Name: rs28729777
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.

rs28729777

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:7651662 (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=0.050924 (13479/264690, TOPMED)
G=0.008609 (1334/154946, GnomAD_exome)
G=0.047018 (6587/140096, GnomAD) (+ 9 more)
G=0.01727 (499/28900, ExAC)
G=0.03578 (516/14420, ALFA)
G=0.02595 (332/12794, GO-ESP)
G=0.0520 (333/6404, 1000G_30x)
G=0.0487 (244/5008, 1000G)
G=0.0006 (1/1774, Korea1K)
G=0.002 (1/534, MGP)
G=0.032 (7/216, Qatari)
A=0.46 (11/24, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP1B2 : 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	14420	A=0.96422	G=0.03578
European	Sub	9824	A=0.9985	G=0.0015
African	Sub	2946	A=0.8435	G=0.1565
African Others	Sub	114	A=0.746	G=0.254
African American	Sub	2832	A=0.8475	G=0.1525
Asian	Sub	112	A=1.000	G=0.000
East Asian	Sub	86	A=1.00	G=0.00
Other Asian	Sub	26	A=1.00	G=0.00
Latin American 1	Sub	146	A=0.973	G=0.027
Latin American 2	Sub	610	A=0.990	G=0.010
South Asian	Sub	98	A=1.00	G=0.00
Other	Sub	684	A=0.956	G=0.044

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=0.949076	G=0.050924
gnomAD - Exomes	Global	Study-wide	154946	A=0.991391	G=0.008609
gnomAD - Exomes	European	Sub	77146	A=0.99940	G=0.00060
gnomAD - Exomes	Asian	Sub	33652	A=0.99905	G=0.00095
gnomAD - Exomes	American	Sub	24986	A=0.99128	G=0.00872
gnomAD - Exomes	Ashkenazi Jewish	Sub	8180	A=0.9999	G=0.0001
gnomAD - Exomes	African	Sub	6692	A=0.8492	G=0.1508
gnomAD - Exomes	Other	Sub	4290	A=0.9935	G=0.0065
gnomAD - Genomes	Global	Study-wide	140096	A=0.952982	G=0.047018
gnomAD - Genomes	European	Sub	75874	A=0.99929	G=0.00071
gnomAD - Genomes	African	Sub	41974	A=0.85327	G=0.14673
gnomAD - Genomes	American	Sub	13652	A=0.97905	G=0.02095
gnomAD - Genomes	Ashkenazi Jewish	Sub	3314	A=1.0000	G=0.0000
gnomAD - Genomes	East Asian	Sub	3128	A=0.9968	G=0.0032
gnomAD - Genomes	Other	Sub	2154	A=0.9638	G=0.0362
ExAC	Global	Study-wide	28900	A=0.98273	G=0.01727
ExAC	Europe	Sub	14676	A=0.99925	G=0.00075
ExAC	Asian	Sub	9720	A=0.9992	G=0.0008
ExAC	African	Sub	2956	A=0.8440	G=0.1560
ExAC	American	Sub	1296	A=0.9853	G=0.0147
ExAC	Other	Sub	252	A=1.000	G=0.000
Allele Frequency Aggregator	Total	Global	14420	A=0.96422	G=0.03578
Allele Frequency Aggregator	European	Sub	9824	A=0.9985	G=0.0015
Allele Frequency Aggregator	African	Sub	2946	A=0.8435	G=0.1565
Allele Frequency Aggregator	Other	Sub	684	A=0.956	G=0.044
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.990	G=0.010
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.973	G=0.027
Allele Frequency Aggregator	Asian	Sub	112	A=1.000	G=0.000
Allele Frequency Aggregator	South Asian	Sub	98	A=1.00	G=0.00
GO Exome Sequencing Project	Global	Study-wide	12794	A=0.97405	G=0.02595
GO Exome Sequencing Project	European American	Sub	8484	A=0.9994	G=0.0006
GO Exome Sequencing Project	African American	Sub	4310	A=0.9241	G=0.0759
1000Genomes_30x	Global	Study-wide	6404	A=0.9480	G=0.0520
1000Genomes_30x	African	Sub	1786	A=0.8180	G=0.1820
1000Genomes_30x	Europe	Sub	1266	A=1.0000	G=0.0000
1000Genomes_30x	South Asian	Sub	1202	A=1.0000	G=0.0000
1000Genomes_30x	East Asian	Sub	1170	A=0.9991	G=0.0009
1000Genomes_30x	American	Sub	980	A=0.993	G=0.007
1000Genomes	Global	Study-wide	5008	A=0.9513	G=0.0487
1000Genomes	African	Sub	1322	A=0.8200	G=0.1800
1000Genomes	East Asian	Sub	1008	A=0.9990	G=0.0010
1000Genomes	Europe	Sub	1006	A=1.0000	G=0.0000
1000Genomes	South Asian	Sub	978	A=1.000	G=0.000
1000Genomes	American	Sub	694	A=0.993	G=0.007
Korean Genome Project	KOREAN	Study-wide	1774	A=0.9994	G=0.0006
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	A=0.998	G=0.002
Qatari	Global	Study-wide	216	A=0.968	G=0.032
SGDP_PRJ	Global	Study-wide	24	A=0.46	G=0.54

