Name: rs2737012
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.

rs2737012

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:89824556 (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: G>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.180056 (47659/264690, TOPMED)
A=0.190123 (26605/139936, GnomAD)
A=0.00011 (3/28258, 14KJPN) (+ 16 more)
A=0.22705 (4289/18890, ALFA)
A=0.00012 (2/16760, 8.3KJPN)
A=0.1096 (702/6404, 1000G_30x)
A=0.1074 (538/5008, 1000G)
A=0.2681 (1201/4480, Estonian)
A=0.2600 (1002/3854, ALSPAC)
A=0.2718 (1008/3708, TWINSUK)
A=0.0003 (1/2922, KOREAN)
A=0.0005 (1/1832, Korea1K)
A=0.255 (254/998, GoNL)
A=0.297 (178/600, NorthernSweden)
A=0.094 (28/298, HapMap)
A=0.167 (36/216, Qatari)
G=0.412 (42/102, SGDP_PRJ)
A=0.35 (14/40, GENOME_DK)
G=0.44 (7/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SNCA : Intron Variant
Publications: 3 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	G=0.77295	A=0.22705
European	Sub	14286	G=0.73016	A=0.26984
African	Sub	2946	G=0.9399	A=0.0601
African Others	Sub	114	G=0.974	A=0.026
African American	Sub	2832	G=0.9386	A=0.0614
Asian	Sub	112	G=1.000	A=0.000
East Asian	Sub	86	G=1.00	A=0.00
Other Asian	Sub	26	G=1.00	A=0.00
Latin American 1	Sub	146	G=0.842	A=0.158
Latin American 2	Sub	610	G=0.852	A=0.148
South Asian	Sub	98	G=0.87	A=0.13
Other	Sub	692	G=0.811	A=0.189

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	G=0.819944	A=0.180056
gnomAD - Genomes	Global	Study-wide	139936	G=0.809877	A=0.190123
gnomAD - Genomes	European	Sub	75764	G=0.73246	A=0.26754
gnomAD - Genomes	African	Sub	41940	G=0.93345	A=0.06655
gnomAD - Genomes	American	Sub	13632	G=0.82064	A=0.17936
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.7933	A=0.2067
gnomAD - Genomes	East Asian	Sub	3126	G=0.9994	A=0.0006
gnomAD - Genomes	Other	Sub	2150	G=0.8093	A=0.1907
14KJPN	JAPANESE	Study-wide	28258	G=0.99989	A=0.00011
Allele Frequency Aggregator	Total	Global	18890	G=0.77295	A=0.22705
Allele Frequency Aggregator	European	Sub	14286	G=0.73016	A=0.26984
Allele Frequency Aggregator	African	Sub	2946	G=0.9399	A=0.0601
Allele Frequency Aggregator	Other	Sub	692	G=0.811	A=0.189
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.852	A=0.148
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.842	A=0.158
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=0.87	A=0.13
8.3KJPN	JAPANESE	Study-wide	16760	G=0.99988	A=0.00012
1000Genomes_30x	Global	Study-wide	6404	G=0.8904	A=0.1096
1000Genomes_30x	African	Sub	1786	G=0.9692	A=0.0308
1000Genomes_30x	Europe	Sub	1266	G=0.7038	A=0.2962
1000Genomes_30x	South Asian	Sub	1202	G=0.9093	A=0.0907
1000Genomes_30x	East Asian	Sub	1170	G=0.9991	A=0.0009
1000Genomes_30x	American	Sub	980	G=0.835	A=0.165
1000Genomes	Global	Study-wide	5008	G=0.8926	A=0.1074
1000Genomes	African	Sub	1322	G=0.9690	A=0.0310
1000Genomes	East Asian	Sub	1008	G=0.9990	A=0.0010
1000Genomes	Europe	Sub	1006	G=0.7008	A=0.2992
1000Genomes	South Asian	Sub	978	G=0.906	A=0.094
1000Genomes	American	Sub	694	G=0.852	A=0.148
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7319	A=0.2681
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7400	A=0.2600
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7282	A=0.2718
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9997	A=0.0003
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9995	A=0.0005
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.745	A=0.255
Northern Sweden	ACPOP	Study-wide	600	G=0.703	A=0.297
HapMap	Global	Study-wide	298	G=0.906	A=0.094
HapMap	African	Sub	112	G=0.991	A=0.009
HapMap	American	Sub	98	G=0.72	A=0.28
HapMap	Asian	Sub	88	G=1.00	A=0.00
Qatari	Global	Study-wide	216	G=0.833	A=0.167
SGDP_PRJ	Global	Study-wide	102	G=0.412	A=0.588
The Danish reference pan genome	Danish	Study-wide	40	G=0.65	A=0.35
Siberian	Global	Study-wide	16	G=0.44	A=0.56

