Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs2298727

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:89821710 (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>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.169666 (44909/264690, TOPMED)
G=0.154316 (21628/140154, GnomAD)
G=0.38400 (10851/28258, 14KJPN) (+ 15 more)
G=0.10503 (1984/18890, ALFA)
G=0.38365 (6430/16760, 8.3KJPN)
G=0.2324 (1488/6404, 1000G_30x)
G=0.2300 (1152/5008, 1000G)
G=0.0364 (163/4480, Estonian)
G=0.0646 (249/3854, ALSPAC)
G=0.0574 (213/3708, TWINSUK)
G=0.3416 (1001/2930, KOREAN)
G=0.071 (71/998, GoNL)
G=0.080 (48/600, NorthernSweden)
T=0.399 (87/218, SGDP_PRJ)
G=0.176 (38/216, Qatari)
G=0.269 (58/216, Vietnamese)
G=0.05 (2/40, GENOME_DK)
T=0.42 (5/12, 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 T=0.89497 G=0.10503
European Sub 14286 T=0.95058 G=0.04942
African Sub 2946 T=0.6629 G=0.3371
African Others Sub 114 T=0.649 G=0.351
African American Sub 2832 T=0.6635 G=0.3365
Asian Sub 112 T=0.625 G=0.375
East Asian Sub 86 T=0.59 G=0.41
Other Asian Sub 26 T=0.73 G=0.27
Latin American 1 Sub 146 T=0.856 G=0.144
Latin American 2 Sub 610 T=0.803 G=0.197
South Asian Sub 98 T=0.94 G=0.06
Other Sub 692 T=0.861 G=0.139


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 T=0.830334 G=0.169666
gnomAD - Genomes Global Study-wide 140154 T=0.845684 G=0.154316
gnomAD - Genomes European Sub 75922 T=0.94102 G=0.05898
gnomAD - Genomes African Sub 41976 T=0.67467 G=0.32533
gnomAD - Genomes American Sub 13654 T=0.86451 G=0.13549
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.9326 G=0.0674
gnomAD - Genomes East Asian Sub 3128 T=0.6493 G=0.3507
gnomAD - Genomes Other Sub 2152 T=0.8499 G=0.1501
14KJPN JAPANESE Study-wide 28258 T=0.61600 G=0.38400
Allele Frequency Aggregator Total Global 18890 T=0.89497 G=0.10503
Allele Frequency Aggregator European Sub 14286 T=0.95058 G=0.04942
Allele Frequency Aggregator African Sub 2946 T=0.6629 G=0.3371
Allele Frequency Aggregator Other Sub 692 T=0.861 G=0.139
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.803 G=0.197
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.856 G=0.144
Allele Frequency Aggregator Asian Sub 112 T=0.625 G=0.375
Allele Frequency Aggregator South Asian Sub 98 T=0.94 G=0.06
8.3KJPN JAPANESE Study-wide 16760 T=0.61635 G=0.38365
1000Genomes_30x Global Study-wide 6404 T=0.7676 G=0.2324
1000Genomes_30x African Sub 1786 T=0.6215 G=0.3785
1000Genomes_30x Europe Sub 1266 T=0.9415 G=0.0585
1000Genomes_30x South Asian Sub 1202 T=0.8577 G=0.1423
1000Genomes_30x East Asian Sub 1170 T=0.6419 G=0.3581
1000Genomes_30x American Sub 980 T=0.849 G=0.151
1000Genomes Global Study-wide 5008 T=0.7700 G=0.2300
1000Genomes African Sub 1322 T=0.6286 G=0.3714
1000Genomes East Asian Sub 1008 T=0.6409 G=0.3591
1000Genomes Europe Sub 1006 T=0.9433 G=0.0567
1000Genomes South Asian Sub 978 T=0.861 G=0.139
1000Genomes American Sub 694 T=0.847 G=0.153
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9636 G=0.0364
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9354 G=0.0646
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9426 G=0.0574
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.6584 C=0.0000, G=0.3416
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.929 G=0.071
Northern Sweden ACPOP Study-wide 600 T=0.920 G=0.080
SGDP_PRJ Global Study-wide 218 T=0.399 G=0.601
Qatari Global Study-wide 216 T=0.824 G=0.176
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.731 G=0.269
The Danish reference pan genome Danish Study-wide 40 T=0.95 G=0.05
Siberian Global Study-wide 12 T=0.42 G=0.58
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.89821710T>C
GRCh38.p14 chr 4 NC_000004.12:g.89821710T>G
GRCh37.p13 chr 4 NC_000004.11:g.90742861T>C
GRCh37.p13 chr 4 NC_000004.11:g.90742861T>G
SNCA RefSeqGene NG_011851.1:g.21587A>G
SNCA RefSeqGene NG_011851.1:g.21587A>C
Gene: SNCA, synuclein alpha (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SNCA transcript variant 1 NM_000345.4:c.306+536A>G N/A Intron Variant
SNCA transcript variant 2 NM_001146054.2:c.306+536A…

