Name: rs7246096
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.

rs7246096

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:35562912 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.174604 (46216/264690, TOPMED)
T=0.174295 (24045/137956, GnomAD)
T=0.15908 (4090/25710, 14KJPN) (+ 15 more)
T=0.15217 (3890/25564, ALFA)
T=0.18142 (3038/16746, 8.3KJPN)
T=0.1871 (1198/6404, 1000G_30x)
T=0.1871 (937/5008, 1000G)
T=0.1250 (560/4480, Estonian)
T=0.1336 (515/3854, ALSPAC)
T=0.1472 (546/3708, TWINSUK)
T=0.1708 (500/2928, KOREAN)
T=0.1632 (299/1832, Korea1K)
T=0.121 (121/998, GoNL)
T=0.120 (72/600, NorthernSweden)
T=0.157 (34/216, Qatari)
G=0.473 (71/150, SGDP_PRJ)
T=0.10 (4/40, GENOME_DK)
G=0.4 (4/10, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP4A : 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	25658	G=0.84757	T=0.15243
European	Sub	20492	G=0.86170	T=0.13830
African	Sub	2970	G=0.7374	T=0.2626
African Others	Sub	114	G=0.772	T=0.228
African American	Sub	2856	G=0.7360	T=0.2640
Asian	Sub	116	G=0.853	T=0.147
East Asian	Sub	88	G=0.85	T=0.15
Other Asian	Sub	28	G=0.86	T=0.14
Latin American 1	Sub	154	G=0.812	T=0.188
Latin American 2	Sub	616	G=0.924	T=0.076
South Asian	Sub	98	G=0.79	T=0.21
Other	Sub	1212	G=0.8490	T=0.1510

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	G=0.825396	T=0.174604
gnomAD - Genomes	Global	Study-wide	137956	G=0.825705	T=0.174295
gnomAD - Genomes	European	Sub	75010	G=0.86054	T=0.13946
gnomAD - Genomes	African	Sub	41100	G=0.73693	T=0.26307
gnomAD - Genomes	American	Sub	13342	G=0.90684	T=0.09316
gnomAD - Genomes	Ashkenazi Jewish	Sub	3304	G=0.8396	T=0.1604
gnomAD - Genomes	East Asian	Sub	3090	G=0.7845	T=0.2155
gnomAD - Genomes	Other	Sub	2110	G=0.8422	T=0.1578
14KJPN	JAPANESE	Study-wide	25710	G=0.84092	T=0.15908
Allele Frequency Aggregator	Total	Global	25564	G=0.84783	T=0.15217
Allele Frequency Aggregator	European	Sub	20416	G=0.86217	T=0.13783
Allele Frequency Aggregator	African	Sub	2970	G=0.7374	T=0.2626
Allele Frequency Aggregator	Other	Sub	1194	G=0.8476	T=0.1524
Allele Frequency Aggregator	Latin American 2	Sub	616	G=0.924	T=0.076
Allele Frequency Aggregator	Latin American 1	Sub	154	G=0.812	T=0.188
Allele Frequency Aggregator	Asian	Sub	116	G=0.853	T=0.147
Allele Frequency Aggregator	South Asian	Sub	98	G=0.79	T=0.21
8.3KJPN	JAPANESE	Study-wide	16746	G=0.81858	T=0.18142
1000Genomes_30x	Global	Study-wide	6404	G=0.8129	T=0.1871
1000Genomes_30x	African	Sub	1786	G=0.7077	T=0.2923
1000Genomes_30x	Europe	Sub	1266	G=0.8776	T=0.1224
1000Genomes_30x	South Asian	Sub	1202	G=0.8195	T=0.1805
1000Genomes_30x	East Asian	Sub	1170	G=0.8043	T=0.1957
1000Genomes_30x	American	Sub	980	G=0.923	T=0.077
1000Genomes	Global	Study-wide	5008	G=0.8129	T=0.1871
1000Genomes	African	Sub	1322	G=0.7141	T=0.2859
1000Genomes	East Asian	Sub	1008	G=0.7976	T=0.2024
1000Genomes	Europe	Sub	1006	G=0.8757	T=0.1243
1000Genomes	South Asian	Sub	978	G=0.818	T=0.182
1000Genomes	American	Sub	694	G=0.925	T=0.075
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8750	T=0.1250
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.8664	T=0.1336
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.8528	T=0.1472
KOREAN population from KRGDB	KOREAN	Study-wide	2928	G=0.8292	T=0.1708
Korean Genome Project	KOREAN	Study-wide	1832	G=0.8368	T=0.1632
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.879	T=0.121
Northern Sweden	ACPOP	Study-wide	600	G=0.880	T=0.120
Qatari	Global	Study-wide	216	G=0.843	T=0.157
SGDP_PRJ	Global	Study-wide	150	G=0.473	T=0.527
The Danish reference pan genome	Danish	Study-wide	40	G=0.90	T=0.10
Siberian	Global	Study-wide	10	G=0.4	T=0.6