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.89824556G>A
GRCh37.p13 chr 4	NC_000004.11:g.90745707G>A
SNCA RefSeqGene	NG_011851.1:g.18741C>T

Gene: SNCA, synuclein alpha (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SNCA transcript variant 1	NM_000345.4:c.164-2168C>T	N/A	Intron Variant
SNCA transcript variant 2	NM_001146054.2:c.164-2168… NM_001146054.2:c.164-2168C>T	N/A	Intron Variant
SNCA transcript variant 3	NM_001146055.2:c.164-2168… NM_001146055.2:c.164-2168C>T	N/A	Intron Variant
SNCA transcript variant 5	NM_001375285.1:c.164-2168… NM_001375285.1:c.164-2168C>T	N/A	Intron Variant
SNCA transcript variant 6	NM_001375286.1:c.164-2168… NM_001375286.1:c.164-2168C>T	N/A	Intron Variant
SNCA transcript variant 7	NM_001375287.1:c.164-2168… NM_001375287.1:c.164-2168C>T	N/A	Intron Variant
SNCA transcript variant 8	NM_001375288.1:c.164-2168… NM_001375288.1:c.164-2168C>T	N/A	Intron Variant
SNCA transcript variant 4	NM_007308.3:c.164-2168C>T	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.164-2168… XM_011532203.2:c.164-2168C>T	N/A	Intron Variant
SNCA transcript variant X2	XM_011532204.4:c.164-2168… XM_011532204.4:c.164-2168C>T	N/A	Intron Variant
SNCA transcript variant X3	XM_011532205.3:c.164-2168… XM_011532205.3:c.164-2168C>T	N/A	Intron Variant
SNCA transcript variant X4	XM_011532206.2:c.164-2168… XM_011532206.2:c.164-2168C>T	N/A	Intron Variant
SNCA transcript variant X5	XM_011532207.2:c.164-2168… XM_011532207.2:c.164-2168C>T	N/A	Intron Variant
SNCA transcript variant X6	XM_047416097.1:c.164-2168… XM_047416097.1:c.164-2168C>T	N/A	Intron Variant

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	G=	A
GRCh38.p14 chr 4	NC_000004.12:g.89824556=	NC_000004.12:g.89824556G>A
GRCh37.p13 chr 4	NC_000004.11:g.90745707=	NC_000004.11:g.90745707G>A
SNCA RefSeqGene	NG_011851.1:g.18741=	NG_011851.1:g.18741C>T
SNCA transcript variant 1	NM_000345.3:c.164-2168=	NM_000345.3:c.164-2168C>T
SNCA transcript variant 1	NM_000345.4:c.164-2168=	NM_000345.4:c.164-2168C>T
SNCA transcript variant 2	NM_001146054.1:c.164-2168=	NM_001146054.1:c.164-2168C>T
SNCA transcript variant 2	NM_001146054.2:c.164-2168=	NM_001146054.2:c.164-2168C>T
SNCA transcript variant 3	NM_001146055.1:c.164-2168=	NM_001146055.1:c.164-2168C>T
SNCA transcript variant 3	NM_001146055.2:c.164-2168=	NM_001146055.2:c.164-2168C>T
SNCA transcript variant 5	NM_001375285.1:c.164-2168=	NM_001375285.1:c.164-2168C>T
SNCA transcript variant 6	NM_001375286.1:c.164-2168=	NM_001375286.1:c.164-2168C>T
SNCA transcript variant 7	NM_001375287.1:c.164-2168=	NM_001375287.1:c.164-2168C>T
SNCA transcript variant 8	NM_001375288.1:c.164-2168=	NM_001375288.1:c.164-2168C>T
SNCA transcript variant 4	NM_007308.2:c.164-2168=	NM_007308.2:c.164-2168C>T
SNCA transcript variant 4	NM_007308.3:c.164-2168=	NM_007308.3:c.164-2168C>T
SNCA transcript variant X1	XM_005263182.1:c.164-2168=	XM_005263182.1:c.164-2168C>T
SNCA transcript variant X2	XM_005263183.1:c.122-2168=	XM_005263183.1:c.122-2168C>T
SNCA transcript variant X3	XM_005263184.1:c.122-2168=	XM_005263184.1:c.122-2168C>T
SNCA transcript variant X4	XM_005263185.1:c.122-2168=	XM_005263185.1:c.122-2168C>T
SNCA transcript variant X5	XM_005263186.1:c.122-2168=	XM_005263186.1:c.122-2168C>T
SNCA transcript variant X6	XM_005263187.1:c.164-2168=	XM_005263187.1:c.164-2168C>T
SNCA transcript variant X7	XM_005263188.1:c.164-2168=	XM_005263188.1:c.164-2168C>T
SNCA transcript variant X8	XM_005263189.1:c.164-2168=	XM_005263189.1:c.164-2168C>T
SNCA transcript variant X1	XM_011532203.2:c.164-2168=	XM_011532203.2:c.164-2168C>T
SNCA transcript variant X2	XM_011532204.4:c.164-2168=	XM_011532204.4:c.164-2168C>T
SNCA transcript variant X3	XM_011532205.3:c.164-2168=	XM_011532205.3:c.164-2168C>T
SNCA transcript variant X4	XM_011532206.2:c.164-2168=	XM_011532206.2:c.164-2168C>T
SNCA transcript variant X5	XM_011532207.2:c.164-2168=	XM_011532207.2:c.164-2168C>T
SNCA transcript variant X6	XM_047416097.1:c.164-2168=	XM_047416097.1:c.164-2168C>T