NM_001146054.2:c.306+536A>G

N/A Intron Variant
SNCA transcript variant 3 NM_001146055.2:c.306+536A…

NM_001146055.2:c.306+536A>G

N/A Intron Variant
SNCA transcript variant 5 NM_001375285.1:c.306+536A…

NM_001375285.1:c.306+536A>G

N/A Intron Variant
SNCA transcript variant 6 NM_001375286.1:c.306+536A…

NM_001375286.1:c.306+536A>G

N/A Intron Variant
SNCA transcript variant 7 NM_001375287.1:c.306+536A…

NM_001375287.1:c.306+536A>G

N/A Intron Variant
SNCA transcript variant 8 NM_001375288.1:c.306+536A…

NM_001375288.1:c.306+536A>G

N/A Intron Variant
SNCA transcript variant 4 NM_007308.3:c.306+536A>G 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.306+536A…

XM_011532203.2:c.306+536A>G

N/A Intron Variant
SNCA transcript variant X2 XM_011532204.4:c.306+536A…

XM_011532204.4:c.306+536A>G

N/A Intron Variant
SNCA transcript variant X3 XM_011532205.3:c.306+536A…

XM_011532205.3:c.306+536A>G

N/A Intron Variant
SNCA transcript variant X4 XM_011532206.2:c.306+536A…

XM_011532206.2:c.306+536A>G

N/A Intron Variant
SNCA transcript variant X5 XM_011532207.2:c.306+536A…

XM_011532207.2:c.306+536A>G

N/A Intron Variant
SNCA transcript variant X6 XM_047416097.1:c.306+536A…

XM_047416097.1:c.306+536A>G

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 T= C G
GRCh38.p14 chr 4 NC_000004.12:g.89821710= NC_000004.12:g.89821710T>C NC_000004.12:g.89821710T>G
GRCh37.p13 chr 4 NC_000004.11:g.90742861= NC_000004.11:g.90742861T>C NC_000004.11:g.90742861T>G
SNCA RefSeqGene NG_011851.1:g.21587= NG_011851.1:g.21587A>G NG_011851.1:g.21587A>C
SNCA transcript variant 1 NM_000345.3:c.306+536= NM_000345.3:c.306+536A>G NM_000345.3:c.306+536A>C
SNCA transcript variant 1 NM_000345.4:c.306+536= NM_000345.4:c.306+536A>G NM_000345.4:c.306+536A>C
SNCA transcript variant 2 NM_001146054.1:c.306+536= NM_001146054.1:c.306+536A>G NM_001146054.1:c.306+536A>C
SNCA transcript variant 2 NM_001146054.2:c.306+536= NM_001146054.2:c.306+536A>G NM_001146054.2:c.306+536A>C
SNCA transcript variant 3 NM_001146055.1:c.306+536= NM_001146055.1:c.306+536A>G NM_001146055.1:c.306+536A>C
SNCA transcript variant 3 NM_001146055.2:c.306+536= NM_001146055.2:c.306+536A>G NM_001146055.2:c.306+536A>C
SNCA transcript variant 5 NM_001375285.1:c.306+536= NM_001375285.1:c.306+536A>G NM_001375285.1:c.306+536A>C
SNCA transcript variant 6 NM_001375286.1:c.306+536= NM_001375286.1:c.306+536A>G NM_001375286.1:c.306+536A>C
SNCA transcript variant 7 NM_001375287.1:c.306+536= NM_001375287.1:c.306+536A>G NM_001375287.1:c.306+536A>C
SNCA transcript variant 8 NM_001375288.1:c.306+536= NM_001375288.1:c.306+536A>G NM_001375288.1:c.306+536A>C
SNCA transcript variant 4 NM_007308.2:c.306+536= NM_007308.2:c.306+536A>G NM_007308.2:c.306+536A>C
SNCA transcript variant 4 NM_007308.3:c.306+536= NM_007308.3:c.306+536A>G NM_007308.3:c.306+536A>C
SNCA transcript variant X1 XM_005263182.1:c.306+536= XM_005263182.1:c.306+536A>G XM_005263182.1:c.306+536A>C
SNCA transcript variant X2 XM_005263183.1:c.264+536= XM_005263183.1:c.264+536A>G XM_005263183.1:c.264+536A>C
SNCA transcript variant X3 XM_005263184.1:c.264+536= XM_005263184.1:c.264+536A>G XM_005263184.1:c.264+536A>C
SNCA transcript variant X4 XM_005263185.1:c.264+536= XM_005263185.1:c.264+536A>G XM_005263185.1:c.264+536A>C
SNCA transcript variant X5 XM_005263186.1:c.264+536= XM_005263186.1:c.264+536A>G XM_005263186.1:c.264+536A>C
SNCA transcript variant X6 XM_005263187.1:c.306+536= XM_005263187.1:c.306+536A>G XM_005263187.1:c.306+536A>C
SNCA transcript variant X7 XM_005263188.1:c.306+536= XM_005263188.1:c.306+536A>G XM_005263188.1:c.306+536A>C
SNCA transcript variant X8 XM_005263189.1:c.306+536= XM_005263189.1:c.306+536A>G XM_005263189.1:c.306+536A>C
SNCA transcript variant X1 XM_011532203.2:c.306+536= XM_011532203.2:c.306+536A>G XM_011532203.2:c.306+536A>C
SNCA transcript variant X2 XM_011532204.4:c.306+536= XM_011532204.4:c.306+536A>G XM_011532204.4:c.306+536A>C
SNCA transcript variant X3 XM_011532205.3:c.306+536= XM_011532205.3:c.306+536A>G XM_011532205.3:c.306+536A>C
SNCA transcript variant X4 XM_011532206.2:c.306+536= XM_011532206.2:c.306+536A>G XM_011532206.2:c.306+536A>C
SNCA transcript variant X5 XM_011532207.2:c.306+536= XM_011532207.2:c.306+536A>G XM_011532207.2:c.306+536A>C
SNCA transcript variant X6 XM_047416097.1:c.306+536= XM_047416097.1:c.306+536A>G XM_047416097.1:c.306+536A>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#.