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.35562912G>T
GRCh37.p13 chr 19	NC_000019.9:g.36053814G>T

Gene: ATP4A, ATPase H+/K+ transporting subunit alpha (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP4A transcript	NM_000704.3:c.217-274C>A	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=	T
GRCh38.p14 chr 19	NC_000019.10:g.35562912=	NC_000019.10:g.35562912G>T
GRCh37.p13 chr 19	NC_000019.9:g.36053814=	NC_000019.9:g.36053814G>T
ATP4A transcript	NM_000704.2:c.217-274=	NM_000704.2:c.217-274C>A
ATP4A transcript	NM_000704.3:c.217-274=	NM_000704.3:c.217-274C>A

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#.

56 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10918998	Jul 11, 2003 (116)
2	1000GENOMES	ss115095235	Jan 25, 2009 (130)
3	ILLUMINA-UK	ss117696896	Dec 01, 2009 (131)
4	COMPLETE_GENOMICS	ss169652352	Jul 04, 2010 (132)
5	BUSHMAN	ss203745205	Jul 04, 2010 (132)
6	1000GENOMES	ss228127887	Jul 14, 2010 (132)
7	1000GENOMES	ss237668438	Jul 15, 2010 (132)
8	1000GENOMES	ss243875753	Jul 15, 2010 (132)
9	GMI	ss283198591	May 04, 2012 (137)
10	ILLUMINA	ss533322324	Sep 08, 2015 (146)
11	TISHKOFF	ss565965624	Apr 25, 2013 (138)
12	SSMP	ss661827466	Apr 25, 2013 (138)
13	EVA-GONL	ss994270230	Aug 21, 2014 (142)
14	JMKIDD_LAB	ss1081884521	Aug 21, 2014 (142)
15	1000GENOMES	ss1363050238	Aug 21, 2014 (142)
16	EVA_GENOME_DK	ss1578629343	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1637912889	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1680906922	Apr 01, 2015 (144)
19	EVA_DECODE	ss1698323806	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1809294405	Sep 08, 2015 (146)
21	WEILL_CORNELL_DGM	ss1937763832	Feb 12, 2016 (147)
22	JJLAB	ss2029660029	Sep 14, 2016 (149)
23	USC_VALOUEV	ss2158198671	Dec 20, 2016 (150)
24	HUMAN_LONGEVITY	ss2225537816	Dec 20, 2016 (150)
25	GRF	ss2702807173	Nov 08, 2017 (151)
26	GNOMAD	ss2962516541	Nov 08, 2017 (151)
27	AFFY	ss2985139721	Nov 08, 2017 (151)
28	AFFY	ss2985771515	Nov 08, 2017 (151)
29	SWEGEN	ss3017419455	Nov 08, 2017 (151)
30	BIOINF_KMB_FNS_UNIBA	ss3028662759	Nov 08, 2017 (151)
31	CSHL	ss3352289766	Nov 08, 2017 (151)
32	ILLUMINA	ss3627925554	Oct 12, 2018 (152)
33	URBANLAB	ss3650911630	Oct 12, 2018 (152)
34	ILLUMINA	ss3653912083	Oct 12, 2018 (152)
35	EGCUT_WGS	ss3684194649	Jul 13, 2019 (153)
36	EVA_DECODE	ss3702708932	Jul 13, 2019 (153)
37	ACPOP	ss3743013242	Jul 13, 2019 (153)
38	EVA	ss3756029769	Jul 13, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3821277559	Jul 13, 2019 (153)
40	EVA	ss3835447941	Apr 27, 2020 (154)
41	SGDP_PRJ	ss3888154058	Apr 27, 2020 (154)
42	KRGDB	ss3938247669	Apr 27, 2020 (154)
43	KOGIC	ss3981276767	Apr 27, 2020 (154)
44	TOPMED	ss5073828068	Apr 26, 2021 (155)
45	TOMMO_GENOMICS	ss5227605885	Apr 26, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5307140234	Oct 16, 2022 (156)
47	EVA	ss5434657574	Oct 16, 2022 (156)
