Name: rs469999
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.

rs469999

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:48241244 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.239650 (63433/264690, TOPMED)
A=0.246955 (34589/140062, GnomAD)
A=0.19265 (5444/28258, 14KJPN) (+ 17 more)
A=0.29339 (7905/26944, ALFA)
A=0.19290 (3233/16760, 8.3KJPN)
A=0.1950 (1249/6404, 1000G_30x)
A=0.1961 (982/5008, 1000G)
A=0.3768 (1688/4480, Estonian)
A=0.3298 (1271/3854, ALSPAC)
A=0.3328 (1234/3708, TWINSUK)
A=0.1055 (309/2930, KOREAN)
A=0.1617 (306/1892, HapMap)
A=0.1174 (215/1832, Korea1K)
A=0.338 (337/998, GoNL)
A=0.362 (217/600, NorthernSweden)
A=0.184 (96/522, SGDP_PRJ)
A=0.199 (43/216, Qatari)
A=0.076 (16/210, Vietnamese)
A=0.20 (10/50, Siberian)
A=0.45 (18/40, GENOME_DK)

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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	26944	A=0.29339	G=0.70661	0.096942	0.510169	0.392889	20
European	Sub	18044	A=0.34355	G=0.65645	0.118377	0.431279	0.450344	0
African	Sub	4050	A=0.0709	G=0.9291	0.005432	0.863704	0.130864	0
African Others	Sub	126	A=0.016	G=0.984	0.0	0.968254	0.031746	0
African American	Sub	3924	A=0.0726	G=0.9274	0.005607	0.860347	0.134047	0
Asian	Sub	160	A=0.081	G=0.919	0.0	0.8375	0.1625	0
East Asian	Sub	102	A=0.059	G=0.941	0.0	0.882353	0.117647	0
Other Asian	Sub	58	A=0.12	G=0.88	0.0	0.758621	0.241379	0
Latin American 1	Sub	292	A=0.233	G=0.767	0.075342	0.609589	0.315068	1
Latin American 2	Sub	2768	A=0.3266	G=0.6734	0.114884	0.461705	0.42341	1
South Asian	Sub	110	A=0.273	G=0.727	0.072727	0.527273	0.4	0
Other	Sub	1520	A=0.2658	G=0.7342	0.069737	0.538158	0.392105	0

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=0.239650	G=0.760350
gnomAD - Genomes	Global	Study-wide	140062	A=0.246955	G=0.753045
gnomAD - Genomes	European	Sub	75826	A=0.33587	G=0.66413
gnomAD - Genomes	African	Sub	41986	A=0.07067	G=0.92933
gnomAD - Genomes	American	Sub	13644	A=0.33018	G=0.66982
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.2319	G=0.7681
gnomAD - Genomes	East Asian	Sub	3132	A=0.1082	G=0.8918
gnomAD - Genomes	Other	Sub	2150	A=0.2507	G=0.7493
14KJPN	JAPANESE	Study-wide	28258	A=0.19265	G=0.80735
Allele Frequency Aggregator	Total	Global	26944	A=0.29339	G=0.70661
Allele Frequency Aggregator	European	Sub	18044	A=0.34355	G=0.65645
Allele Frequency Aggregator	African	Sub	4050	A=0.0709	G=0.9291
Allele Frequency Aggregator	Latin American 2	Sub	2768	A=0.3266	G=0.6734
Allele Frequency Aggregator	Other	Sub	1520	A=0.2658	G=0.7342
Allele Frequency Aggregator	Latin American 1	Sub	292	A=0.233	G=0.767
Allele Frequency Aggregator	Asian	Sub	160	A=0.081	G=0.919
Allele Frequency Aggregator	South Asian	Sub	110	A=0.273	G=0.727
8.3KJPN	JAPANESE	Study-wide	16760	A=0.19290	G=0.80710
1000Genomes_30x	Global	Study-wide	6404	A=0.1950	G=0.8050
1000Genomes_30x	African	Sub	1786	A=0.0252	G=0.9748
1000Genomes_30x	Europe	Sub	1266	A=0.2907	G=0.7093
1000Genomes_30x	South Asian	Sub	1202	A=0.3319	G=0.6681
1000Genomes_30x	East Asian	Sub	1170	A=0.0949	G=0.9051
1000Genomes_30x	American	Sub	980	A=0.333	G=0.667
1000Genomes	Global	Study-wide	5008	A=0.1961	G=0.8039
1000Genomes	African	Sub	1322	A=0.0310	G=0.9690
1000Genomes	East Asian	Sub	1008	A=0.0923	G=0.9077
1000Genomes	Europe	Sub	1006	A=0.2913	G=0.7087
1000Genomes	South Asian	Sub	978	A=0.333	G=0.667
1000Genomes	American	Sub	694	A=0.330	G=0.670
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.3768	G=0.6232
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.3298	G=0.6702
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.3328	G=0.6672
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.1055	G=0.8945
HapMap	Global	Study-wide	1892	A=0.1617	G=0.8383
HapMap	American	Sub	770	A=0.249	G=0.751
HapMap	African	Sub	692	A=0.046	G=0.954
HapMap	Asian	Sub	254	A=0.146	G=0.854
HapMap	Europe	Sub	176	A=0.256	G=0.744
Korean Genome Project	KOREAN	Study-wide	1832	A=0.1174	G=0.8826
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.338	G=0.662
Northern Sweden	ACPOP	Study-wide	600	A=0.362	G=0.638
SGDP_PRJ	Global	Study-wide	522	A=0.184	G=0.816
Qatari	Global	Study-wide	216	A=0.199	G=0.801
A Vietnamese Genetic Variation Database	Global	Study-wide	210	A=0.076	G=0.924
Siberian	Global	Study-wide	50	A=0.20	G=0.80
The Danish reference pan genome	Danish	Study-wide	40	A=0.45	G=0.55

