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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.

rs2737004

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:89829571 (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
G=0.180139 (47681/264690, TOPMED)
G=0.190007 (26631/140158, GnomAD)
G=0.00011 (3/28258, 14KJPN) (+ 15 more)
G=0.22721 (4292/18890, ALFA)
G=0.00012 (2/16760, 8.3KJPN)
G=0.1096 (702/6404, 1000G_30x)
G=0.1074 (538/5008, 1000G)
G=0.2683 (1202/4480, Estonian)
G=0.2610 (1006/3854, ALSPAC)
G=0.2721 (1009/3708, TWINSUK)
G=0.0005 (1/1832, Korea1K)
G=0.255 (254/998, GoNL)
G=0.297 (178/600, NorthernSweden)
G=0.125 (41/328, HapMap)
G=0.162 (35/216, Qatari)
A=0.412 (42/102, SGDP_PRJ)
G=0.35 (14/40, GENOME_DK)
A=0.44 (7/16, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SNCA : 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 18890 A=0.77279 G=0.22721
European Sub 14286 A=0.72995 G=0.27005
African Sub 2946 A=0.9399 G=0.0601
African Others Sub 114 A=0.974 G=0.026
African American Sub 2832 A=0.9386 G=0.0614
Asian Sub 112 A=1.000 G=0.000
East Asian Sub 86 A=1.00 G=0.00
Other Asian Sub 26 A=1.00 G=0.00
Latin American 1 Sub 146 A=0.842 G=0.158
Latin American 2 Sub 610 A=0.852 G=0.148
South Asian Sub 98 A=0.87 G=0.13
Other Sub 692 A=0.811 G=0.189


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
TopMed Global Study-wide 264690 A=0.819861 G=0.180139
gnomAD - Genomes Global Study-wide 140158 A=0.809993 G=0.190007
gnomAD - Genomes European Sub 75872 A=0.73279 G=0.26721
gnomAD - Genomes African Sub 42032 A=0.93315 G=0.06685
gnomAD - Genomes American Sub 13644 A=0.82065 G=0.17935
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.7933 G=0.2067
gnomAD - Genomes East Asian Sub 3132 A=0.9994 G=0.0006
gnomAD - Genomes Other Sub 2154 A=0.8092 G=0.1908
14KJPN JAPANESE Study-wide 28258 A=0.99989 G=0.00011
Allele Frequency Aggregator Total Global 18890 A=0.77279 G=0.22721
Allele Frequency Aggregator European Sub 14286 A=0.72995 G=0.27005
Allele Frequency Aggregator African Sub 2946 A=0.9399 G=0.0601
Allele Frequency Aggregator Other Sub 692 A=0.811 G=0.189
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.852 G=0.148
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.842 G=0.158
Allele Frequency Aggregator Asian Sub 112 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=0.87 G=0.13
8.3KJPN JAPANESE Study-wide 16760 A=0.99988 G=0.00012
1000Genomes_30x Global Study-wide 6404 A=0.8904 G=0.1096
1000Genomes_30x African Sub 1786 A=0.9692 G=0.0308
1000Genomes_30x Europe Sub 1266 A=0.7038 G=0.2962
1000Genomes_30x South Asian Sub 1202 A=0.9093 G=0.0907
1000Genomes_30x East Asian Sub 1170 A=0.9991 G=0.0009
1000Genomes_30x American Sub 980 A=0.835 G=0.165
1000Genomes Global Study-wide 5008 A=0.8926 G=0.1074
1000Genomes African Sub 1322 A=0.9690 G=0.0310
1000Genomes East Asian Sub 1008 A=0.9990 G=0.0010
1000Genomes Europe Sub 1006 A=0.7008 G=0.2992
1000Genomes South Asian Sub 978 A=0.906 G=0.094
1000Genomes American Sub 694 A=0.852 G=0.148
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.7317 G=0.2683
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.7390 G=0.2610
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.7279 G=0.2721
Korean Genome Project KOREAN Study-wide 1832 A=0.9995 G=0.0005
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.745 G=0.255
Northern Sweden ACPOP Study-wide 600 A=0.703 G=0.297
HapMap Global Study-wide 328 A=0.875 G=0.125
HapMap African Sub 120 A=0.975 G=0.025
HapMap American Sub 118 A=0.678 G=0.322
HapMap Asian Sub 90 A=1.00 G=0.00
Qatari Global Study-wide 216 A=0.838 G=0.162
SGDP_PRJ Global Study-wide 102 A=0.412 G=0.588
The Danish reference pan genome Danish Study-wide 40 A=0.65 G=0.35
Siberian Global Study-wide 16 A=0.44 G=0.56
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.p14 chr 4 NC_000004.12:g.89829571A>G
GRCh37.p13 chr 4 NC_000004.11:g.90750722A>G
SNCA RefSeqGene NG_011851.1:g.13726T>C
Gene: SNCA, synuclein alpha (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SNCA transcript variant 1 NM_000345.4:c.122-1387T>C N/A Intron Variant
SNCA transcript variant 2 NM_001146054.2:c.122-1387…

