Name: rs34059732
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.

rs34059732

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:116382709 (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: insGT
Variation Type: Indel Insertion and Deletion
Frequency: T=0.248649 (65815/264690, TOPMED)
T=0.239327 (33501/139980, GnomAD)
insGT=0.33005 (9326/28256, 14KJPN) (+ 11 more)
T=0.26199 (4852/18520, ALFA)
insGT=0.33210 (5566/16760, 8.3KJPN)
T=0.2879 (1844/6404, 1000G_30x)
T=0.2995 (1500/5008, 1000G)
T=0.3116 (1396/4480, Estonian)
T=0.2680 (1033/3854, ALSPAC)
T=0.2667 (989/3708, TWINSUK)
T=0.241 (241/998, GoNL)
T=0.337 (202/600, NorthernSweden)
insGT=0.229 (49/214, Vietnamese)
T=0.20 (8/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP1A1 : 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	18520	T=0.26199	TGT=0.73801
European	Sub	14152	T=0.29183	TGT=0.70817
African	Sub	2898	T=0.0611	TGT=0.9389
African Others	Sub	114	T=0.000	TGT=1.000
African American	Sub	2784	T=0.0636	TGT=0.9364
Asian	Sub	112	T=0.768	TGT=0.232
East Asian	Sub	86	T=0.78	TGT=0.22
Other Asian	Sub	26	T=0.73	TGT=0.27
Latin American 1	Sub	146	T=0.308	TGT=0.692
Latin American 2	Sub	610	T=0.431	TGT=0.569
South Asian	Sub	98	T=0.13	TGT=0.87
Other	Sub	504	T=0.274	TGT=0.726

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	- No frequency provided	insGT=0.751351
gnomAD - Genomes	Global	Study-wide	139980	- No frequency provided	insGT=0.760673
gnomAD - Genomes	European	Sub	75760	- No frequency provided	insGT=0.70791
gnomAD - Genomes	African	Sub	41996	- No frequency provided	insGT=0.93895
gnomAD - Genomes	American	Sub	13636	- No frequency provided	insGT=0.66332
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	- No frequency provided	insGT=0.5819
gnomAD - Genomes	East Asian	Sub	3120	- No frequency provided	insGT=0.2888
gnomAD - Genomes	Other	Sub	2146	- No frequency provided	insGT=0.7162
14KJPN	JAPANESE	Study-wide	28256	- No frequency provided	insGT=0.33005
Allele Frequency Aggregator	Total	Global	18520	T=0.26199	insGT=0.73801
Allele Frequency Aggregator	European	Sub	14152	T=0.29183	insGT=0.70817
Allele Frequency Aggregator	African	Sub	2898	T=0.0611	insGT=0.9389
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.431	insGT=0.569
Allele Frequency Aggregator	Other	Sub	504	T=0.274	insGT=0.726
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.308	insGT=0.692
Allele Frequency Aggregator	Asian	Sub	112	T=0.768	insGT=0.232
Allele Frequency Aggregator	South Asian	Sub	98	T=0.13	insGT=0.87
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	insGT=0.33210
1000Genomes_30x	Global	Study-wide	6404	- No frequency provided	insGT=0.7121
1000Genomes_30x	African	Sub	1786	- No frequency provided	insGT=0.9894
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	insGT=0.7125
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	insGT=0.7812
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	insGT=0.2692
1000Genomes_30x	American	Sub	980	- No frequency provided	insGT=0.650
1000Genomes	Global	Study-wide	5008	- No frequency provided	insGT=0.7005
1000Genomes	African	Sub	1322	- No frequency provided	insGT=0.9871
1000Genomes	East Asian	Sub	1008	- No frequency provided	insGT=0.2698
1000Genomes	Europe	Sub	1006	- No frequency provided	insGT=0.7058
1000Genomes	South Asian	Sub	978	- No frequency provided	insGT=0.788
1000Genomes	American	Sub	694	- No frequency provided	insGT=0.648
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	insGT=0.6884
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	- No frequency provided	insGT=0.7320
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	- No frequency provided	insGT=0.7333
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	- No frequency provided	insGT=0.759
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	insGT=0.663
A Vietnamese Genetic Variation Database	Global	Study-wide	214	- No frequency provided	insGT=0.229
The Danish reference pan genome	Danish	Study-wide	40	- No frequency provided	insGT=0.80