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 22	NC_000022.11:g.48241244A>G
GRCh37.p13 chr 22	NC_000022.10:g.48637056A>G

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
GRCh38.p14 chr 22	NC_000022.11:g.48241244=	NC_000022.11:g.48241244A>G
GRCh37.p13 chr 22	NC_000022.10:g.48637056=	NC_000022.10:g.48637056A>G

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#.

89 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC	ss640251	Jul 21, 2000 (80)
2	SC_SNP	ss8022931	Apr 21, 2003 (117)
3	WI_SSAHASNP	ss12531878	Jul 11, 2003 (116)
4	SC_SNP	ss13372569	Dec 05, 2003 (119)
5	CSHL-HAPMAP	ss16924506	Feb 27, 2004 (120)
6	SSAHASNP	ss21856188	Apr 05, 2004 (121)
7	AFFY	ss66180466	Dec 01, 2006 (127)
8	AFFY	ss76244897	Dec 07, 2007 (129)
9	HGSV	ss77372224	Dec 07, 2007 (129)
10	HGSV	ss78876285	Dec 07, 2007 (129)
11	KRIBB_YJKIM	ss81422592	Dec 15, 2007 (130)
12	BCMHGSC_JDW	ss91948496	Mar 24, 2008 (129)
13	HUMANGENOME_JCVI	ss96105923	Feb 06, 2009 (130)
14	BGI	ss106232823	Feb 06, 2009 (130)
15	1000GENOMES	ss112713382	Jan 25, 2009 (130)
16	1000GENOMES	ss114335752	Jan 25, 2009 (130)
17	ILLUMINA-UK	ss117438031	Feb 14, 2009 (130)
18	ENSEMBL	ss138368970	Dec 01, 2009 (131)
19	ENSEMBL	ss139319389	Dec 01, 2009 (131)
20	GMI	ss157280379	Dec 01, 2009 (131)
21	COMPLETE_GENOMICS	ss168130736	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss169535852	Jul 04, 2010 (132)
23	AFFY	ss172954473	Jul 04, 2010 (132)
24	BUSHMAN	ss204118001	Jul 04, 2010 (132)
25	BCM-HGSC-SUB	ss208822802	Jul 04, 2010 (132)
26	1000GENOMES	ss228729419	Jul 14, 2010 (132)
27	1000GENOMES	ss238103291	Jul 15, 2010 (132)
28	1000GENOMES	ss244213508	Jul 15, 2010 (132)
29	GMI	ss283668564	May 04, 2012 (137)
30	GMI	ss287584554	Apr 25, 2013 (138)
31	PJP	ss292725892	May 09, 2011 (134)
32	TISHKOFF	ss566705036	Apr 25, 2013 (138)
33	SSMP	ss662632643	Apr 25, 2013 (138)
34	EVA-GONL	ss995449535	Aug 21, 2014 (142)
35	JMKIDD_LAB	ss1082727661	Aug 21, 2014 (142)
36	1000GENOMES	ss1367547127	Aug 21, 2014 (142)
37	DDI	ss1429286342	Apr 01, 2015 (144)
38	EVA_GENOME_DK	ss1579788871	Apr 01, 2015 (144)
39	EVA_UK10K_ALSPAC	ss1640193629	Apr 01, 2015 (144)
40	EVA_UK10K_TWINSUK	ss1683187662	Apr 01, 2015 (144)
41	EVA_DECODE	ss1699520527	Apr 01, 2015 (144)
42	EVA_SVP	ss1713748278	Apr 01, 2015 (144)
43	HAMMER_LAB	ss1809844183	Sep 08, 2015 (146)
44	WEILL_CORNELL_DGM	ss1939021746	Feb 12, 2016 (147)
45	GENOMED	ss1969290507	Jul 19, 2016 (147)
46	JJLAB	ss2030282800	Sep 14, 2016 (149)
47	USC_VALOUEV	ss2158906644	Dec 20, 2016 (150)
48	HUMAN_LONGEVITY	ss2248107095	Dec 20, 2016 (150)