NM_001146054.2:c.122-1387T>C

N/A Intron Variant
SNCA transcript variant 3 NM_001146055.2:c.122-1387…

NM_001146055.2:c.122-1387T>C

N/A Intron Variant
SNCA transcript variant 5 NM_001375285.1:c.122-1387…

NM_001375285.1:c.122-1387T>C

N/A Intron Variant
SNCA transcript variant 6 NM_001375286.1:c.122-1387…

NM_001375286.1:c.122-1387T>C

N/A Intron Variant
SNCA transcript variant 7 NM_001375287.1:c.122-1387…

NM_001375287.1:c.122-1387T>C

N/A Intron Variant
SNCA transcript variant 8 NM_001375288.1:c.122-1387…

NM_001375288.1:c.122-1387T>C

N/A Intron Variant
SNCA transcript variant 4 NM_007308.3:c.122-1387T>C N/A Intron Variant
SNCA transcript variant 9 NM_001375290.1:c. N/A Genic Upstream Transcript Variant
SNCA transcript variant 10 NR_164674.1:n. N/A Intron Variant
SNCA transcript variant 11 NR_164675.1:n. N/A Intron Variant
SNCA transcript variant 12 NR_164676.1:n. N/A Intron Variant
SNCA transcript variant X1 XM_011532203.2:c.122-1387…

XM_011532203.2:c.122-1387T>C

N/A Intron Variant
SNCA transcript variant X2 XM_011532204.4:c.122-1387…

XM_011532204.4:c.122-1387T>C

N/A Intron Variant
SNCA transcript variant X3 XM_011532205.3:c.122-1387…

XM_011532205.3:c.122-1387T>C

N/A Intron Variant
SNCA transcript variant X4 XM_011532206.2:c.122-1387…

XM_011532206.2:c.122-1387T>C

N/A Intron Variant
SNCA transcript variant X5 XM_011532207.2:c.122-1387…

XM_011532207.2:c.122-1387T>C

N/A Intron Variant
SNCA transcript variant X6 XM_047416097.1:c.122-1387…

XM_047416097.1:c.122-1387T>C

N/A Intron Variant
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
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 A= G
GRCh38.p14 chr 4 NC_000004.12:g.89829571= NC_000004.12:g.89829571A>G
GRCh37.p13 chr 4 NC_000004.11:g.90750722= NC_000004.11:g.90750722A>G
SNCA RefSeqGene NG_011851.1:g.13726= NG_011851.1:g.13726T>C
SNCA transcript variant 1 NM_000345.3:c.122-1387= NM_000345.3:c.122-1387T>C
SNCA transcript variant 1 NM_000345.4:c.122-1387= NM_000345.4:c.122-1387T>C
SNCA transcript variant 2 NM_001146054.1:c.122-1387= NM_001146054.1:c.122-1387T>C
SNCA transcript variant 2 NM_001146054.2:c.122-1387= NM_001146054.2:c.122-1387T>C
SNCA transcript variant 3 NM_001146055.1:c.122-1387= NM_001146055.1:c.122-1387T>C
SNCA transcript variant 3 NM_001146055.2:c.122-1387= NM_001146055.2:c.122-1387T>C
SNCA transcript variant 5 NM_001375285.1:c.122-1387= NM_001375285.1:c.122-1387T>C
SNCA transcript variant 6 NM_001375286.1:c.122-1387= NM_001375286.1:c.122-1387T>C
SNCA transcript variant 7 NM_001375287.1:c.122-1387= NM_001375287.1:c.122-1387T>C
SNCA transcript variant 8 NM_001375288.1:c.122-1387= NM_001375288.1:c.122-1387T>C
SNCA transcript variant 4 NM_007308.2:c.122-1387= NM_007308.2:c.122-1387T>C
SNCA transcript variant 4 NM_007308.3:c.122-1387= NM_007308.3:c.122-1387T>C
SNCA transcript variant X1 XM_005263182.1:c.122-1387= XM_005263182.1:c.122-1387T>C
SNCA transcript variant X2 XM_005263183.1:c.121+5976= XM_005263183.1:c.121+5976T>C
SNCA transcript variant X3 XM_005263184.1:c.121+5976= XM_005263184.1:c.121+5976T>C
SNCA transcript variant X4 XM_005263185.1:c.121+5976= XM_005263185.1:c.121+5976T>C
SNCA transcript variant X5 XM_005263186.1:c.121+5976= XM_005263186.1:c.121+5976T>C
SNCA transcript variant X6 XM_005263187.1:c.122-1387= XM_005263187.1:c.122-1387T>C
SNCA transcript variant X7 XM_005263188.1:c.122-1387= XM_005263188.1:c.122-1387T>C
SNCA transcript variant X8 XM_005263189.1:c.122-1387= XM_005263189.1:c.122-1387T>C
SNCA transcript variant X1 XM_011532203.2:c.122-1387= XM_011532203.2:c.122-1387T>C
SNCA transcript variant X2 XM_011532204.4:c.122-1387= XM_011532204.4:c.122-1387T>C
SNCA transcript variant X3 XM_011532205.3:c.122-1387= XM_011532205.3:c.122-1387T>C
SNCA transcript variant X4 XM_011532206.2:c.122-1387= XM_011532206.2:c.122-1387T>C
SNCA transcript variant X5 XM_011532207.2:c.122-1387= XM_011532207.2:c.122-1387T>C
SNCA transcript variant X6 XM_047416097.1:c.122-1387= XM_047416097.1:c.122-1387T>C
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#.

