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dbSNP Short Genetic Variations

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.

rs6430538

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr2:134782397 (GRCh38.p12) 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 / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.491889 (64584/131298, ALFA Project)
C=0.356484 (44763/125568, TOPMED)
C=0.17827 (14004/78556, PAGE_STUDY) (+ 15 more)
C=0.40754 (12774/31344, GnomAD)
C=0.1891 (947/5008, 1000G)
T=0.4413 (1977/4480, Estonian)
T=0.4009 (1545/3854, ALSPAC)
T=0.3894 (1444/3708, TWINSUK)
C=0.0126 (37/2930, KOREAN)
C=0.0142 (26/1832, Korea1K)
C=0.1608 (257/1598, HapMap)
T=0.369 (368/998, GoNL)
T=0.335 (201/600, NorthernSweden)
C=0.088 (46/522, SGDP_PRJ)
C=0.046 (10/216, Qatari)
C=0.009 (2/212, Vietnamese)
T=0.38 (15/40, GENOME_DK)
C=0.20 (8/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
4 citations
Genomic View
See rs on genome
Help

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.p12 chr 2 NC_000002.12:g.134782397C>A
GRCh38.p12 chr 2 NC_000002.12:g.134782397C>G
GRCh38.p12 chr 2 NC_000002.12:g.134782397C>T
GRCh37.p13 chr 2 NC_000002.11:g.135539967C>A
GRCh37.p13 chr 2 NC_000002.11:g.135539967C>G
GRCh37.p13 chr 2 NC_000002.11:g.135539967C>T
Help

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

ALFA Allele Frequency (New)
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: 20200227123210
Population Group Sample Size Ref Allele Alt Allele
Total Global 131298 C=0.508111 T=0.491889
European Sub 112698 C=0.544136 T=0.455864
African Sub 3752 C=0.1085 T=0.8915
African Others Sub 134 C=0.007 T=0.993
African American Sub 3618 C=0.1122 T=0.8878
Asian Sub 252 C=0.016 T=0.984
East Asian Sub 150 C=0.007 T=0.993
Other Asian Sub 102 C=0.029 T=0.971
Latin American 1 Sub 704 C=0.375 T=0.625
Latin American 2 Sub 7570 C=0.2787 T=0.7213
South Asian Sub 70 C=0.23 T=0.77
Other Sub 6252 C=0.4143 T=0.5857


Help

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
ALFA Total Global 131298 C=0.508111 T=0.491889
ALFA European Sub 112698 C=0.544136 T=0.455864
ALFA Latin American 2 Sub 7570 C=0.2787 T=0.7213
ALFA Other Sub 6252 C=0.4143 T=0.5857
ALFA African Sub 3752 C=0.1085 T=0.8915
ALFA Latin American 1 Sub 704 C=0.375 T=0.625
ALFA Asian Sub 252 C=0.016 T=0.984
ALFA South Asian Sub 70 C=0.23 T=0.77
TopMed Global Study-wide 125568 C=0.356484 T=0.643516
The PAGE Study Global Study-wide 78556 C=0.17827 T=0.82173
The PAGE Study AfricanAmerican Sub 32470 C=0.12378 T=0.87622
The PAGE Study Mexican Sub 10776 C=0.27209 T=0.72791
The PAGE Study Asian Sub 8302 C=0.0554 T=0.9446
The PAGE Study PuertoRican Sub 7900 C=0.2547 T=0.7453
The PAGE Study NativeHawaiian Sub 4524 C=0.1501 T=0.8499
The PAGE Study Cuban Sub 4228 C=0.3186 T=0.6814
The PAGE Study Dominican Sub 3826 C=0.2020 T=0.7980
The PAGE Study CentralAmerican Sub 2446 C=0.2212 T=0.7788
The PAGE Study SouthAmerican Sub 1974 C=0.2599 T=0.7401
The PAGE Study NativeAmerican Sub 1254 C=0.4322 T=0.5678
The PAGE Study SouthAsian Sub 856 C=0.217 T=0.783
gnomAD - Genomes Global Study-wide 31344 C=0.40754 T=0.59246
gnomAD - Genomes European Sub 18876 C=0.58333 T=0.41667
gnomAD - Genomes African Sub 8690 C=0.1015 T=0.8985
gnomAD - Genomes East Asian Sub 1556 C=0.0141 T=0.9859
gnomAD - Genomes Other Sub 1086 C=0.5055 T=0.4945
gnomAD - Genomes American Sub 846 C=0.290 T=0.710
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.224 T=0.776
1000Genomes Global Study-wide 5008 C=0.1891 T=0.8109
1000Genomes African Sub 1322 C=0.0197 T=0.9803
1000Genomes East Asian Sub 1008 C=0.0159 T=0.9841
1000Genomes Europe Sub 1006 C=0.5030 T=0.4970
1000Genomes South Asian Sub 978 C=0.198 T=0.802
1000Genomes American Sub 694 C=0.295 T=0.705
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5587 T=0.4413
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.5991 T=0.4009
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.6106 T=0.3894
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.0126 A=0.0000, G=0.0000, T=0.9874
Korean Genome Project KOREAN Study-wide 1832 C=0.0142 T=0.9858
HapMap Global Study-wide 1598 C=0.1608 T=0.8392
HapMap American Sub 766 C=0.269 T=0.731
HapMap African Sub 406 C=0.007 T=0.993
HapMap Asian Sub 254 C=0.035 T=0.965
HapMap Europe Sub 172 C=0.227 T=0.773
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.631 T=0.369
Northern Sweden ACPOP Study-wide 600 C=0.665 T=0.335
SGDP_PRJ Global Study-wide 522 C=0.088 T=0.912
Qatari Global Study-wide 216 C=0.046 T=0.954
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.009 T=0.991
The Danish reference pan genome Danish Study-wide 40 C=0.62 T=0.38
Siberian Global Study-wide 40 C=0.20 T=0.80
Help