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#.

53 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3863760	Sep 28, 2001 (100)
2	WI_SSAHASNP	ss6464092	Feb 20, 2003 (111)
3	ABI	ss44578840	Mar 14, 2006 (126)
4	1000GENOMES	ss108127842	Jan 23, 2009 (130)
5	ENSEMBL	ss144368730	Dec 01, 2009 (131)
6	1000GENOMES	ss221062833	Jul 14, 2010 (132)
7	1000GENOMES	ss232490160	Jul 14, 2010 (132)
8	BL	ss253329246	May 09, 2011 (134)
9	GMI	ss284955848	Apr 25, 2013 (138)
10	SSMP	ss651483519	Apr 25, 2013 (138)
11	EVA-GONL	ss980375527	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1071733703	Aug 21, 2014 (142)
13	1000GENOMES	ss1310714176	Aug 21, 2014 (142)
14	EVA_GENOME_DK	ss1580660716	Apr 01, 2015 (144)
15	EVA_DECODE	ss1589877871	Apr 01, 2015 (144)
16	EVA_UK10K_ALSPAC	ss1610595527	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1653589560	Apr 01, 2015 (144)
18	WEILL_CORNELL_DGM	ss1923619513	Feb 12, 2016 (147)
19	JJLAB	ss2022394842	Sep 14, 2016 (149)
20	USC_VALOUEV	ss2150524683	Dec 20, 2016 (150)
21	HUMAN_LONGEVITY	ss2264859669	Dec 20, 2016 (150)
22	SYSTEMSBIOZJU	ss2625699891	Nov 08, 2017 (151)
23	GNOMAD	ss2812083373	Nov 08, 2017 (151)
24	SWEGEN	ss2995099975	Nov 08, 2017 (151)
25	BIOINF_KMB_FNS_UNIBA	ss3024973555	Nov 08, 2017 (151)
26	CSHL	ss3345832527	Nov 08, 2017 (151)
27	URBANLAB	ss3647788241	Oct 12, 2018 (152)
28	EGCUT_WGS	ss3662987826	Jul 13, 2019 (153)
29	EVA_DECODE	ss3712526414	Jul 13, 2019 (153)
30	ACPOP	ss3731363823	Jul 13, 2019 (153)
31	EVA	ss3762090429	Jul 13, 2019 (153)
32	PACBIO	ss3784785279	Jul 13, 2019 (153)
33	PACBIO	ss3790232677	Jul 13, 2019 (153)
34	PACBIO	ss3795108050	Jul 13, 2019 (153)
35	KHV_HUMAN_GENOMES	ss3805237009	Jul 13, 2019 (153)
36	EVA	ss3828670333	Apr 26, 2020 (154)
37	EVA	ss3837777088	Apr 26, 2020 (154)
38	EVA	ss3843215136	Apr 26, 2020 (154)
39	SGDP_PRJ	ss3859471037	Apr 26, 2020 (154)
40	KRGDB	ss3905742358	Apr 26, 2020 (154)
41	KOGIC	ss3954625123	Apr 26, 2020 (154)
42	TOPMED	ss4622256974	Apr 26, 2021 (155)
43	TOMMO_GENOMICS	ss5166788333	Apr 26, 2021 (155)
44	1000G_HIGH_COVERAGE	ss5260054593	Oct 13, 2022 (156)
45	HUGCELL_USP	ss5458723156	Oct 13, 2022 (156)
46	EVA	ss5507613188	Oct 13, 2022 (156)
47	1000G_HIGH_COVERAGE	ss5541586499	Oct 13, 2022 (156)
48	SANFORD_IMAGENETICS	ss5635530609	Oct 13, 2022 (156)
49	TOMMO_GENOMICS	ss5701437089	Oct 13, 2022 (156)
50	YY_MCH	ss5805297851	Oct 13, 2022 (156)
51	EVA	ss5844330765	Oct 13, 2022 (156)
52	EVA	ss5864414157	Oct 13, 2022 (156)
53	EVA	ss5963915491	Oct 13, 2022 (156)
54	1000Genomes	NC_000004.11 - 90745707	Oct 12, 2018 (152)
55	1000Genomes_30x	NC_000004.12 - 89824556	Oct 13, 2022 (156)
56	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 90745707	Oct 12, 2018 (152)
