Name: rs10889805
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.

rs10889805

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:69305121 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.369527 (97810/264690, TOPMED)
A=0.387615 (54280/140036, GnomAD)
A=0.30929 (8740/28258, 14KJPN) (+ 16 more)
A=0.38507 (7274/18890, ALFA)
A=0.31122 (5216/16760, 8.3KJPN)
A=0.3663 (2346/6404, 1000G_30x)
A=0.3666 (1836/5008, 1000G)
A=0.4491 (2012/4480, Estonian)
A=0.3282 (1265/3854, ALSPAC)
A=0.3314 (1229/3708, TWINSUK)
A=0.3648 (1069/2930, KOREAN)
A=0.3684 (675/1832, Korea1K)
A=0.340 (339/998, GoNL)
A=0.375 (225/600, NorthernSweden)
C=0.361 (107/296, SGDP_PRJ)
A=0.384 (83/216, Qatari)
A=0.266 (57/214, Vietnamese)
A=0.30 (12/40, GENOME_DK)
C=0.46 (12/26, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	C=0.61493	A=0.38507
European	Sub	14286	C=0.62054	A=0.37946
African	Sub	2946	C=0.5428	A=0.4572
African Others	Sub	114	C=0.544	A=0.456
African American	Sub	2832	C=0.5427	A=0.4573
Asian	Sub	112	C=0.732	A=0.268
East Asian	Sub	86	C=0.72	A=0.28
Other Asian	Sub	26	C=0.77	A=0.23
Latin American 1	Sub	146	C=0.603	A=0.397
Latin American 2	Sub	610	C=0.790	A=0.210
South Asian	Sub	98	C=0.70	A=0.30
Other	Sub	692	C=0.623	A=0.377

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=0.630473	A=0.369527
gnomAD - Genomes	Global	Study-wide	140036	C=0.612385	A=0.387615
gnomAD - Genomes	European	Sub	75856	C=0.63623	A=0.36377
gnomAD - Genomes	African	Sub	41950	C=0.52551	A=0.47449
gnomAD - Genomes	American	Sub	13636	C=0.72221	A=0.27779
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	C=0.6540	A=0.3460
gnomAD - Genomes	East Asian	Sub	3128	C=0.6694	A=0.3306
gnomAD - Genomes	Other	Sub	2148	C=0.6224	A=0.3776
14KJPN	JAPANESE	Study-wide	28258	C=0.69071	A=0.30929
Allele Frequency Aggregator	Total	Global	18890	C=0.61493	A=0.38507
Allele Frequency Aggregator	European	Sub	14286	C=0.62054	A=0.37946
Allele Frequency Aggregator	African	Sub	2946	C=0.5428	A=0.4572
Allele Frequency Aggregator	Other	Sub	692	C=0.623	A=0.377
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.790	A=0.210
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.603	A=0.397
Allele Frequency Aggregator	Asian	Sub	112	C=0.732	A=0.268
Allele Frequency Aggregator	South Asian	Sub	98	C=0.70	A=0.30
8.3KJPN	JAPANESE	Study-wide	16760	C=0.68878	A=0.31122
1000Genomes_30x	Global	Study-wide	6404	C=0.6337	A=0.3663
1000Genomes_30x	African	Sub	1786	C=0.4748	A=0.5252
1000Genomes_30x	Europe	Sub	1266	C=0.6319	A=0.3681
1000Genomes_30x	South Asian	Sub	1202	C=0.7022	A=0.2978
1000Genomes_30x	East Asian	Sub	1170	C=0.6991	A=0.3009
1000Genomes_30x	American	Sub	980	C=0.763	A=0.237
1000Genomes	Global	Study-wide	5008	C=0.6334	A=0.3666
1000Genomes	African	Sub	1322	C=0.4713	A=0.5287
1000Genomes	East Asian	Sub	1008	C=0.6974	A=0.3026
1000Genomes	Europe	Sub	1006	C=0.6252	A=0.3748
1000Genomes	South Asian	Sub	978	C=0.706	A=0.294
1000Genomes	American	Sub	694	C=0.759	A=0.241
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.5509	A=0.4491
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6718	A=0.3282
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6686	A=0.3314
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6352	A=0.3648
Korean Genome Project	KOREAN	Study-wide	1832	C=0.6316	A=0.3684
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.660	A=0.340
Northern Sweden	ACPOP	Study-wide	600	C=0.625	A=0.375
SGDP_PRJ	Global	Study-wide	296	C=0.361	A=0.639
Qatari	Global	Study-wide	216	C=0.616	A=0.384
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.734	A=0.266
The Danish reference pan genome	Danish	Study-wide	40	C=0.70	A=0.30
Siberian	Global	Study-wide	26	C=0.46	A=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 1	NC_000001.11:g.69305121C>A
GRCh37.p13 chr 1	NC_000001.10:g.69770804C>A