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 G T
GRCh38.p12 chr 2 NC_000002.12:g.134782397= NC_000002.12:g.134782397C>A NC_000002.12:g.134782397C>G NC_000002.12:g.134782397C>T
GRCh37.p13 chr 2 NC_000002.11:g.135539967= NC_000002.11:g.135539967C>A NC_000002.11:g.135539967C>G NC_000002.11:g.135539967C>T
Help

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#.

98 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9957515 Jul 11, 2003 (116)
2 WI_SSAHASNP ss11479007 Jul 11, 2003 (116)
3 CSHL-HAPMAP ss19454490 Feb 27, 2004 (120)
4 ABI ss44262209 Mar 13, 2006 (126)
5 AFFY ss66182665 Dec 01, 2006 (127)
6 ILLUMINA ss75241996 Dec 06, 2007 (129)
7 AFFY ss76249389 Dec 08, 2007 (130)
8 KRIBB_YJKIM ss82226962 Dec 16, 2007 (130)
9 HGSV ss85104449 Dec 14, 2007 (130)
10 BCMHGSC_JDW ss91357089 Mar 24, 2008 (129)
11 BGI ss106120954 Feb 04, 2009 (130)
12 1000GENOMES ss110960069 Jan 25, 2009 (130)
13 ILLUMINA-UK ss117886225 Feb 14, 2009 (130)
14 ENSEMBL ss138536685 Dec 01, 2009 (131)
15 GMI ss157713975 Dec 01, 2009 (131)
16 ILLUMINA ss160772421 Dec 01, 2009 (131)
17 ENSEMBL ss161184979 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss164284966 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss165271610 Jul 04, 2010 (132)
20 AFFY ss172970779 Jul 04, 2010 (132)
21 ILLUMINA ss173998570 Jul 04, 2010 (132)
22 BUSHMAN ss201091303 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss205845937 Jul 04, 2010 (132)
24 1000GENOMES ss219525581 Jul 14, 2010 (132)
25 1000GENOMES ss231372367 Jul 14, 2010 (132)
26 1000GENOMES ss238878747 Jul 15, 2010 (132)
27 GMI ss276691451 May 04, 2012 (137)
28 PJP ss292373260 May 09, 2011 (134)
29 ILLUMINA ss481237672 May 04, 2012 (137)
30 ILLUMINA ss481261305 May 04, 2012 (137)
31 ILLUMINA ss482247204 Sep 08, 2015 (146)
32 ILLUMINA ss485414179 May 04, 2012 (137)
33 ILLUMINA ss537347410 Sep 08, 2015 (146)
34 TISHKOFF ss555893333 Apr 25, 2013 (138)
35 SSMP ss649520597 Apr 25, 2013 (138)
36 ILLUMINA ss778939352 Sep 08, 2015 (146)
37 ILLUMINA ss783152526 Sep 08, 2015 (146)
38 ILLUMINA ss784108457 Sep 08, 2015 (146)
39 ILLUMINA ss832411750 Sep 08, 2015 (146)
40 ILLUMINA ss834401040 Sep 08, 2015 (146)
41 EVA-GONL ss977385433 Aug 21, 2014 (142)
42 JMKIDD_LAB ss1069515948 Aug 21, 2014 (142)
43 1000GENOMES ss1299433647 Aug 21, 2014 (142)
44 DDI ss1428748822 Apr 01, 2015 (144)
45 EVA_GENOME_DK ss1579097431 Apr 01, 2015 (144)
46 EVA_DECODE ss1586813872 Apr 01, 2015 (144)
47 EVA_UK10K_ALSPAC ss1604620154 Apr 01, 2015 (144)
48 EVA_UK10K_TWINSUK ss1647614187 Apr 01, 2015 (144)
49 EVA_SVP ss1712491938 Apr 01, 2015 (144)
50 ILLUMINA ss1752312195 Sep 08, 2015 (146)
51 HAMMER_LAB ss1797572173 Sep 08, 2015 (146)
52 WEILL_CORNELL_DGM ss1920643823 Feb 12, 2016 (147)
53 ILLUMINA ss1946052476 Feb 12, 2016 (147)
54 ILLUMINA ss1958460764 Feb 12, 2016 (147)
55 GENOMED ss1968894970 Jul 19, 2016 (147)
56 JJLAB ss2020845930 Sep 14, 2016 (149)
57 USC_VALOUEV ss2148911805 Dec 20, 2016 (150)
58 HUMAN_LONGEVITY ss2234491436 Dec 20, 2016 (150)