49	SYSTEMSBIOZJU	ss2629637591	Nov 08, 2017 (151)
50	ILLUMINA	ss2635114081	Nov 08, 2017 (151)
51	GRF	ss2704659665	Nov 08, 2017 (151)
52	GNOMAD	ss2975472381	Nov 08, 2017 (151)
53	SWEGEN	ss3019461571	Nov 08, 2017 (151)
54	ILLUMINA	ss3022197127	Nov 08, 2017 (151)
55	BIOINF_KMB_FNS_UNIBA	ss3028978383	Nov 08, 2017 (151)
56	CSHL	ss3352881863	Nov 08, 2017 (151)
57	URBANLAB	ss3651198478	Oct 12, 2018 (152)
58	ILLUMINA	ss3652661904	Oct 12, 2018 (152)
59	EGCUT_WGS	ss3685951294	Jul 13, 2019 (153)
60	EVA_DECODE	ss3708392934	Jul 13, 2019 (153)
61	ILLUMINA	ss3725977700	Jul 13, 2019 (153)
62	ACPOP	ss3744016243	Jul 13, 2019 (153)
63	EVA	ss3759502328	Jul 13, 2019 (153)
64	PACBIO	ss3788851954	Jul 13, 2019 (153)
65	PACBIO	ss3793713712	Jul 13, 2019 (153)
66	PACBIO	ss3798600229	Jul 13, 2019 (153)
67	KHV_HUMAN_GENOMES	ss3822658898	Jul 13, 2019 (153)
68	EVA	ss3836040164	Apr 27, 2020 (154)
69	EVA	ss3841647982	Apr 27, 2020 (154)
70	EVA	ss3847163434	Apr 27, 2020 (154)
71	SGDP_PRJ	ss3890755684	Apr 27, 2020 (154)
72	KRGDB	ss3941163116	Apr 27, 2020 (154)
73	KOGIC	ss3983846175	Apr 27, 2020 (154)
74	TOPMED	ss5112515752	Apr 26, 2021 (155)
75	TOMMO_GENOMICS	ss5233081295	Apr 26, 2021 (155)
76	1000G_HIGH_COVERAGE	ss5311444207	Oct 16, 2022 (156)
77	EVA	ss5441931042	Oct 16, 2022 (156)
78	HUGCELL_USP	ss5503252360	Oct 16, 2022 (156)
79	1000G_HIGH_COVERAGE	ss5619154484	Oct 16, 2022 (156)
80	SANFORD_IMAGENETICS	ss5624505879	Oct 16, 2022 (156)
81	SANFORD_IMAGENETICS	ss5664683531	Oct 16, 2022 (156)
82	TOMMO_GENOMICS	ss5794349925	Oct 16, 2022 (156)
83	YY_MCH	ss5818793452	Oct 16, 2022 (156)
84	EVA	ss5822205871	Oct 16, 2022 (156)
85	EVA	ss5847948760	Oct 16, 2022 (156)
86	EVA	ss5853432268	Oct 16, 2022 (156)
87	EVA	ss5882206705	Oct 16, 2022 (156)
88	EVA	ss5959543380	Oct 16, 2022 (156)
89	EVA	ss5979640943	Oct 16, 2022 (156)
90	1000Genomes	NC_000022.10 - 48637056	Oct 12, 2018 (152)
91	1000Genomes_30x	NC_000022.11 - 48241244	Oct 16, 2022 (156)
92	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 48637056	Oct 12, 2018 (152)
93	Genetic variation in the Estonian population	NC_000022.10 - 48637056	Oct 12, 2018 (152)
94	The Danish reference pan genome	NC_000022.10 - 48637056	Apr 27, 2020 (154)
95	gnomAD - Genomes	NC_000022.11 - 48241244	Apr 26, 2021 (155)
96	Genome of the Netherlands Release 5	NC_000022.10 - 48637056	Apr 27, 2020 (154)
97	HapMap	NC_000022.11 - 48241244	Apr 27, 2020 (154)
98	KOREAN population from KRGDB	NC_000022.10 - 48637056	Apr 27, 2020 (154)
99	Korean Genome Project	NC_000022.11 - 48241244	Apr 27, 2020 (154)
100	Northern Sweden	NC_000022.10 - 48637056	Jul 13, 2019 (153)
