Name: rs406449
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.

rs406449

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:249875 (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: T>A / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.348936 (92360/264690, TOPMED)
T=0.349065 (48890/140060, GnomAD)
T=0.33930 (9588/28258, 14KJPN) (+ 17 more)
T=0.38878 (7344/18890, ALFA)
T=0.34141 (5722/16760, 8.3KJPN)
T=0.3265 (2091/6404, 1000G_30x)
T=0.3289 (1647/5008, 1000G)
T=0.4609 (2065/4480, Estonian)
T=0.4017 (1548/3854, ALSPAC)
T=0.3954 (1466/3708, TWINSUK)
T=0.3065 (898/2930, KOREAN)
T=0.3129 (592/1892, HapMap)
T=0.3073 (563/1832, Korea1K)
T=0.449 (448/998, GoNL)
T=0.392 (235/600, NorthernSweden)
T=0.270 (130/482, SGDP_PRJ)
T=0.389 (84/216, Qatari)
T=0.364 (78/214, Vietnamese)
T=0.38 (18/48, Siberian)
T=0.42 (17/40, 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18890	T=0.38878	A=0.61122
European	Sub	14286	T=0.42615	A=0.57385
African	Sub	2946	T=0.1914	A=0.8086
African Others	Sub	114	T=0.184	A=0.816
African American	Sub	2832	T=0.1917	A=0.8083
Asian	Sub	112	T=0.384	A=0.616
East Asian	Sub	86	T=0.38	A=0.62
Other Asian	Sub	26	T=0.38	A=0.62
Latin American 1	Sub	146	T=0.253	A=0.747
Latin American 2	Sub	610	T=0.513	A=0.487
South Asian	Sub	98	T=0.44	A=0.56
Other	Sub	692	T=0.370	A=0.630

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	T=0.348936	A=0.651064
gnomAD - Genomes	Global	Study-wide	140060	T=0.349065	A=0.650935
gnomAD - Genomes	European	Sub	75868	T=0.40978	A=0.59022
gnomAD - Genomes	African	Sub	41954	T=0.19717	A=0.80283
gnomAD - Genomes	American	Sub	13640	T=0.45447	A=0.54553
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.4759	A=0.5241
gnomAD - Genomes	East Asian	Sub	3124	T=0.3214	A=0.6786
gnomAD - Genomes	Other	Sub	2152	T=0.3462	A=0.6538
14KJPN	JAPANESE	Study-wide	28258	T=0.33930	A=0.66070
Allele Frequency Aggregator	Total	Global	18890	T=0.38878	A=0.61122
Allele Frequency Aggregator	European	Sub	14286	T=0.42615	A=0.57385
Allele Frequency Aggregator	African	Sub	2946	T=0.1914	A=0.8086
Allele Frequency Aggregator	Other	Sub	692	T=0.370	A=0.630
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.513	A=0.487
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.253	A=0.747
Allele Frequency Aggregator	Asian	Sub	112	T=0.384	A=0.616
Allele Frequency Aggregator	South Asian	Sub	98	T=0.44	A=0.56
8.3KJPN	JAPANESE	Study-wide	16760	T=0.34141	A=0.65859
1000Genomes_30x	Global	Study-wide	6404	T=0.3265	A=0.6735
1000Genomes_30x	African	Sub	1786	T=0.1529	A=0.8471
1000Genomes_30x	Europe	Sub	1266	T=0.3847	A=0.6153
1000Genomes_30x	South Asian	Sub	1202	T=0.3952	A=0.6048
1000Genomes_30x	East Asian	Sub	1170	T=0.3692	A=0.6308
1000Genomes_30x	American	Sub	980	T=0.433	A=0.567
1000Genomes	Global	Study-wide	5008	T=0.3289	A=0.6711
1000Genomes	African	Sub	1322	T=0.1619	A=0.8381
1000Genomes	East Asian	Sub	1008	T=0.3651	A=0.6349
1000Genomes	Europe	Sub	1006	T=0.3797	A=0.6203
1000Genomes	South Asian	Sub	978	T=0.385	A=0.615
1000Genomes	American	Sub	694	T=0.441	A=0.559
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.4609	A=0.5391
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.4017	A=0.5983
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.3954	A=0.6046
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3065	A=0.6935, C=0.0000, G=0.0000
HapMap	Global	Study-wide	1892	T=0.3129	A=0.6871
HapMap	American	Sub	770	T=0.374	A=0.626
HapMap	African	Sub	692	T=0.189	A=0.811
HapMap	Asian	Sub	254	T=0.398	A=0.602
HapMap	Europe	Sub	176	T=0.409	A=0.591
Korean Genome Project	KOREAN	Study-wide	1832	T=0.3073	A=0.6927
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.449	A=0.551
Northern Sweden	ACPOP	Study-wide	600	T=0.392	A=0.608
SGDP_PRJ	Global	Study-wide	482	T=0.270	A=0.730
Qatari	Global	Study-wide	216	T=0.389	A=0.611
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.364	A=0.636
Siberian	Global	Study-wide	48	T=0.38	A=0.62
The Danish reference pan genome	Danish	Study-wide	40	T=0.42	A=0.57

