	May 09, 2011 (134)
19	GMI	ss283411364	May 04, 2012 (137)
20	GMI	ss287470129	Apr 25, 2013 (138)
21	PJP	ss292577458	May 09, 2011 (134)
22	TISHKOFF	ss566303904	Apr 25, 2013 (138)
23	SSMP	ss662184041	Apr 25, 2013 (138)
24	EVA-GONL	ss994808185	Aug 21, 2014 (142)
25	JMKIDD_LAB	ss1082266790	Aug 21, 2014 (142)
26	1000GENOMES	ss1365114927	Aug 21, 2014 (142)
27	DDI	ss1429077819	Apr 01, 2015 (144)
28	EVA_GENOME_DK	ss1579538327	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1638962918	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1681956951	Apr 01, 2015 (144)
31	EVA_DECODE	ss1698870164	Apr 01, 2015 (144)
32	HAMMER_LAB	ss1809540054	Sep 08, 2015 (146)
33	WEILL_CORNELL_DGM	ss1938324845	Feb 12, 2016 (147)
34	JJLAB	ss2029941974	Sep 14, 2016 (149)
35	USC_VALOUEV	ss2158512169	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2243458428	Dec 20, 2016 (150)
37	SYSTEMSBIOZJU	ss2629465150	Nov 08, 2017 (151)
38	GRF	ss2704207516	Nov 08, 2017 (151)
39	GNOMAD	ss2968392865	Nov 08, 2017 (151)
40	SWEGEN	ss3018321318	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3028803757	Nov 08, 2017 (151)
42	CSHL	ss3352549126	Nov 08, 2017 (151)
43	EGCUT_WGS	ss3685005211	Jul 13, 2019 (153)
44	EVA_DECODE	ss3707118591	Jul 13, 2019 (153)
45	ACPOP	ss3743466330	Jul 13, 2019 (153)
46	EVA	ss3758750271	Jul 13, 2019 (153)
47	PACBIO	ss3788670142	Jul 13, 2019 (153)
48	PACBIO	ss3793557492	Jul 13, 2019 (153)
49	PACBIO	ss3798444535	Jul 13, 2019 (153)
50	KHV_HUMAN_GENOMES	ss3821907364	Jul 13, 2019 (153)
51	EVA	ss3835714465	Apr 27, 2020 (154)
52	EVA	ss3841480884	Apr 27, 2020 (154)
53	EVA	ss3846993995	Apr 27, 2020 (154)
54	SGDP_PRJ	ss3889281653	Apr 27, 2020 (154)
55	KRGDB	ss3939591787	Apr 27, 2020 (154)
56	KOGIC	ss3982460316	Apr 27, 2020 (154)
57	TOPMED	ss5091580900	Apr 27, 2021 (155)
58	TOMMO_GENOMICS	ss5230046282	Apr 27, 2021 (155)
59	1000G_HIGH_COVERAGE	ss5309103689	Oct 13, 2022 (156)
60	EVA	ss5437961162	Oct 13, 2022 (156)
61	HUGCELL_USP	ss5501352702	Oct 13, 2022 (156)
62	EVA	ss5512241284	Oct 13, 2022 (156)
63	1000G_HIGH_COVERAGE	ss5615706670	Oct 13, 2022 (156)
64	SANFORD_IMAGENETICS	ss5663381596	Oct 13, 2022 (156)
65	TOMMO_GENOMICS	ss5789972677	Oct 13, 2022 (156)
66	YY_MCH	ss5818120148	Oct 13, 2022 (156)
67	EVA	ss5845810547	Oct 13, 2022 (156)
68	EVA	ss5853177593	Oct 13, 2022 (156)
69	EVA	ss5923777123	Oct 13, 2022 (156)
70	EVA	ss5958307330	Oct 13, 2022 (156)
71	EVA	ss5981093294	Oct 13, 2022 (156)
72	1000Genomes	NC_000020.10 - 50260636	Oct 12, 2018 (152)
73	1000Genomes_30x	NC_000020.11 - 51644097	Oct 13, 2022 (156)
74	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 50260636	Oct 12, 2018 (152)
75	Genetic variation in the Estonian population	NC_000020.10 - 50260636	Oct 12, 2018 (152)
76	The Danish reference pan genome	NC_000020.10 - 50260636	Apr 27, 2020 (154)
77	gnomAD - Genomes	NC_000020.11 - 51644097	Apr 27, 2021 (155)
78	Genome of the Netherlands Release 5	NC_000020.10 - 50260636	Apr 27, 2020 (154)
79	KOREAN population from KRGDB	NC_000020.10 - 50260636	Apr 27, 2020 (154)
80	Korean Genome Project	NC_000020.11 - 51644097	Apr 27, 2020 (154)
81	Northern Sweden	NC_000020.10 - 50260636	Jul 13, 2019 (153)
82	Qatari	NC_000020.10 - 50260636	Apr 27, 2020 (154)
83	SGDP_PRJ	NC_000020.10 - 50260636	Apr 27, 2020 (154)
84	Siberian	NC_000020.10 - 50260636	Apr 27, 2020 (154)
85	8.3KJPN	NC_000020.10 - 50260636	Apr 27, 2021 (155)
86	14KJPN	NC_000020.11 - 51644097	Oct 13, 2022 (156)
87	TopMed	NC_000020.11 - 51644097	Apr 27, 2021 (155)
88	UK 10K study - Twins	NC_000020.10 - 50260636	Oct 12, 2018 (152)
89	A Vietnamese Genetic Variation Database	NC_000020.10 - 50260636	Jul 13, 2019 (153)
90	ALFA	NC_000020.11 - 51644097	Apr 27, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
46769181, ss3939591787	NC_000020.10:50260635:T:A	NC_000020.11:51644096:T:A	(self)
ss78980262, ss91723249, ss112088198, ss117573256, ss168264443, ss172143107, ss203914239, ss255701618, ss283411364, ss287470129, ss292577458, ss1698870164	NC_000020.9:49694042:T:C	NC_000020.11:51644096:T:C	(self)
78589953, 43508704, 30743459, 5703266, 19378472, 46769181, 16751195, 20366767, 41298633, 11028523, 88015589, 43508704, 9597203, ss228395954, ss237861782, ss244027861, ss566303904, ss662184041, ss994808185, ss1082266790, ss1365114927, ss1429077819, ss1579538327, ss1638962918, ss1681956951, ss1809540054, ss1938324845, ss2029941974, ss2158512169, ss2629465150, ss2704207516, ss2968392865, ss3018321318, ss3352549126, ss3685005211, ss3743466330, ss3758750271, ss3788670142, ss3793557492, ss3798444535, ss3835714465, ss3841480884, ss3889281653, ss3939591787, ss5230046282, ss5437961162, ss5512241284, ss5663381596, ss5845810547, ss5958307330, ss5981093294	NC_000020.10:50260635:T:C	NC_000020.11:51644096:T:C	(self)
103232605, 554340404, 38838317, 123809781, 366689845, 6619112218, ss2243458428, ss3028803757, ss3707118591, ss3821907364, ss3846993995, ss3982460316, ss5091580900, ss5309103689, ss5501352702, ss5615706670, ss5789972677, ss5818120148, ss5853177593, ss5923777123	NC_000020.11:51644096:T:C	NC_000020.11:51644096:T:C	(self)
ss17698473	NT_011362.8:15313543:T:C	NC_000020.11:51644096:T:C	(self)
ss3398766, ss8379769, ss41400806, ss138256212, ss156510771, ss161329840	NT_011362.10:20456727:T:C	NC_000020.11:51644096: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 rs2426337

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2426337