Name: rs3800570
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.

rs3800570

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:138726587 (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: C>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.123847 (32781/264690, TOPMED)
G=0.122478 (17165/140148, GnomAD)
G=0.14895 (4209/28258, 14KJPN) (+ 19 more)
G=0.10119 (2134/21088, ALFA)
G=0.14894 (2496/16758, 8.3KJPN)
G=0.1541 (987/6404, 1000G_30x)
G=0.1554 (778/5008, 1000G)
G=0.1025 (459/4480, Estonian)
G=0.0654 (252/3854, ALSPAC)
G=0.0720 (267/3708, TWINSUK)
G=0.1454 (426/2930, KOREAN)
G=0.1612 (305/1892, HapMap)
G=0.1294 (237/1832, Korea1K)
G=0.1546 (175/1132, Daghestan)
G=0.054 (54/998, GoNL)
G=0.097 (58/600, NorthernSweden)
G=0.162 (35/216, Qatari)
G=0.140 (30/214, Vietnamese)
C=0.433 (77/178, SGDP_PRJ)
G=0.03 (1/40, GENOME_DK)
C=0.50 (7/14, Siberian)
G=0.50 (7/14, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP6V0A4 : 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	21088	C=0.89881	G=0.10119
European	Sub	16446	C=0.91749	G=0.08251
African	Sub	2946	C=0.7953	G=0.2047
African Others	Sub	114	C=0.816	G=0.184
African American	Sub	2832	C=0.7945	G=0.2055
Asian	Sub	112	C=0.786	G=0.214
East Asian	Sub	86	C=0.78	G=0.22
Other Asian	Sub	26	C=0.81	G=0.19
Latin American 1	Sub	146	C=0.870	G=0.130
Latin American 2	Sub	610	C=0.925	G=0.075
South Asian	Sub	98	C=0.84	G=0.16
Other	Sub	730	C=0.905	G=0.095

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	C=0.876153	G=0.123847
gnomAD - Genomes	Global	Study-wide	140148	C=0.877522	G=0.122478
gnomAD - Genomes	European	Sub	75912	C=0.91813	G=0.08187
gnomAD - Genomes	African	Sub	41978	C=0.79318	G=0.20682
gnomAD - Genomes	American	Sub	13662	C=0.91765	G=0.08235
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.8858	G=0.1142
gnomAD - Genomes	East Asian	Sub	3126	C=0.8372	G=0.1628
gnomAD - Genomes	Other	Sub	2150	C=0.8814	G=0.1186
14KJPN	JAPANESE	Study-wide	28258	C=0.85105	G=0.14895
Allele Frequency Aggregator	Total	Global	21088	C=0.89881	G=0.10119
Allele Frequency Aggregator	European	Sub	16446	C=0.91749	G=0.08251
Allele Frequency Aggregator	African	Sub	2946	C=0.7953	G=0.2047
Allele Frequency Aggregator	Other	Sub	730	C=0.905	G=0.095
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.925	G=0.075
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.870	G=0.130
Allele Frequency Aggregator	Asian	Sub	112	C=0.786	G=0.214
Allele Frequency Aggregator	South Asian	Sub	98	C=0.84	G=0.16
8.3KJPN	JAPANESE	Study-wide	16758	C=0.85106	G=0.14894
1000Genomes_30x	Global	Study-wide	6404	C=0.8459	G=0.1541
1000Genomes_30x	African	Sub	1786	C=0.7548	G=0.2452
1000Genomes_30x	Europe	Sub	1266	C=0.9147	G=0.0853
1000Genomes_30x	South Asian	Sub	1202	C=0.8353	G=0.1647
1000Genomes_30x	East Asian	Sub	1170	C=0.8607	G=0.1393
1000Genomes_30x	American	Sub	980	C=0.918	G=0.082
1000Genomes	Global	Study-wide	5008	C=0.8446	G=0.1554
1000Genomes	African	Sub	1322	C=0.7534	G=0.2466
1000Genomes	East Asian	Sub	1008	C=0.8651	G=0.1349
1000Genomes	Europe	Sub	1006	C=0.9056	G=0.0944
1000Genomes	South Asian	Sub	978	C=0.830	G=0.170
1000Genomes	American	Sub	694	C=0.921	G=0.079
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8975	G=0.1025
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9346	G=0.0654
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9280	G=0.0720
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.8546	G=0.1454
HapMap	Global	Study-wide	1892	C=0.8388	G=0.1612
HapMap	American	Sub	770	C=0.871	G=0.129
HapMap	African	Sub	692	C=0.786	G=0.214
HapMap	Asian	Sub	254	C=0.843	G=0.157
HapMap	Europe	Sub	176	C=0.898	G=0.102
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8706	G=0.1294
Genome-wide autozygosity in Daghestan	Global	Study-wide	1132	C=0.8454	G=0.1546
Genome-wide autozygosity in Daghestan	Daghestan	Sub	626	C=0.824	G=0.176
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	C=0.868	G=0.132
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	C=0.902	G=0.098
Genome-wide autozygosity in Daghestan	Europe	Sub	108	C=0.898	G=0.102
Genome-wide autozygosity in Daghestan	South Asian	Sub	96	C=0.83	G=0.17
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	C=0.81	G=0.19
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.946	G=0.054
Northern Sweden	ACPOP	Study-wide	600	C=0.903	G=0.097
Qatari	Global	Study-wide	216	C=0.838	G=0.162
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.860	G=0.140
SGDP_PRJ	Global	Study-wide	178	C=0.433	G=0.567
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	G=0.03
Siberian	Global	Study-wide	14	C=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 7	NC_000007.14:g.138726587C>G
GRCh37.p13 chr 7	NC_000007.13:g.138411332C>G
ATP6V0A4 RefSeqGene (LRG_1175)	NG_008145.1:g.76610G>C