59 TOPMED ss2400850500 Dec 20, 2016 (150)
60 SYSTEMSBIOZJU ss2624929608 Nov 08, 2017 (151)
61 ILLUMINA ss2633676200 Nov 08, 2017 (151)
62 GRF ss2703536125 Nov 08, 2017 (151)
63 ILLUMINA ss2710912429 Nov 08, 2017 (151)
64 GNOMAD ss2779962038 Nov 08, 2017 (151)
65 SWEGEN ss2990472031 Nov 08, 2017 (151)
66 BIOINF_KMB_FNS_UNIBA ss3024186350 Nov 08, 2017 (151)
67 TOPMED ss3323671302 Nov 08, 2017 (151)
68 CSHL ss3344493812 Nov 08, 2017 (151)
69 ILLUMINA ss3625765884 Oct 11, 2018 (152)
70 ILLUMINA ss3628171326 Oct 11, 2018 (152)
71 ILLUMINA ss3631639670 Oct 11, 2018 (152)
72 ILLUMINA ss3633217217 Oct 11, 2018 (152)
73 ILLUMINA ss3633929718 Oct 11, 2018 (152)
74 ILLUMINA ss3634788524 Oct 11, 2018 (152)
75 ILLUMINA ss3635615568 Oct 11, 2018 (152)
76 ILLUMINA ss3636477430 Oct 11, 2018 (152)
77 ILLUMINA ss3637367511 Oct 11, 2018 (152)
78 ILLUMINA ss3638288962 Oct 11, 2018 (152)
79 ILLUMINA ss3640495823 Oct 11, 2018 (152)
80 ILLUMINA ss3643255778 Oct 11, 2018 (152)
81 ILLUMINA ss3644755195 Oct 11, 2018 (152)
82 EGCUT_WGS ss3658314024 Jul 13, 2019 (153)
83 EVA_DECODE ss3704943540 Jul 13, 2019 (153)
84 ACPOP ss3728890359 Jul 13, 2019 (153)
85 ILLUMINA ss3744182897 Jul 13, 2019 (153)
86 ILLUMINA ss3744480194 Jul 13, 2019 (153)
87 ILLUMINA ss3745088377 Jul 13, 2019 (153)
88 EVA ss3757414225 Jul 13, 2019 (153)
89 PAGE_CC ss3770950188 Jul 13, 2019 (153)
90 ILLUMINA ss3772585054 Jul 13, 2019 (153)
91 PACBIO ss3784001321 Jul 13, 2019 (153)
92 PACBIO ss3789563933 Jul 13, 2019 (153)
93 PACBIO ss3794436865 Jul 13, 2019 (153)
94 KHV_HUMAN_GENOMES ss3801781760 Jul 13, 2019 (153)
95 EVA ss3827234210 Apr 25, 2020 (154)
96 SGDP_PRJ ss3853470489 Apr 25, 2020 (154)
97 KRGDB ss3899030269 Apr 25, 2020 (154)
98 KOGIC ss3949021102 Apr 25, 2020 (154)
99 1000Genomes NC_000002.11 - 135539967 Oct 11, 2018 (152)
100 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 135539967 Oct 11, 2018 (152)
101 Genetic variation in the Estonian population NC_000002.11 - 135539967 Oct 11, 2018 (152)
102 The Danish reference pan genome NC_000002.11 - 135539967 Apr 25, 2020 (154)
103 gnomAD - Genomes NC_000002.11 - 135539967 Jul 13, 2019 (153)
104 Genome of the Netherlands Release 5 NC_000002.11 - 135539967 Apr 25, 2020 (154)
105 HapMap NC_000002.12 - 134782397 Apr 25, 2020 (154)
106 KOREAN population from KRGDB NC_000002.11 - 135539967 Apr 25, 2020 (154)
107 Korean Genome Project NC_000002.12 - 134782397 Apr 25, 2020 (154)
108 Northern Sweden NC_000002.11 - 135539967 Jul 13, 2019 (153)
109 The PAGE Study NC_000002.12 - 134782397 Jul 13, 2019 (153)
110 Qatari NC_000002.11 - 135539967 Apr 25, 2020 (154)
111 SGDP_PRJ NC_000002.11 - 135539967 Apr 25, 2020 (154)
112 Siberian NC_000002.11 - 135539967 Apr 25, 2020 (154)
113 TopMed NC_000002.12 - 134782397 Oct 11, 2018 (152)
114 UK 10K study - Twins NC_000002.11 - 135539967 Oct 11, 2018 (152)
115 A Vietnamese Genetic Variation Database NC_000002.11 - 135539967 Jul 13, 2019 (153)
116 dbGaP Population Frequency Project NC_000002.12 - 134782397 Apr 25, 2020 (154)
Help