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 17	NC_000017.11:g.7651662A>G
GRCh38.p14 chr 17	NC_000017.11:g.7651662A>T
GRCh37.p13 chr 17	NC_000017.10:g.7554980A>G
GRCh37.p13 chr 17	NC_000017.10:g.7554980A>T

Gene: ATP1B2, ATPase Na+/K+ transporting subunit beta 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP1B2 transcript variant 2	NM_001303263.2:c.-5-2179A… NM_001303263.2:c.-5-2179A>G	N/A	Intron Variant
ATP1B2 transcript variant 1	NM_001678.5:c.112+32A>G	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	A=	G	T
GRCh38.p14 chr 17	NC_000017.11:g.7651662=	NC_000017.11:g.7651662A>G	NC_000017.11:g.7651662A>T
GRCh37.p13 chr 17	NC_000017.10:g.7554980=	NC_000017.10:g.7554980A>G	NC_000017.10:g.7554980A>T
ATP1B2 transcript variant 2	NM_001303263.2:c.-5-2179=	NM_001303263.2:c.-5-2179A>G	NM_001303263.2:c.-5-2179A>T
ATP1B2 transcript	NM_001678.3:c.112+32=	NM_001678.3:c.112+32A>G	NM_001678.3:c.112+32A>T
ATP1B2 transcript variant 1	NM_001678.5:c.112+32=	NM_001678.5:c.112+32A>G	NM_001678.5:c.112+32A>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#.

