Name: rs147165312
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.

rs147165312

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:89818710 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.005941 (833/140212, GnomAD)
A=0.00331 (62/18754, ALFA)
A=0.0061 (39/6404, 1000G_30x) (+ 11 more)
A=0.0064 (32/5008, 1000G)
A=0.0098 (44/4480, Estonian)
A=0.0054 (21/3854, ALSPAC)
A=0.0059 (22/3708, TWINSUK)
A=0.008 (8/998, GoNL)
A=0.008 (5/600, NorthernSweden)
A=0.014 (3/216, Qatari)
T=0.5 (3/6, SGDP_PRJ)
A=0.5 (3/6, SGDP_PRJ)
T=0.5 (1/2, Siberian)
A=0.5 (1/2, 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	18754	T=0.99669	A=0.00331, C=0.00000
European	Sub	14168	T=0.99577	A=0.00423, C=0.00000
African	Sub	2944	T=0.9997	A=0.0003, C=0.0000
African Others	Sub	114	T=1.000	A=0.000, C=0.000
African American	Sub	2830	T=0.9996	A=0.0004, C=0.0000
Asian	Sub	112	T=1.000	A=0.000, C=0.000
East Asian	Sub	86	T=1.00	A=0.00, C=0.00
Other Asian	Sub	26	T=1.00	A=0.00, C=0.00
Latin American 1	Sub	142	T=1.000	A=0.000, C=0.000
Latin American 2	Sub	608	T=1.000	A=0.000, C=0.000
South Asian	Sub	92	T=1.00	A=0.00, C=0.00
Other	Sub	688	T=0.999	A=0.001, C=0.000

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
gnomAD - Genomes	Global	Study-wide	140212	T=0.994059	A=0.005941
gnomAD - Genomes	European	Sub	75928	T=0.99098	A=0.00902
gnomAD - Genomes	African	Sub	42044	T=0.99943	A=0.00057
gnomAD - Genomes	American	Sub	13642	T=0.99611	A=0.00389
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.9831	A=0.0169
gnomAD - Genomes	East Asian	Sub	3128	T=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2150	T=0.9930	A=0.0070
Allele Frequency Aggregator	Total	Global	18754	T=0.99669	A=0.00331, C=0.00000
Allele Frequency Aggregator	European	Sub	14168	T=0.99577	A=0.00423, C=0.00000
Allele Frequency Aggregator	African	Sub	2944	T=0.9997	A=0.0003, C=0.0000
Allele Frequency Aggregator	Other	Sub	688	T=0.999	A=0.001, C=0.000
Allele Frequency Aggregator	Latin American 2	Sub	608	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	142	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Asian	Sub	112	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	South Asian	Sub	92	T=1.00	A=0.00, C=0.00
1000Genomes_30x	Global	Study-wide	6404	T=0.9939	A=0.0061
1000Genomes_30x	African	Sub	1786	T=1.0000	A=0.0000
1000Genomes_30x	Europe	Sub	1266	T=0.9905	A=0.0095
1000Genomes_30x	South Asian	Sub	1202	T=0.9800	A=0.0200
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	T=0.997	A=0.003
1000Genomes	Global	Study-wide	5008	T=0.9936	A=0.0064
1000Genomes	African	Sub	1322	T=1.0000	A=0.0000
1000Genomes	East Asian	Sub	1008	T=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	T=0.9881	A=0.0119
1000Genomes	South Asian	Sub	978	T=0.982	A=0.018
1000Genomes	American	Sub	694	T=0.997	A=0.003
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9902	A=0.0098
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9946	A=0.0054
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9941	A=0.0059
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.992	A=0.008
Northern Sweden	ACPOP	Study-wide	600	T=0.992	A=0.008
Qatari	Global	Study-wide	216	T=0.986	A=0.014
SGDP_PRJ	Global	Study-wide	6	T=0.5	A=0.5
Siberian	Global	Study-wide	2	T=0.5	A=0.5