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)
rs56558360 May 24, 2008 (130)
rs57760959 May 24, 2008 (130)
rs61421215 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
6207663, ss3899030269 NC_000002.11:135539966:C:A NC_000002.12:134782396:C:A
6207663, ss3899030269 NC_000002.11:135539966:C:G NC_000002.12:134782396:C:G
ss85104449 NC_000002.9:135373698:C:T NC_000002.12:134782396:C:T (self)
ss91357089, ss110960069, ss117886225, ss164284966, ss165271610, ss201091303, ss205845937, ss276691451, ss292373260, ss481237672, ss1586813872, ss1712491938, ss3643255778 NC_000002.10:135256436:C:T NC_000002.12:134782396:C:T (self)
10453222, 5757675, 4052272, 5262370, 28542069, 2531468, 6207663, 2175224, 2685753, 5487469, 1428159, 5757675, 1245950, ss219525581, ss231372367, ss238878747, ss481261305, ss482247204, ss485414179, ss537347410, ss555893333, ss649520597, ss778939352, ss783152526, ss784108457, ss832411750, ss834401040, ss977385433, ss1069515948, ss1299433647, ss1428748822, ss1579097431, ss1604620154, ss1647614187, ss1752312195, ss1797572173, ss1920643823, ss1946052476, ss1958460764, ss1968894970, ss2020845930, ss2148911805, ss2400850500, ss2624929608, ss2633676200, ss2703536125, ss2710912429, ss2779962038, ss2990472031, ss3344493812, ss3625765884, ss3628171326, ss3631639670, ss3633217217, ss3633929718, ss3634788524, ss3635615568, ss3636477430, ss3637367511, ss3638288962, ss3640495823, ss3644755195, ss3658314024, ss3728890359, ss3744182897, ss3744480194, ss3745088377, ss3757414225, ss3772585054, ss3784001321, ss3789563933, ss3794436865, ss3827234210, ss3853470489, ss3899030269 NC_000002.11:135539966:C:T NC_000002.12:134782396:C:T (self)
1898846, 5399103, 171657, 205055512, 311345736, ss2234491436, ss3024186350, ss3323671302, ss3704943540, ss3770950188, ss3801781760, ss3949021102 NC_000002.12:134782396:C:T NC_000002.12:134782396:C:T (self)
ss9957515, ss11479007 NT_005058.13:4148865:C:T NC_000002.12:134782396:C:T (self)
ss19454490 NT_005058.14:4148975:C:T NC_000002.12:134782396:C:T (self)
ss44262209, ss66182665, ss75241996, ss76249389, ss82226962, ss106120954, ss138536685, ss157713975, ss160772421, ss161184979, ss172970779, ss173998570 NT_022135.16:25288629:C:T NC_000002.12:134782396:C:T (self)
Help

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

4 citations for rs6430538
PMID Title Author Year Journal
28927418 A systematic review and integrative approach to decode the common molecular link between levodopa response and Parkinson's disease. Guin D et al. 2017 BMC medical genomics
30719275 Polymorphisms of <i>ACMSD</i>-<i>TMEM163</i>, <i>MCCC1</i>, and <i>BCKDK</i>-<i>STX1B</i> Are Not Associated with Parkinson's Disease in Taiwan. Chang KH et al. 2019 Parkinson's disease
30880162 Association of three candidate genetic variants in ACMSD/TMEM163, GPNMB and BCKDK /STX1B with sporadic Parkinson's disease in Han Chinese. Wang L et al. 2019 Neuroscience letters
31430546 A replication study of GWAS-genetic risk variants associated with Parkinson's disease in a Spanish population. Tejera-Parrado C et al. 2019 Neuroscience letters
Help

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.

Software version is: 2.0.1.post531+5874462