32 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss35509976	May 24, 2005 (125)
2	COMPLETE_GENOMICS	ss169011127	Jul 04, 2010 (132)
3	1000GENOMES	ss227449774	Jul 14, 2010 (132)
4	1000GENOMES	ss491115317	May 04, 2012 (137)
5	SSMP	ss660940196	Apr 25, 2013 (138)
6	NHLBI-ESP	ss713354996	Apr 25, 2013 (138)
7	1000GENOMES	ss1357812713	Aug 21, 2014 (142)
8	EVA_EXAC	ss1692579262	Apr 01, 2015 (144)
9	EVA_MGP	ss1711446972	Apr 01, 2015 (144)
10	WEILL_CORNELL_DGM	ss1936345795	Feb 12, 2016 (147)
11	HUMAN_LONGEVITY	ss2215318188	Dec 20, 2016 (150)
12	GNOMAD	ss2742409581	Nov 08, 2017 (151)
13	GNOMAD	ss2749679593	Nov 08, 2017 (151)
14	GNOMAD	ss2947434287	Nov 08, 2017 (151)
15	AFFY	ss2985722739	Nov 08, 2017 (151)
16	KHV_HUMAN_GENOMES	ss3819691573	Jul 13, 2019 (153)
17	EVA	ss3825073808	Apr 27, 2020 (154)
18	SGDP_PRJ	ss3885289371	Apr 27, 2020 (154)
19	KOGIC	ss3978353690	Apr 27, 2020 (154)
20	EVA	ss3986711473	Apr 27, 2021 (155)
21	TOPMED	ss5028665092	Apr 27, 2021 (155)
22	TOMMO_GENOMICS	ss5221388485	Apr 27, 2021 (155)
23	TOMMO_GENOMICS	ss5221388486	Apr 27, 2021 (155)
24	1000G_HIGH_COVERAGE	ss5302343917	Oct 17, 2022 (156)
25	EVA	ss5426240184	Oct 17, 2022 (156)
26	HUGCELL_USP	ss5495527077	Oct 17, 2022 (156)
27	1000G_HIGH_COVERAGE	ss5605658645	Oct 17, 2022 (156)
28	SANFORD_IMAGENETICS	ss5659676347	Oct 17, 2022 (156)
29	TOMMO_GENOMICS	ss5776952997	Oct 17, 2022 (156)
30	TOMMO_GENOMICS	ss5776952998	Oct 17, 2022 (156)
31	EVA	ss5913133756	Oct 17, 2022 (156)
32	EVA	ss5951086627	Oct 17, 2022 (156)
33	1000Genomes	NC_000017.10 - 7554980	Oct 12, 2018 (152)
34	1000Genomes_30x	NC_000017.11 - 7651662	Oct 17, 2022 (156)
35	ExAC	NC_000017.10 - 7554980	Oct 12, 2018 (152)
36	gnomAD - Genomes	NC_000017.11 - 7651662	Apr 27, 2021 (155)
37	gnomAD - Exomes	NC_000017.10 - 7554980	Jul 13, 2019 (153)
38	GO Exome Sequencing Project	NC_000017.10 - 7554980	Oct 12, 2018 (152)
39	Korean Genome Project	NC_000017.11 - 7651662	Apr 27, 2020 (154)
40	Medical Genome Project healthy controls from Spanish population	NC_000017.10 - 7554980	Apr 27, 2020 (154)
41	Qatari	NC_000017.10 - 7554980	Apr 27, 2020 (154)
42	SGDP_PRJ	NC_000017.10 - 7554980	Apr 27, 2020 (154)
43	8.3KJPN Submission ignored due to conflicting rows: Row 79357792 (NC_000017.10:7554979:A:T 1/16758) Row 79357793 (NC_000017.10:7554979:A:G 4/16758)	-	Apr 27, 2021 (155)
44	8.3KJPN Submission ignored due to conflicting rows: Row 79357792 (NC_000017.10:7554979:A:T 1/16758) Row 79357793 (NC_000017.10:7554979:A:G 4/16758)	-	Apr 27, 2021 (155)
45	14KJPN Submission ignored due to conflicting rows: Row 110790101 (NC_000017.11:7651661:A:T 1/28256) Row 110790102 (NC_000017.11:7651661:A:G 6/28256)	-	Oct 17, 2022 (156)
46	14KJPN Submission ignored due to conflicting rows: Row 110790101 (NC_000017.11:7651661:A:T 1/28256) Row 110790102 (NC_000017.11:7651661:A:G 6/28256)	-	Oct 17, 2022 (156)
47	TopMed	NC_000017.11 - 7651662	Apr 27, 2021 (155)
48	ALFA	NC_000017.11 - 7651662	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
ss35509976, ss169011127	NC_000017.9:7495704:A:G	NC_000017.11:7651661:A:G	(self)
71023352, 3007002, 11707636, 1530938, 562732, 18387717, 37306351, ss227449774, ss491115317, ss660940196, ss713354996, ss1357812713, ss1692579262, ss1711446972, ss1936345795, ss2742409581, ss2749679593, ss2947434287, ss2985722739, ss3825073808, ss3885289371, ss3986711473, ss5221388486, ss5426240184, ss5659676347, ss5951086627	NC_000017.10:7554979:A:G	NC_000017.11:7651661:A:G	(self)
93184580, 500814891, 34731691, 244210754, 9666552057, ss2215318188, ss3819691573, ss3978353690, ss5028665092, ss5302343917, ss5495527077, ss5605658645, ss5776952998, ss5913133756	NC_000017.11:7651661:A:G	NC_000017.11:7651661:A:G	(self)
ss5221388485	NC_000017.10:7554979:A:T	NC_000017.11:7651661:A:T	(self)
ss5776952997	NC_000017.11:7651661:A:T	NC_000017.11:7651661:A:T

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs28729777

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

rs28729777