58 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3863751 Sep 28, 2001 (100)
2 SSAHASNP ss22201981 Apr 05, 2004 (126)
3 ABI ss42386182 Mar 10, 2006 (126)
4 EGP_SNPS ss46533335 Mar 10, 2006 (126)
5 HUMANGENOME_JCVI ss98980433 Feb 05, 2009 (130)
6 1000GENOMES ss108127997 Jan 23, 2009 (130)
7 ENSEMBL ss133410531 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss166882911 Jul 04, 2010 (132)
9 BUSHMAN ss198840391 Jul 04, 2010 (132)
10 1000GENOMES ss221062869 Jul 14, 2010 (132)
11 1000GENOMES ss232490205 Jul 14, 2010 (132)
12 BL ss253329333 May 09, 2011 (134)
13 GMI ss284955895 Apr 25, 2013 (138)
14 SSMP ss651483569 Apr 25, 2013 (138)
15 EVA-GONL ss980375602 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1071733763 Aug 21, 2014 (142)
17 1000GENOMES ss1310714342 Aug 21, 2014 (142)
18 EVA_GENOME_DK ss1580660762 Apr 01, 2015 (144)
19 EVA_DECODE ss1589877945 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1610595628 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1653589661 Apr 01, 2015 (144)
22 WEILL_CORNELL_DGM ss1923619582 Feb 12, 2016 (147)
23 JJLAB ss2022394896 Sep 14, 2016 (149)
24 USC_VALOUEV ss2150524736 Dec 20, 2016 (150)
25 HUMAN_LONGEVITY ss2264859975 Dec 20, 2016 (150)
26 SYSTEMSBIOZJU ss2625699924 Nov 08, 2017 (151)
27 GNOMAD ss2812083769 Nov 08, 2017 (151)
28 AFFY ss2985922040 Nov 08, 2017 (151)
29 SWEGEN ss2995100076 Nov 08, 2017 (151)
30 BIOINF_KMB_FNS_UNIBA ss3024973596 Nov 08, 2017 (151)
31 CSHL ss3345832579 Nov 08, 2017 (151)
32 URBANLAB ss3647788286 Oct 12, 2018 (152)
33 EGCUT_WGS ss3662987926 Jul 13, 2019 (153)
34 EVA_DECODE ss3712526537 Jul 13, 2019 (153)
35 ACPOP ss3731363905 Jul 13, 2019 (153)
36 EVA ss3762090495 Jul 13, 2019 (153)
37 PACBIO ss3784785325 Jul 13, 2019 (153)
38 PACBIO ss3790232723 Jul 13, 2019 (153)
39 PACBIO ss3795108097 Jul 13, 2019 (153)
40 KHV_HUMAN_GENOMES ss3805237090 Jul 13, 2019 (153)
41 EVA ss3828670395 Apr 26, 2020 (154)
42 EVA ss3837777136 Apr 26, 2020 (154)
43 EVA ss3843215185 Apr 26, 2020 (154)
44 SGDP_PRJ ss3859471139 Apr 26, 2020 (154)
45 KOGIC ss3954625223 Apr 26, 2020 (154)
46 TOPMED ss4622258113 Apr 26, 2021 (155)
47 TOMMO_GENOMICS ss5166788515 Apr 26, 2021 (155)
48 1000G_HIGH_COVERAGE ss5260054757 Oct 13, 2022 (156)
49 EVA ss5350548122 Oct 13, 2022 (156)
50 HUGCELL_USP ss5458723318 Oct 13, 2022 (156)
51 EVA ss5507613245 Oct 13, 2022 (156)
52 1000G_HIGH_COVERAGE ss5541586704 Oct 13, 2022 (156)
53 SANFORD_IMAGENETICS ss5635530709 Oct 13, 2022 (156)
54 TOMMO_GENOMICS ss5701437306 Oct 13, 2022 (156)
55 YY_MCH ss5805297918 Oct 13, 2022 (156)
56 EVA ss5844330855 Oct 13, 2022 (156)
57 EVA ss5864414336 Oct 13, 2022 (156)
58 EVA ss5963915596 Oct 13, 2022 (156)