48	HUGCELL_USP	ss5499680608	Oct 16, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5612823546	Oct 16, 2022 (156)
50	SANFORD_IMAGENETICS	ss5662333001	Oct 16, 2022 (156)
51	TOMMO_GENOMICS	ss5786188550	Oct 16, 2022 (156)
52	YY_MCH	ss5817573688	Oct 16, 2022 (156)
53	EVA	ss5840509453	Oct 16, 2022 (156)
54	EVA	ss5852278187	Oct 16, 2022 (156)
55	EVA	ss5927990605	Oct 16, 2022 (156)
56	EVA	ss5953749244	Oct 16, 2022 (156)
57	1000Genomes	NC_000019.9 - 36053814	Oct 12, 2018 (152)
58	1000Genomes_30x	NC_000019.10 - 35562912	Oct 16, 2022 (156)
59	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 36053814	Oct 12, 2018 (152)
60	Genetic variation in the Estonian population	NC_000019.9 - 36053814	Oct 12, 2018 (152)
61	The Danish reference pan genome	NC_000019.9 - 36053814	Apr 27, 2020 (154)
62	gnomAD - Genomes	NC_000019.10 - 35562912	Apr 26, 2021 (155)
63	Genome of the Netherlands Release 5	NC_000019.9 - 36053814	Apr 27, 2020 (154)
64	KOREAN population from KRGDB	NC_000019.9 - 36053814	Apr 27, 2020 (154)
65	Korean Genome Project	NC_000019.10 - 35562912	Apr 27, 2020 (154)
66	Northern Sweden	NC_000019.9 - 36053814	Jul 13, 2019 (153)
67	Qatari	NC_000019.9 - 36053814	Apr 27, 2020 (154)
68	SGDP_PRJ	NC_000019.9 - 36053814	Apr 27, 2020 (154)
69	Siberian	NC_000019.9 - 36053814	Apr 27, 2020 (154)
70	8.3KJPN	NC_000019.9 - 36053814	Apr 26, 2021 (155)
71	14KJPN	NC_000019.10 - 35562912	Oct 16, 2022 (156)
72	TopMed	NC_000019.10 - 35562912	Apr 26, 2021 (155)
73	UK 10K study - Twins	NC_000019.9 - 36053814	Oct 12, 2018 (152)
74	ALFA	NC_000019.10 - 35562912	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss115095235, ss117696896, ss169652352, ss203745205, ss283198591, ss1698323806	NC_000019.8:40745653:G:T	NC_000019.10:35562911:G:T	(self)
76453021, 42347978, 29932897, 4812272, 18865872, 45425063, 16298107, 19805754, 40171038, 10715025, 85575192, 42347978, ss228127887, ss237668438, ss243875753, ss533322324, ss565965624, ss661827466, ss994270230, ss1081884521, ss1363050238, ss1578629343, ss1637912889, ss1680906922, ss1809294405, ss1937763832, ss2029660029, ss2158198671, ss2702807173, ss2962516541, ss2985139721, ss2985771515, ss3017419455, ss3352289766, ss3627925554, ss3653912083, ss3684194649, ss3743013242, ss3756029769, ss3835447941, ss3888154058, ss3938247669, ss5227605885, ss5434657574, ss5662333001, ss5840509453, ss5953749244	NC_000019.9:36053813:G:T	NC_000019.10:35562911:G:T	(self)
100349481, 539179470, 37654768, 120025654, 289373732, 7596775433, ss2225537816, ss3028662759, ss3650911630, ss3702708932, ss3821277559, ss3981276767, ss5073828068, ss5307140234, ss5499680608, ss5612823546, ss5786188550, ss5817573688, ss5852278187, ss5927990605	NC_000019.10:35562911:G:T	NC_000019.10:35562911:G:T	(self)
ss10918998	NT_011109.15:8322031:G:T	NC_000019.10:35562911:G: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 rs7246096

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

rs7246096