101	Qatari	NC_000022.10 - 48637056	Apr 27, 2020 (154)
102	SGDP_PRJ	NC_000022.10 - 48637056	Apr 27, 2020 (154)
103	Siberian	NC_000022.10 - 48637056	Apr 27, 2020 (154)
104	8.3KJPN	NC_000022.10 - 48637056	Apr 26, 2021 (155)
105	14KJPN	NC_000022.11 - 48241244	Oct 16, 2022 (156)
106	TopMed	NC_000022.11 - 48241244	Apr 26, 2021 (155)
107	UK 10K study - Twins	NC_000022.10 - 48637056	Oct 12, 2018 (152)
108	A Vietnamese Genetic Variation Database	NC_000022.10 - 48637056	Jul 13, 2019 (153)
109	ALFA	NC_000022.11 - 48241244	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)
rs5768463	Aug 27, 2003 (117)
rs59124721	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77372224, ss78876285	NC_000022.8:46957574:A:G	NC_000022.11:48241243:A:G	(self)
ss91948496, ss112713382, ss114335752, ss117438031, ss168130736, ss169535852, ss204118001, ss208822802, ss283668564, ss287584554, ss292725892, ss1699520527, ss1713748278, ss2635114081	NC_000022.9:47015719:A:G	NC_000022.11:48241243:A:G	(self)
81112866, 44868128, 31689542, 5953810, 19988781, 48340510, 17301108, 21063668, 42772664, 11422998, 91050602, 44868128, 9892912, ss228729419, ss238103291, ss244213508, ss566705036, ss662632643, ss995449535, ss1082727661, ss1367547127, ss1429286342, ss1579788871, ss1640193629, ss1683187662, ss1809844183, ss1939021746, ss1969290507, ss2030282800, ss2158906644, ss2629637591, ss2704659665, ss2975472381, ss3019461571, ss3022197127, ss3352881863, ss3652661904, ss3685951294, ss3744016243, ss3759502328, ss3788851954, ss3793713712, ss3798600229, ss3836040164, ss3841647982, ss3890755684, ss3941163116, ss5233081295, ss5441931042, ss5624505879, ss5664683531, ss5822205871, ss5847948760, ss5959543380, ss5979640943	NC_000022.10:48637055:A:G	NC_000022.11:48241243:A:G	(self)
106680419, 572716752, 2275896, 40224176, 128187029, 387624699, 12374358709, ss2248107095, ss3028978383, ss3651198478, ss3708392934, ss3725977700, ss3822658898, ss3847163434, ss3983846175, ss5112515752, ss5311444207, ss5503252360, ss5619154484, ss5794349925, ss5818793452, ss5853432268, ss5882206705	NC_000022.11:48241243:A:G	NC_000022.11:48241243:A:G	(self)
ss640251, ss8022931, ss66180466, ss76244897, ss81422592, ss96105923, ss106232823, ss138368970, ss139319389, ss157280379, ss172954473	NT_011520.12:28027624:A:G	NC_000022.11:48241243:A:G	(self)
ss12531878, ss13372569, ss16924506, ss21856188	NT_011523.9:2216939:A:G	NC_000022.11:48241243:A: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 rs469999

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

rs469999