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 20	NC_000020.11:g.249875T>A
GRCh38.p14 chr 20	NC_000020.11:g.249875T>C
GRCh38.p14 chr 20	NC_000020.11:g.249875T>G
GRCh37.p13 chr 20	NC_000020.10:g.230516T>A
GRCh37.p13 chr 20	NC_000020.10:g.230516T>C
GRCh37.p13 chr 20	NC_000020.10:g.230516T>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	T=	A	C	G
GRCh38.p14 chr 20	NC_000020.11:g.249875=	NC_000020.11:g.249875T>A	NC_000020.11:g.249875T>C	NC_000020.11:g.249875T>G
GRCh37.p13 chr 20	NC_000020.10:g.230516=	NC_000020.10:g.230516T>A	NC_000020.10:g.230516T>C	NC_000020.10:g.230516T>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#.

82 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss531115	Jul 16, 2000 (80)
2	SC_JCM	ss3391021	Sep 28, 2001 (126)
3	SC_SNP	ss8341654	Apr 21, 2003 (126)
4	CSHL-HAPMAP	ss16900900	Feb 27, 2004 (126)
5	ABI	ss41437342	Mar 11, 2006 (126)
6	AFFY	ss66229928	Dec 01, 2006 (127)
7	AFFY	ss76375976	Dec 08, 2007 (130)
8	HGSV	ss78440180	Dec 06, 2007 (129)
9	KRIBB_YJKIM	ss81420458	Dec 15, 2007 (130)
10	HGSV	ss83692925	Dec 15, 2007 (130)
11	BCMHGSC_JDW	ss91612065	Mar 24, 2008 (129)
12	BGI	ss103712457	Dec 01, 2009 (131)
13	1000GENOMES	ss111583062	Jan 25, 2009 (130)
14	1000GENOMES	ss115347663	Jan 25, 2009 (130)
15	ILLUMINA-UK	ss117452563	Dec 01, 2009 (131)
16	ENSEMBL	ss138196965	Dec 01, 2009 (131)
17	GMI	ss156061344	Dec 01, 2009 (131)
18	ENSEMBL	ss161309280	Dec 01, 2009 (131)
19	COMPLETE_GENOMICS	ss167639879	Jul 04, 2010 (132)
20	COMPLETE_GENOMICS	ss168832073	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss171805601	Jul 04, 2010 (132)
22	AFFY	ss173417518	Jun 24, 2010 (142)
23	BUSHMAN	ss203804452	Jul 04, 2010 (132)
24	BCM-HGSC-SUB	ss208581030	Jul 04, 2010 (132)
25	1000GENOMES	ss228211328	Jul 14, 2010 (132)
26	1000GENOMES	ss237730440	Jul 15, 2010 (132)
27	1000GENOMES	ss243923905	Jul 15, 2010 (132)
28	BL	ss255420757	May 09, 2011 (134)
29	GMI	ss283269522	May 04, 2012 (137)
30	GMI	ss287408642	Apr 25, 2013 (138)
31	PJP	ss292559921	May 09, 2011 (134)
32	TISHKOFF	ss566083378	Apr 25, 2013 (138)
33	SSMP	ss661954335	Apr 25, 2013 (138)
34	EVA-GONL	ss994458225	Aug 21, 2014 (142)
35	JMKIDD_LAB	ss1082010526	Aug 21, 2014 (142)
36	1000GENOMES	ss1363770582	Aug 21, 2014 (142)
37	DDI	ss1428971067	Apr 01, 2015 (144)
38	EVA_GENOME_DK	ss1579403178	Apr 01, 2015 (144)
39	EVA_UK10K_ALSPAC	ss1638251725	Apr 01, 2015 (144)
40	EVA_UK10K_TWINSUK	ss1681245758	Apr 01, 2015 (144)
41	EVA_DECODE	ss1698511771	Apr 01, 2015 (144)
42	EVA_SVP	ss1713672468	Apr 01, 2015 (144)
43	HAMMER_LAB	ss1809384343	Sep 08, 2015 (146)