Gene: ATP6V0A4, ATPase H+ transporting V0 subunit a4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP6V0A4 transcript variant 1	NM_020632.3:c.2010+2174G>C	N/A	Intron Variant
ATP6V0A4 transcript variant 2	NM_130840.3:c.2010+2174G>C	N/A	Intron Variant
ATP6V0A4 transcript variant 3	NM_130841.3:c.2010+2174G>C	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	C=	G
GRCh38.p14 chr 7	NC_000007.14:g.138726587=	NC_000007.14:g.138726587C>G
GRCh37.p13 chr 7	NC_000007.13:g.138411332=	NC_000007.13:g.138411332C>G
ATP6V0A4 RefSeqGene (LRG_1175)	NG_008145.1:g.76610=	NG_008145.1:g.76610G>C
ATP6V0A4 transcript variant 1	NM_020632.2:c.2010+2174=	NM_020632.2:c.2010+2174G>C
ATP6V0A4 transcript variant 1	NM_020632.3:c.2010+2174=	NM_020632.3:c.2010+2174G>C
ATP6V0A4 transcript variant 2	NM_130840.2:c.2010+2174=	NM_130840.2:c.2010+2174G>C
ATP6V0A4 transcript variant 2	NM_130840.3:c.2010+2174=	NM_130840.3:c.2010+2174G>C
ATP6V0A4 transcript variant 3	NM_130841.2:c.2010+2174=	NM_130841.2:c.2010+2174G>C
ATP6V0A4 transcript variant 3	NM_130841.3:c.2010+2174=	NM_130841.3:c.2010+2174G>C
ATP6V0A4 transcript variant X1	XM_005250393.1:c.2010+2174=	XM_005250393.1:c.2010+2174G>C
ATP6V0A4 transcript variant X2	XM_005250394.1:c.2010+2174=	XM_005250394.1:c.2010+2174G>C

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#.