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 1	NC_000001.11:g.116382709_116382710insGT
GRCh37.p13 chr 1	NC_000001.10:g.116925331_116925332insGT
ATP1A1 RefSeqGene	NG_047036.1:g.15525_15526insGT

Gene: ATP1A1, ATPase Na+/K+ transporting subunit alpha 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP1A1 transcript variant 1	NM_000701.8:c.13-1305_13-… NM_000701.8:c.13-1305_13-1304insGT	N/A	Intron Variant
ATP1A1 transcript variant 3	NM_001160233.2:c.13-1305_… NM_001160233.2:c.13-1305_13-1304insGT	N/A	Intron Variant
ATP1A1 transcript variant 4	NM_001160234.2:c.	N/A	Genic 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	T=	insGT
GRCh38.p14 chr 1	NC_000001.11:g.116382709=	NC_000001.11:g.116382709_116382710insGT
GRCh37.p13 chr 1	NC_000001.10:g.116925331=	NC_000001.10:g.116925331_116925332insGT
ATP1A1 RefSeqGene	NG_047036.1:g.15525=	NG_047036.1:g.15525_15526insGT
ATP1A1 transcript variant 1	NM_000701.7:c.13-1305=	NM_000701.7:c.13-1305_13-1304insGT
ATP1A1 transcript variant 1	NM_000701.8:c.13-1305=	NM_000701.8:c.13-1305_13-1304insGT
ATP1A1 transcript variant 3	NM_001160233.1:c.13-1305=	NM_001160233.1:c.13-1305_13-1304insGT
ATP1A1 transcript variant 3	NM_001160233.2:c.13-1305=	NM_001160233.2:c.13-1305_13-1304insGT
ATP1A1 transcript variant X1	XM_005270890.1:c.-81-1305=	XM_005270890.1:c.-81-1305_-81-1304insGT

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#.