57	Genetic variation in the Estonian population	NC_000004.11 - 90745707	Oct 12, 2018 (152)
58	The Danish reference pan genome	NC_000004.11 - 90745707	Apr 26, 2020 (154)
59	gnomAD - Genomes	NC_000004.12 - 89824556	Apr 26, 2021 (155)
60	Genome of the Netherlands Release 5	NC_000004.11 - 90745707	Apr 26, 2020 (154)
61	HapMap	NC_000004.12 - 89824556	Apr 26, 2020 (154)
62	KOREAN population from KRGDB	NC_000004.11 - 90745707	Apr 26, 2020 (154)
63	Korean Genome Project	NC_000004.12 - 89824556	Apr 26, 2020 (154)
64	Northern Sweden	NC_000004.11 - 90745707	Jul 13, 2019 (153)
65	Qatari	NC_000004.11 - 90745707	Apr 26, 2020 (154)
66	SGDP_PRJ	NC_000004.11 - 90745707	Apr 26, 2020 (154)
67	Siberian	NC_000004.11 - 90745707	Apr 26, 2020 (154)
68	8.3KJPN	NC_000004.11 - 90745707	Apr 26, 2021 (155)
69	14KJPN	NC_000004.12 - 89824556	Oct 13, 2022 (156)
70	TopMed	NC_000004.12 - 89824556	Apr 26, 2021 (155)
71	UK 10K study - Twins	NC_000004.11 - 90745707	Oct 12, 2018 (152)
72	ALFA	NC_000004.12 - 89824556	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss108127842, ss253329246, ss284955848, ss1589877871	NC_000004.10:90964729:G:A	NC_000004.12:89824555:G:A	(self)
22146028, 12318291, 8726074, 6825655, 5440651, 12919752, 4648688, 5661443, 11488017, 3041037, 24757640, 12318291, ss221062833, ss232490160, ss651483519, ss980375527, ss1071733703, ss1310714176, ss1580660716, ss1610595527, ss1653589560, ss1923619513, ss2022394842, ss2150524683, ss2625699891, ss2812083373, ss2995099975, ss3345832527, ss3662987826, ss3731363823, ss3762090429, ss3784785279, ss3790232677, ss3795108050, ss3828670333, ss3837777088, ss3859471037, ss3905742358, ss5166788333, ss5507613188, ss5635530609, ss5844330765, ss5963915491	NC_000004.11:90745706:G:A	NC_000004.12:89824555:G:A	(self)
29112434, 156850406, 2658858, 11003124, 35274193, 459634530, 7131760839, ss2264859669, ss3024973555, ss3647788241, ss3712526414, ss3805237009, ss3843215136, ss3954625123, ss4622256974, ss5260054593, ss5458723156, ss5541586499, ss5701437089, ss5805297851, ss5864414157	NC_000004.12:89824555:G:A	NC_000004.12:89824555:G:A	(self)
ss3863760, ss6464092, ss44578840, ss144368730	NT_016354.19:15293427:G:A	NC_000004.12:89824555:G:A	(self)

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

3 citations for rs2737012

PMID	Title	Author	Year	Journal
15637659	Linkage disequilibrium patterns and tagSNP transferability among European populations.	Mueller JC et al.	2005	American journal of human genetics
22025277	Genetic variants of α-synuclein are not associated with essential tremor.	Ross OA et al.	2011	Movement disorders
22912757	Evaluation of the role of SNCA variants in survival without neurological disease.	Heckman MG et al.	2012	PloS one

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

rs2737012