44	WEILL_CORNELL_DGM	ss1937966745	Feb 12, 2016 (147)
45	GENOMED	ss1969071409	Jul 19, 2016 (147)
46	JJLAB	ss2029758152	Sep 14, 2016 (149)
47	USC_VALOUEV	ss2158312605	Dec 20, 2016 (150)
48	HUMAN_LONGEVITY	ss2240722601	Dec 20, 2016 (150)
49	SYSTEMSBIOZJU	ss2629376854	Nov 08, 2017 (151)
50	GRF	ss2703984022	Nov 08, 2017 (151)
51	GNOMAD	ss2964615858	Nov 08, 2017 (151)
52	SWEGEN	ss3017746107	Nov 08, 2017 (151)
53	BIOINF_KMB_FNS_UNIBA	ss3028710799	Nov 08, 2017 (151)
54	CSHL	ss3352380881	Nov 08, 2017 (151)
55	URBANLAB	ss3650953388	Oct 12, 2018 (152)
56	EGCUT_WGS	ss3684458553	Jul 13, 2019 (153)
57	EVA_DECODE	ss3706407703	Jul 13, 2019 (153)
58	ACPOP	ss3743180293	Jul 13, 2019 (153)
59	EVA	ss3758327719	Jul 13, 2019 (153)
60	PACBIO	ss3788577174	Jul 13, 2019 (153)
61	PACBIO	ss3793480668	Jul 13, 2019 (153)
62	PACBIO	ss3798367814	Jul 13, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3821500635	Jul 13, 2019 (153)
64	EVA	ss3835545673	Apr 27, 2020 (154)
65	EVA	ss3841395958	Apr 27, 2020 (154)
66	EVA	ss3846903229	Apr 27, 2020 (154)
67	SGDP_PRJ	ss3888573050	Apr 27, 2020 (154)
68	KRGDB	ss3938750109	Apr 27, 2020 (154)
69	KOGIC	ss3981680905	Apr 27, 2020 (154)
70	TOPMED	ss5079773387	Apr 26, 2021 (155)
71	TOMMO_GENOMICS	ss5228511120	Apr 26, 2021 (155)
72	1000G_HIGH_COVERAGE	ss5307824785	Oct 13, 2022 (156)
73	EVA	ss5435790093	Oct 13, 2022 (156)
74	HUGCELL_USP	ss5500249602	Oct 13, 2022 (156)
75	1000G_HIGH_COVERAGE	ss5613783052	Oct 13, 2022 (156)
76	SANFORD_IMAGENETICS	ss5662713874	Oct 13, 2022 (156)
77	TOMMO_GENOMICS	ss5787404399	Oct 13, 2022 (156)
78	YY_MCH	ss5817749903	Oct 13, 2022 (156)
79	EVA	ss5845339040	Oct 13, 2022 (156)
80	EVA	ss5853034766	Oct 13, 2022 (156)
81	EVA	ss5922376223	Oct 13, 2022 (156)
82	EVA	ss5957609566	Oct 13, 2022 (156)
83	1000Genomes	NC_000020.10 - 230516	Oct 12, 2018 (152)
84	1000Genomes_30x	NC_000020.11 - 249875	Oct 13, 2022 (156)
85	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 230516	Oct 12, 2018 (152)
86	Genetic variation in the Estonian population	NC_000020.10 - 230516	Oct 12, 2018 (152)
87	The Danish reference pan genome	NC_000020.10 - 230516	Apr 27, 2020 (154)
88	gnomAD - Genomes	NC_000020.11 - 249875	Apr 26, 2021 (155)
89	Genome of the Netherlands Release 5	NC_000020.10 - 230516	Apr 27, 2020 (154)
90	HapMap	NC_000020.11 - 249875	Apr 27, 2020 (154)
91	KOREAN population from KRGDB	NC_000020.10 - 230516	Apr 27, 2020 (154)
92	Korean Genome Project	NC_000020.11 - 249875	Apr 27, 2020 (154)
93	Northern Sweden	NC_000020.10 - 230516	Jul 13, 2019 (153)