55 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ABI	ss41176305	Mar 13, 2006 (126)
2	HGSV	ss77949779	Dec 07, 2007 (129)
3	HGSV	ss79721759	Dec 15, 2007 (130)
4	HGSV	ss81112801	Dec 15, 2007 (130)
5	BCMHGSC_JDW	ss103801343	Dec 01, 2009 (131)
6	BL	ss255937653	May 09, 2011 (135)
7	GMI	ss287679895	May 09, 2011 (134)
8	GMI	ss288030547	May 04, 2012 (138)
9	1000GENOMES	ss326079404	May 09, 2011 (135)
10	1000GENOMES	ss326082417	May 09, 2011 (135)
11	1000GENOMES	ss326108402	May 09, 2011 (135)
12	1000GENOMES	ss498980610	May 04, 2012 (138)
13	LUNTER	ss550974357	Apr 25, 2013 (138)
14	LUNTER	ss550989316	Apr 25, 2013 (138)
15	LUNTER	ss552800708	Apr 25, 2013 (138)
16	TISHKOFF	ss554352490	Apr 25, 2013 (138)
17	SSMP	ss663112634	Apr 01, 2015 (144)
18	BILGI_BIOE	ss666107548	Apr 25, 2013 (138)
19	EVA-GONL	ss975607486	Aug 21, 2014 (142)
20	1000GENOMES	ss1367827353	Aug 21, 2014 (142)
21	DDI	ss1536245275	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1574012956	Apr 01, 2015 (144)
23	EVA_DECODE	ss1584989548	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1701155748	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1701155761	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1794984007	Sep 08, 2015 (146)
27	GENOMED	ss1966849817	Jul 19, 2016 (147)
28	JJLAB	ss2030345267	Sep 14, 2016 (149)
29	GNOMAD	ss2759961357	Nov 08, 2017 (151)
30	SWEGEN	ss2987495893	Nov 08, 2017 (151)
31	MCHAISSO	ss3063604878	Nov 08, 2017 (151)
32	MCHAISSO	ss3065323106	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3645067938	Oct 11, 2018 (152)
34	EGCUT_WGS	ss3655586945	Jul 12, 2019 (153)
35	EVA_DECODE	ss3687600319	Jul 12, 2019 (153)
36	ACPOP	ss3727419573	Jul 12, 2019 (153)
37	PACBIO	ss3783529601	Jul 12, 2019 (153)
38	PACBIO	ss3789169854	Jul 12, 2019 (153)
39	PACBIO	ss3794042813	Jul 12, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3799717079	Jul 12, 2019 (153)
41	EVA	ss3826388470	Apr 25, 2020 (154)
42	EVA	ss3836585481	Apr 25, 2020 (154)
43	EVA	ss3841994015	Apr 25, 2020 (154)
44	TOPMED	ss4464860604	Apr 25, 2021 (155)
45	TOMMO_GENOMICS	ss5145838204	Apr 25, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5243729991	Oct 12, 2022 (156)
47	HUGCELL_USP	ss5444642551	Oct 12, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5516786535	Oct 12, 2022 (156)
49	SANFORD_IMAGENETICS	ss5626367197	Oct 12, 2022 (156)
50	TOMMO_GENOMICS	ss5671153422	Oct 12, 2022 (156)
51	YY_MCH	ss5800961175	Oct 12, 2022 (156)
52	EVA	ss5832531570	Oct 12, 2022 (156)
53	EVA	ss5849081816	Oct 12, 2022 (156)
54	EVA	ss5909941735	Oct 12, 2022 (156)
55	EVA	ss5938237336	Oct 12, 2022 (156)
56	1000Genomes	NC_000001.10 - 116925331	Oct 11, 2018 (152)
57	1000Genomes_30x	NC_000001.11 - 116382709	Oct 12, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 116925331	Oct 11, 2018 (152)
59	Genetic variation in the Estonian population	NC_000001.10 - 116925331	Oct 11, 2018 (152)
60	The Danish reference pan genome	NC_000001.10 - 116925331	Apr 25, 2020 (154)
61	gnomAD - Genomes	NC_000001.11 - 116382709	Apr 25, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000001.10 - 116925331	Apr 25, 2020 (154)
63	Northern Sweden	NC_000001.10 - 116925331	Jul 12, 2019 (153)
64	8.3KJPN	NC_000001.10 - 116925331	Apr 25, 2021 (155)
65	14KJPN	NC_000001.11 - 116382709	Oct 12, 2022 (156)
66	TopMed	NC_000001.11 - 116382709	Apr 25, 2021 (155)
67	UK 10K study - Twins	NC_000001.10 - 116925331	Oct 11, 2018 (152)
68	A Vietnamese Genetic Variation Database	NC_000001.10 - 116925331	Jul 12, 2019 (153)
69	ALFA	NC_000001.11 - 116382709	Apr 25, 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)
rs149413563	Sep 17, 2011 (135)
rs201254981	Apr 25, 2013 (138)
rs59053780	May 26, 2008 (130)
rs144336378	Apr 25, 2013 (138)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss255937653, ss288030547, ss326079404, ss326082417, ss326108402, ss550974357, ss550989316, ss552800708, ss1584989548	NC_000001.9:116726853::TG	NC_000001.11:116382708:T:TGT	(self)
3353603, 1858041, 1325193, 168329, 807866, 704438, 3807511, 1858041, 401690, ss498980610, ss663112634, ss666107548, ss975607486, ss1367827353, ss1536245275, ss1574012956, ss1701155748, ss1701155761, ss1794984007, ss1966849817, ss2030345267, ss2759961357, ss2987495893, ss3655586945, ss3727419573, ss3783529601, ss3789169854, ss3794042813, ss3826388470, ss3836585481, ss5145838204, ss5626367197, ss5832531570, ss5938237336	NC_000001.10:116925330::TG	NC_000001.11:116382708:T:TGT	(self)
ss554352490	NC_000001.10:116925331::GT	NC_000001.11:116382708:T:TGT	(self)
4312470, 23718785, 4990526, 28466939, ss3063604878, ss3065323106, ss3645067938, ss3687600319, ss3799717079, ss3841994015, ss4464860604, ss5243729991, ss5444642551, ss5516786535, ss5671153422, ss5800961175, ss5849081816, ss5909941735	NC_000001.11:116382708::TG	NC_000001.11:116382708:T:TGT	(self)
198385532	NC_000001.11:116382708:T:TGT	NC_000001.11:116382708:T:TGT	(self)
ss41176305, ss287679895	NT_032977.9:86897248::TG	NC_000001.11:116382708:T:TGT	(self)
ss77949779, ss79721759, ss81112801, ss103801343	NT_032977.9:86897249::GT	NC_000001.11:116382708:T:TGT	(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 rs34059732

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

rs34059732