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=	A
GRCh38.p14 chr 1	NC_000001.11:g.69305121=	NC_000001.11:g.69305121C>A
GRCh37.p13 chr 1	NC_000001.10:g.69770804=	NC_000001.10:g.69770804C>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#.

64 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss16384110	Feb 27, 2004 (120)
2	SC_SNP	ss18135790	Feb 27, 2004 (120)
3	SC_SNP	ss18243012	Feb 27, 2004 (120)
4	ABI	ss41239637	Mar 14, 2006 (126)
5	HGSV	ss82745551	Dec 14, 2007 (130)
6	BCMHGSC_JDW	ss87520464	Mar 23, 2008 (129)
7	BGI	ss102750460	Dec 01, 2009 (131)
8	1000GENOMES	ss110602356	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss118781991	Dec 01, 2009 (131)
10	ENSEMBL	ss137991477	Dec 01, 2009 (131)
11	ENSEMBL	ss161270810	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss163489117	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss164499655	Jul 04, 2010 (132)
14	BUSHMAN	ss198587320	Jul 04, 2010 (132)
15	1000GENOMES	ss218440133	Jul 14, 2010 (132)
16	1000GENOMES	ss230574953	Jul 14, 2010 (132)
17	1000GENOMES	ss238261325	Jul 15, 2010 (132)
18	BL	ss253165943	May 09, 2011 (134)
19	GMI	ss275866014	May 04, 2012 (137)
20	GMI	ss284067751	Apr 25, 2013 (138)
21	PJP	ss290531949	May 09, 2011 (134)
22	TISHKOFF	ss554222907	Apr 25, 2013 (138)
23	SSMP	ss648103097	Apr 25, 2013 (138)
24	EVA-GONL	ss975264016	Aug 21, 2014 (142)
25	JMKIDD_LAB	ss1067967137	Aug 21, 2014 (142)
26	1000GENOMES	ss1291288649	Aug 21, 2014 (142)
27	DDI	ss1425842973	Apr 01, 2015 (144)
28	EVA_GENOME_DK	ss1574130657	Apr 01, 2015 (144)
29	EVA_DECODE	ss1584634403	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1600385080	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1643379113	Apr 01, 2015 (144)
32	HAMMER_LAB	ss1794517455	Sep 08, 2015 (146)
33	WEILL_CORNELL_DGM	ss1918471669	Feb 12, 2016 (147)
34	JJLAB	ss2019753196	Sep 14, 2016 (149)
35	USC_VALOUEV	ss2147769525	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2163330081	Dec 20, 2016 (150)
37	SYSTEMSBIOZJU	ss2624389968	Nov 08, 2017 (151)
38	GRF	ss2697688064	Nov 08, 2017 (151)
39	GNOMAD	ss2756267398	Nov 08, 2017 (151)
40	SWEGEN	ss2986974656	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3023638575	Nov 08, 2017 (151)
42	CSHL	ss3343500408	Nov 08, 2017 (151)
43	EGCUT_WGS	ss3655046509	Jul 12, 2019 (153)
44	EVA_DECODE	ss3686966496	Jul 12, 2019 (153)
45	ACPOP	ss3727134014	Jul 12, 2019 (153)
46	EVA	ss3746326291	Jul 12, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3799332727	Jul 12, 2019 (153)
48	EVA	ss3826223064	Apr 25, 2020 (154)
49	SGDP_PRJ	ss3849054188	Apr 25, 2020 (154)
50	KRGDB	ss3894085133	Apr 25, 2020 (154)
51	KOGIC	ss3944705532	Apr 25, 2020 (154)
52	TOPMED	ss4453243386	Apr 25, 2021 (155)
53	TOMMO_GENOMICS	ss5144392534	Apr 25, 2021 (155)
54	1000G_HIGH_COVERAGE	ss5242612820	Oct 12, 2022 (156)
55	EVA	ss5319361471	Oct 12, 2022 (156)
56	HUGCELL_USP	ss5443641955	Oct 12, 2022 (156)
57	1000G_HIGH_COVERAGE	ss5515064160	Oct 12, 2022 (156)
58	SANFORD_IMAGENETICS	ss5625726304	Oct 12, 2022 (156)
59	TOMMO_GENOMICS	ss5669291350	Oct 12, 2022 (156)