94	Qatari	NC_000020.10 - 230516	Apr 27, 2020 (154)
95	SGDP_PRJ	NC_000020.10 - 230516	Apr 27, 2020 (154)
96	Siberian	NC_000020.10 - 230516	Apr 27, 2020 (154)
97	8.3KJPN	NC_000020.10 - 230516	Apr 26, 2021 (155)
98	14KJPN	NC_000020.11 - 249875	Oct 13, 2022 (156)
99	TopMed	NC_000020.11 - 249875	Apr 26, 2021 (155)
100	UK 10K study - Twins	NC_000020.10 - 230516	Oct 12, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000020.10 - 230516	Jul 13, 2019 (153)
102	ALFA	NC_000020.11 - 249875	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)
rs2422497	Mar 11, 2006 (126)
rs6034748	Mar 11, 2006 (126)
rs56611114	May 25, 2008 (130)
rs59316031	Feb 27, 2009 (130)
rs60214542	May 25, 2008 (130)
rs111196828	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss66229928, ss76375976, ss78440180, ss83692925, ss91612065, ss111583062, ss115347663, ss117452563, ss167639879, ss168832073, ss171805601, ss173417518, ss203804452, ss208581030, ss255420757, ss283269522, ss287408642, ss292559921, ss1698511771, ss1713672468	NC_000020.9:178515:T:A	NC_000020.11:249874:T:A	(self)
77200083, 42728332, 30196801, 5568117, 19039016, 45927503, 16465158, 20008667, 40590030, 10828959, 86480427, 42728332, 9432989, ss228211328, ss237730440, ss243923905, ss566083378, ss661954335, ss994458225, ss1082010526, ss1363770582, ss1428971067, ss1579403178, ss1638251725, ss1681245758, ss1809384343, ss1937966745, ss1969071409, ss2029758152, ss2158312605, ss2629376854, ss2703984022, ss2964615858, ss3017746107, ss3352380881, ss3684458553, ss3743180293, ss3758327719, ss3788577174, ss3793480668, ss3798367814, ss3835545673, ss3841395958, ss3888573050, ss3938750109, ss5228511120, ss5435790093, ss5662713874, ss5845339040, ss5957609566	NC_000020.10:230515:T:A	NC_000020.11:249874:T:A	(self)
101308987, 544412796, 2047918, 38058906, 121241503, 354882332, 1794515663, ss2240722601, ss3028710799, ss3650953388, ss3706407703, ss3821500635, ss3846903229, ss3981680905, ss5079773387, ss5307824785, ss5500249602, ss5613783052, ss5787404399, ss5817749903, ss5853034766, ss5922376223	NC_000020.11:249874:T:A	NC_000020.11:249874:T:A	(self)
ss531115, ss3391021, ss8341654, ss16900900, ss41437342, ss81420458, ss103712457, ss138196965, ss156061344, ss161309280	NT_011387.8:170515:T:A	NC_000020.11:249874:T:A	(self)
45927503, ss3938750109	NC_000020.10:230515:T:C	NC_000020.11:249874:T:C	(self)
45927503, ss3938750109	NC_000020.10:230515:T:G	NC_000020.11:249874:T: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 rs406449

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

rs406449