54 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3243742 Sep 28, 2001 (100)
2 EGP_SNPS ss46533390 Mar 14, 2006 (126)
3 HGSV ss78831185 Dec 07, 2007 (129)
4 HGSV ss82269509 Dec 15, 2007 (130)
5 BGI ss104093199 Dec 01, 2009 (131)
6 ILLUMINA-UK ss117088937 Feb 14, 2009 (130)
7 GMI ss157591848 Dec 01, 2009 (131)
8 BUSHMAN ss198840183 Jul 04, 2010 (132)
9 1000GENOMES ss221062823 Jul 14, 2010 (132)
10 1000GENOMES ss232490147 Jul 14, 2010 (132)
11 1000GENOMES ss239761534 Jul 15, 2010 (132)
12 GMI ss277820476 May 04, 2012 (137)
13 SSMP ss651483494 Apr 25, 2013 (138)
14 EVA-GONL ss980375483 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1071733675 Aug 21, 2014 (142)
16 1000GENOMES ss1310714084 Aug 21, 2014 (142)
17 DDI ss1429962238 Apr 01, 2015 (144)
18 EVA_GENOME_DK ss1580660699 Apr 01, 2015 (144)
19 EVA_DECODE ss1589877836 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1610595476 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1653589509 Apr 01, 2015 (144)
22 HAMMER_LAB ss1801820087 Sep 08, 2015 (146)
23 WEILL_CORNELL_DGM ss1923619479 Feb 12, 2016 (147)
24 GENOMED ss1969802496 Jul 19, 2016 (147)
25 JJLAB ss2022394817 Sep 14, 2016 (149)
26 USC_VALOUEV ss2150524657 Dec 20, 2016 (150)
27 HUMAN_LONGEVITY ss2264859482 Dec 20, 2016 (150)
28 SYSTEMSBIOZJU ss2625699870 Nov 08, 2017 (151)
29 GRF ss2706000651 Nov 08, 2017 (151)
30 GNOMAD ss2812083141 Nov 08, 2017 (151)
31 SWEGEN ss2995099918 Nov 08, 2017 (151)
32 CSHL ss3345832499 Nov 08, 2017 (151)
33 EGCUT_WGS ss3662987772 Jul 13, 2019 (153)
34 EVA_DECODE ss3712526351 Jul 13, 2019 (153)
35 ACPOP ss3731363787 Jul 13, 2019 (153)
36 EVA ss3762090394 Jul 13, 2019 (153)
37 KHV_HUMAN_GENOMES ss3805236977 Jul 13, 2019 (153)
38 EVA ss3828670303 Apr 26, 2020 (154)
39 SGDP_PRJ ss3859470995 Apr 26, 2020 (154)
40 KRGDB ss3905742320 Apr 26, 2020 (154)
41 TOPMED ss4622256255 Apr 26, 2021 (155)
42 TOMMO_GENOMICS ss5166788240 Apr 26, 2021 (155)
43 1000G_HIGH_COVERAGE ss5260054514 Oct 13, 2022 (156)
44 EVA ss5350547774 Oct 13, 2022 (156)
45 HUGCELL_USP ss5458723077 Oct 13, 2022 (156)
46 EVA ss5507613163 Oct 13, 2022 (156)
47 1000G_HIGH_COVERAGE ss5541586381 Oct 13, 2022 (156)
48 SANFORD_IMAGENETICS ss5635530557 Oct 13, 2022 (156)
49 TOMMO_GENOMICS ss5701436970 Oct 13, 2022 (156)
50 YY_MCH ss5805297817 Oct 13, 2022 (156)
51 EVA ss5844330717 Oct 13, 2022 (156)
52 EVA ss5854328724 Oct 13, 2022 (156)
53 EVA ss5864414061 Oct 13, 2022 (156)
54 EVA ss5963915441 Oct 13, 2022 (156)
55 1000Genomes NC_000004.11 - 90742861 Oct 12, 2018 (152)
56 1000Genomes_30x NC_000004.12 - 89821710 Oct 13, 2022 (156)