66 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss4986953	Aug 28, 2002 (107)
2	WUGSC_SSAHASNP	ss14581574	Dec 05, 2003 (120)
3	PERLEGEN	ss23448294	Sep 20, 2004 (123)
4	AFFY	ss66414761	Dec 01, 2006 (127)
5	AFFY	ss76175772	Dec 07, 2007 (129)
6	KRIBB_YJKIM	ss81961138	Dec 14, 2007 (130)
7	1000GENOMES	ss114516652	Jan 25, 2009 (130)
8	ILLUMINA-UK	ss116339208	Feb 14, 2009 (130)
9	COMPLETE_GENOMICS	ss165518790	Jul 04, 2010 (132)
10	AFFY	ss172716478	Jul 04, 2010 (132)
11	ILLUMINA	ss173644593	Jul 04, 2010 (132)
12	BUSHMAN	ss198370505	Jul 04, 2010 (132)
13	1000GENOMES	ss223364528	Jul 14, 2010 (132)
14	1000GENOMES	ss234192158	Jul 15, 2010 (132)
15	1000GENOMES	ss241100164	Jul 15, 2010 (132)
16	BL	ss254715873	May 09, 2011 (134)
17	GMI	ss279555450	May 04, 2012 (137)
18	ILLUMINA	ss537196549	Sep 08, 2015 (146)
19	TISHKOFF	ss560342552	Apr 25, 2013 (138)
20	SSMP	ss654754886	Apr 25, 2013 (138)
21	EVA-GONL	ss984868020	Aug 21, 2014 (142)
22	JMKIDD_LAB	ss1075032886	Aug 21, 2014 (142)
23	1000GENOMES	ss1327397954	Aug 21, 2014 (142)
24	HAMMER_LAB	ss1397507906	Sep 08, 2015 (146)
25	DDI	ss1431299411	Apr 01, 2015 (144)
26	EVA_GENOME_DK	ss1582428586	Apr 01, 2015 (144)
27	EVA_DECODE	ss1594457097	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1619358047	Apr 01, 2015 (144)
29	EVA_UK10K_TWINSUK	ss1662352080	Apr 01, 2015 (144)
30	EVA_SVP	ss1712992252	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1805249802	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1928123858	Feb 12, 2016 (147)
33	JJLAB	ss2024751875	Sep 14, 2016 (149)
34	USC_VALOUEV	ss2152974142	Dec 20, 2016 (150)
35	HUMAN_LONGEVITY	ss2298402764	Dec 20, 2016 (150)
36	SYSTEMSBIOZJU	ss2626863470	Nov 08, 2017 (151)
37	GRF	ss2708696026	Nov 08, 2017 (151)
38	ILLUMINA	ss2711122657	Nov 08, 2017 (151)
39	GNOMAD	ss2859857352	Nov 08, 2017 (151)
40	SWEGEN	ss3002141757	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3026165342	Nov 08, 2017 (151)
42	CSHL	ss3347874357	Nov 08, 2017 (151)
43	ILLUMINA	ss3629927821	Oct 12, 2018 (152)
44	ILLUMINA	ss3638727273	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3669899829	Jul 13, 2019 (153)
46	EVA_DECODE	ss3720822928	Jul 13, 2019 (153)
47	ACPOP	ss3735129234	Jul 13, 2019 (153)
48	EVA	ss3767241635	Jul 13, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3810407844	Jul 13, 2019 (153)
50	SGDP_PRJ	ss3868533168	Apr 26, 2020 (154)
51	KRGDB	ss3915901666	Apr 26, 2020 (154)
52	KOGIC	ss3962714378	Apr 26, 2020 (154)
53	EVA	ss4017362410	Apr 26, 2021 (155)
54	TOPMED	ss4766067371	Apr 26, 2021 (155)
55	TOMMO_GENOMICS	ss5185886059	Apr 26, 2021 (155)
56	1000G_HIGH_COVERAGE	ss5274970543	Oct 13, 2022 (156)
57	EVA	ss5377205347	Oct 13, 2022 (156)
58	HUGCELL_USP	ss5471832356	Oct 13, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5564245186	Oct 13, 2022 (156)
60	SANFORD_IMAGENETICS	ss5644118240	Oct 13, 2022 (156)
61	TOMMO_GENOMICS	ss5726971244	Oct 13, 2022 (156)
62	YY_MCH	ss5809150258	Oct 13, 2022 (156)
63	EVA	ss5823615925	Oct 13, 2022 (156)
64	EVA	ss5856124086	Oct 13, 2022 (156)
65	EVA	ss5861152647	Oct 13, 2022 (156)
66	EVA	ss5973322687	Oct 13, 2022 (156)