60	YY_MCH	ss5800682211	Oct 12, 2022 (156)
61	EVA	ss5832093264	Oct 12, 2022 (156)
62	EVA	ss5848948551	Oct 12, 2022 (156)
63	EVA	ss5908657663	Oct 12, 2022 (156)
64	EVA	ss5937566009	Oct 12, 2022 (156)
65	1000Genomes	NC_000001.10 - 69770804	Oct 11, 2018 (152)
66	1000Genomes_30x	NC_000001.11 - 69305121	Oct 12, 2022 (156)
67	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 69770804	Oct 11, 2018 (152)
68	Genetic variation in the Estonian population	NC_000001.10 - 69770804	Oct 11, 2018 (152)
69	The Danish reference pan genome	NC_000001.10 - 69770804	Apr 25, 2020 (154)
70	gnomAD - Genomes	NC_000001.11 - 69305121	Apr 25, 2021 (155)
71	Genome of the Netherlands Release 5	NC_000001.10 - 69770804	Apr 25, 2020 (154)
72	KOREAN population from KRGDB	NC_000001.10 - 69770804	Apr 25, 2020 (154)
73	Korean Genome Project	NC_000001.11 - 69305121	Apr 25, 2020 (154)
74	Northern Sweden	NC_000001.10 - 69770804	Jul 12, 2019 (153)
75	Qatari	NC_000001.10 - 69770804	Apr 25, 2020 (154)
76	SGDP_PRJ	NC_000001.10 - 69770804	Apr 25, 2020 (154)
77	Siberian	NC_000001.10 - 69770804	Apr 25, 2020 (154)
78	8.3KJPN	NC_000001.10 - 69770804	Apr 25, 2021 (155)
79	14KJPN	NC_000001.11 - 69305121	Oct 12, 2022 (156)
80	TopMed	NC_000001.11 - 69305121	Apr 25, 2021 (155)
81	UK 10K study - Twins	NC_000001.10 - 69770804	Oct 11, 2018 (152)
82	A Vietnamese Genetic Variation Database	NC_000001.10 - 69770804	Jul 12, 2019 (153)
83	ALFA	NC_000001.11 - 69305121	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)
rs57343956	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss82745551	NC_000001.8:69482824:C:A	NC_000001.11:69305120:C:A	(self)
ss87520464, ss110602356, ss118781991, ss163489117, ss164499655, ss198587320, ss253165943, ss275866014, ss284067751, ss290531949, ss1584634403	NC_000001.9:69543391:C:A	NC_000001.11:69305120:C:A	(self)
2021254, 1108545, 784757, 1543058, 473151, 1262527, 418879, 513599, 1071168, 285879, 2361841, 1108545, 232302, ss218440133, ss230574953, ss238261325, ss554222907, ss648103097, ss975264016, ss1067967137, ss1291288649, ss1425842973, ss1574130657, ss1600385080, ss1643379113, ss1794517455, ss1918471669, ss2019753196, ss2147769525, ss2624389968, ss2697688064, ss2756267398, ss2986974656, ss3343500408, ss3655046509, ss3727134014, ss3746326291, ss3826223064, ss3849054188, ss3894085133, ss5144392534, ss5319361471, ss5625726304, ss5832093264, ss5937566009	NC_000001.10:69770803:C:A	NC_000001.11:69305120:C:A	(self)
2590095, 14256403, 1083533, 3128454, 16849721, 8773592387, ss2163330081, ss3023638575, ss3686966496, ss3799332727, ss3944705532, ss4453243386, ss5242612820, ss5443641955, ss5515064160, ss5669291350, ss5800682211, ss5848948551, ss5908657663	NC_000001.11:69305120:C:A	NC_000001.11:69305120:C:A	(self)
ss16384110, ss18135790, ss18243012	NT_032977.6:31333872:C:A	NC_000001.11:69305120:C:A	(self)
ss41239637, ss102750460, ss137991477, ss161270810	NT_032977.9:39742721:C:A	NC_000001.11:69305120:C:A	(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 rs10889805

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

rs10889805