57 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 90742861 Oct 12, 2018 (152)
58 Genetic variation in the Estonian population NC_000004.11 - 90742861 Oct 12, 2018 (152)
59 The Danish reference pan genome NC_000004.11 - 90742861 Apr 26, 2020 (154)
60 gnomAD - Genomes NC_000004.12 - 89821710 Apr 26, 2021 (155)
61 Genome of the Netherlands Release 5 NC_000004.11 - 90742861 Apr 26, 2020 (154)
62 KOREAN population from KRGDB NC_000004.11 - 90742861 Apr 26, 2020 (154)
63 Northern Sweden NC_000004.11 - 90742861 Jul 13, 2019 (153)
64 Qatari NC_000004.11 - 90742861 Apr 26, 2020 (154)
65 SGDP_PRJ NC_000004.11 - 90742861 Apr 26, 2020 (154)
66 Siberian NC_000004.11 - 90742861 Apr 26, 2020 (154)
67 8.3KJPN NC_000004.11 - 90742861 Apr 26, 2021 (155)
68 14KJPN NC_000004.12 - 89821710 Oct 13, 2022 (156)
69 TopMed NC_000004.12 - 89821710 Apr 26, 2021 (155)
70 UK 10K study - Twins NC_000004.11 - 90742861 Oct 12, 2018 (152)
71 A Vietnamese Genetic Variation Database NC_000004.11 - 90742861 Jul 13, 2019 (153)
72 ALFA NC_000004.12 - 89821710 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)
rs59505087 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
12919714, ss3905742320 NC_000004.11:90742860:T:C NC_000004.12:89821709:T:C (self)
ss78831185, ss82269509 NC_000004.9:91100038:T:G NC_000004.12:89821709:T:G (self)
ss117088937, ss198840183, ss277820476, ss1589877836 NC_000004.10:90961883:T:G NC_000004.12:89821709:T:G (self)
22145931, 12318233, 8726020, 6825638, 5440607, 12919714, 4648652, 5661409, 11487975, 3041011, 24757547, 12318233, 2710271, ss221062823, ss232490147, ss239761534, ss651483494, ss980375483, ss1071733675, ss1310714084, ss1429962238, ss1580660699, ss1610595476, ss1653589509, ss1801820087, ss1923619479, ss1969802496, ss2022394817, ss2150524657, ss2625699870, ss2706000651, ss2812083141, ss2995099918, ss3345832499, ss3662987772, ss3731363787, ss3762090394, ss3828670303, ss3859470995, ss3905742320, ss5166788240, ss5350547774, ss5507613163, ss5635530557, ss5844330717, ss5963915441 NC_000004.11:90742860:T:G NC_000004.12:89821709:T:G (self)
29112316, 156849852, 35274074, 459633811, 11975334578, ss2264859482, ss3712526351, ss3805236977, ss4622256255, ss5260054514, ss5458723077, ss5541586381, ss5701436970, ss5805297817, ss5854328724, ss5864414061 NC_000004.12:89821709:T:G NC_000004.12:89821709:T:G (self)
ss3243742, ss46533390, ss104093199, ss157591848 NT_016354.19:15290581:T:G NC_000004.12:89821709:T: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 rs2298727

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.post774+babeb33