59 1000Genomes NC_000004.11 - 90750722 Oct 12, 2018 (152)
60 1000Genomes_30x NC_000004.12 - 89829571 Oct 13, 2022 (156)
61 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 90750722 Oct 12, 2018 (152)
62 Genetic variation in the Estonian population NC_000004.11 - 90750722 Oct 12, 2018 (152)
63 The Danish reference pan genome NC_000004.11 - 90750722 Apr 26, 2020 (154)
64 gnomAD - Genomes NC_000004.12 - 89829571 Apr 26, 2021 (155)
65 Genome of the Netherlands Release 5 NC_000004.11 - 90750722 Apr 26, 2020 (154)
66 HapMap NC_000004.12 - 89829571 Apr 26, 2020 (154)
67 Korean Genome Project NC_000004.12 - 89829571 Apr 26, 2020 (154)
68 Northern Sweden NC_000004.11 - 90750722 Jul 13, 2019 (153)
69 Qatari NC_000004.11 - 90750722 Apr 26, 2020 (154)
70 SGDP_PRJ NC_000004.11 - 90750722 Apr 26, 2020 (154)
71 Siberian NC_000004.11 - 90750722 Apr 26, 2020 (154)
72 8.3KJPN NC_000004.11 - 90750722 Apr 26, 2021 (155)
73 14KJPN NC_000004.12 - 89829571 Oct 13, 2022 (156)
74 TopMed NC_000004.12 - 89829571 Apr 26, 2021 (155)
75 UK 10K study - Twins NC_000004.11 - 90750722 Oct 12, 2018 (152)
76 ALFA NC_000004.12 - 89829571 Apr 26, 2021 (155)
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)
rs13148411 Mar 10, 2006 (126)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss108127997, ss166882911, ss198840391, ss253329333, ss284955895, ss1589877945 NC_000004.10:90969744:A:G NC_000004.12:89829570:A:G (self)
22146204, 12318411, 8726174, 6825701, 5440726, 4648770, 5661512, 11488119, 3041090, 24757822, 12318411, ss221062869, ss232490205, ss651483569, ss980375602, ss1071733763, ss1310714342, ss1580660762, ss1610595628, ss1653589661, ss1923619582, ss2022394896, ss2150524736, ss2625699924, ss2812083769, ss2985922040, ss2995100076, ss3345832579, ss3662987926, ss3731363905, ss3762090495, ss3784785325, ss3790232723, ss3795108097, ss3828670395, ss3837777136, ss3859471139, ss5166788515, ss5350548122, ss5507613245, ss5635530709, ss5844330855, ss5963915596 NC_000004.11:90750721:A:G NC_000004.12:89829570:A:G (self)
29112639, 156851428, 2658885, 11003224, 35274410, 459635669, 5462023415, ss2264859975, ss3024973596, ss3647788286, ss3712526537, ss3805237090, ss3843215185, ss3954625223, ss4622258113, ss5260054757, ss5458723318, ss5541586704, ss5701437306, ss5805297918, ss5864414336 NC_000004.12:89829570:A:G NC_000004.12:89829570:A:G (self)
ss22201981 NT_016354.16:15245425:A:G NC_000004.12:89829570:A:G (self)
ss3863751, ss42386182, ss46533335, ss98980433, ss133410531 NT_016354.19:15298442:A:G NC_000004.12:89829570:A:G (self)
Help

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

No publications for rs2737004

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.post761+d5e8e07