67	1000Genomes	NC_000007.13 - 138411332	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000007.14 - 138726587	Oct 13, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 138411332	Oct 12, 2018 (152)
70	Genome-wide autozygosity in Daghestan	NC_000007.12 - 138061872	Apr 26, 2020 (154)
71	Genetic variation in the Estonian population	NC_000007.13 - 138411332	Oct 12, 2018 (152)
72	The Danish reference pan genome	NC_000007.13 - 138411332	Apr 26, 2020 (154)
73	gnomAD - Genomes	NC_000007.14 - 138726587	Apr 26, 2021 (155)
74	Genome of the Netherlands Release 5	NC_000007.13 - 138411332	Apr 26, 2020 (154)
75	HapMap	NC_000007.14 - 138726587	Apr 26, 2020 (154)
76	KOREAN population from KRGDB	NC_000007.13 - 138411332	Apr 26, 2020 (154)
77	Korean Genome Project	NC_000007.14 - 138726587	Apr 26, 2020 (154)
78	Northern Sweden	NC_000007.13 - 138411332	Jul 13, 2019 (153)
79	Qatari	NC_000007.13 - 138411332	Apr 26, 2020 (154)
80	SGDP_PRJ	NC_000007.13 - 138411332	Apr 26, 2020 (154)
81	Siberian	NC_000007.13 - 138411332	Apr 26, 2020 (154)
82	8.3KJPN	NC_000007.13 - 138411332	Apr 26, 2021 (155)
83	14KJPN	NC_000007.14 - 138726587	Oct 13, 2022 (156)
84	TopMed	NC_000007.14 - 138726587	Apr 26, 2021 (155)
85	UK 10K study - Twins	NC_000007.13 - 138411332	Oct 12, 2018 (152)
86	A Vietnamese Genetic Variation Database	NC_000007.13 - 138411332	Jul 13, 2019 (153)
87	ALFA	NC_000007.14 - 138726587	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)
rs10376048	Feb 27, 2004 (120)
rs57985062	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
481910, ss66414761, ss76175772, ss114516652, ss116339208, ss165518790, ss172716478, ss198370505, ss254715873, ss279555450, ss1397507906, ss1594457097, ss1712992252	NC_000007.12:138061871:C:G	NC_000007.14:138726586:C:G	(self)
39451711, 21957765, 15638077, 8593524, 9796869, 23079060, 8414099, 10165788, 20550148, 5490496, 43855366, 21957765, 4889892, ss223364528, ss234192158, ss241100164, ss537196549, ss560342552, ss654754886, ss984868020, ss1075032886, ss1327397954, ss1431299411, ss1582428586, ss1619358047, ss1662352080, ss1805249802, ss1928123858, ss2024751875, ss2152974142, ss2626863470, ss2708696026, ss2711122657, ss2859857352, ss3002141757, ss3347874357, ss3629927821, ss3638727273, ss3669899829, ss3735129234, ss3767241635, ss3868533168, ss3915901666, ss4017362410, ss5185886059, ss5377205347, ss5644118240, ss5823615925, ss5973322687	NC_000007.13:138411331:C:G	NC_000007.14:138726586:C:G	(self)
51771121, 278588250, 3506788, 19092379, 60808348, 603444930, 968141243, ss2298402764, ss3026165342, ss3720822928, ss3810407844, ss3962714378, ss4766067371, ss5274970543, ss5471832356, ss5564245186, ss5726971244, ss5809150258, ss5856124086, ss5861152647	NC_000007.14:138726586:C:G	NC_000007.14:138726586:C:G	(self)
ss14581574	NT_007933.13:63447909:C:G	NC_000007.14:138726586:C:G	(self)
ss4986953, ss23448294, ss81961138, ss173644593	NT_007933.15:76444174:C:G	NC_000007.14:138726586:C:G	(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 rs3800570

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

rs3800570