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.89818710T>A
GRCh38.p14 chr 4	NC_000004.12:g.89818710T>C
GRCh37.p13 chr 4	NC_000004.11:g.90739861T>A
GRCh37.p13 chr 4	NC_000004.11:g.90739861T>C
SNCA RefSeqGene	NG_011851.1:g.24587A>T
SNCA RefSeqGene	NG_011851.1:g.24587A>G

Gene: SNCA, synuclein alpha (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SNCA transcript variant 1	NM_000345.4:c.306+3536A>T	N/A	Intron Variant
SNCA transcript variant 2	NM_001146054.2:c.306+3536… NM_001146054.2:c.306+3536A>T	N/A	Intron Variant
SNCA transcript variant 3	NM_001146055.2:c.306+3536… NM_001146055.2:c.306+3536A>T	N/A	Intron Variant
SNCA transcript variant 5	NM_001375285.1:c.306+3536… NM_001375285.1:c.306+3536A>T	N/A	Intron Variant
SNCA transcript variant 6	NM_001375286.1:c.306+3536… NM_001375286.1:c.306+3536A>T	N/A	Intron Variant
SNCA transcript variant 7	NM_001375287.1:c.306+3536… NM_001375287.1:c.306+3536A>T	N/A	Intron Variant
SNCA transcript variant 8	NM_001375288.1:c.306+3536… NM_001375288.1:c.306+3536A>T	N/A	Intron Variant
SNCA transcript variant 4	NM_007308.3:c.306+3536A>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.306+3536… XM_011532203.2:c.306+3536A>T	N/A	Intron Variant
SNCA transcript variant X2	XM_011532204.4:c.306+3536… XM_011532204.4:c.306+3536A>T	N/A	Intron Variant
SNCA transcript variant X3	XM_011532205.3:c.306+3536… XM_011532205.3:c.306+3536A>T	N/A	Intron Variant
SNCA transcript variant X4	XM_011532206.2:c.306+3536… XM_011532206.2:c.306+3536A>T	N/A	Intron Variant
SNCA transcript variant X5	XM_011532207.2:c.306+3536… XM_011532207.2:c.306+3536A>T	N/A	Intron Variant
SNCA transcript variant X6	XM_047416097.1:c.306+3536… XM_047416097.1:c.306+3536A>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	T=	A	C
GRCh38.p14 chr 4	NC_000004.12:g.89818710=	NC_000004.12:g.89818710T>A	NC_000004.12:g.89818710T>C
GRCh37.p13 chr 4	NC_000004.11:g.90739861=	NC_000004.11:g.90739861T>A	NC_000004.11:g.90739861T>C
SNCA RefSeqGene	NG_011851.1:g.24587=	NG_011851.1:g.24587A>T	NG_011851.1:g.24587A>G
SNCA transcript variant 1	NM_000345.3:c.306+3536=	NM_000345.3:c.306+3536A>T	NM_000345.3:c.306+3536A>G
SNCA transcript variant 1	NM_000345.4:c.306+3536=	NM_000345.4:c.306+3536A>T	NM_000345.4:c.306+3536A>G
SNCA transcript variant 2	NM_001146054.1:c.306+3536=	NM_001146054.1:c.306+3536A>T	NM_001146054.1:c.306+3536A>G
SNCA transcript variant 2	NM_001146054.2:c.306+3536=	NM_001146054.2:c.306+3536A>T	NM_001146054.2:c.306+3536A>G
SNCA transcript variant 3	NM_001146055.1:c.306+3536=	NM_001146055.1:c.306+3536A>T	NM_001146055.1:c.306+3536A>G
SNCA transcript variant 3	NM_001146055.2:c.306+3536=	NM_001146055.2:c.306+3536A>T	NM_001146055.2:c.306+3536A>G
SNCA transcript variant 5	NM_001375285.1:c.306+3536=	NM_001375285.1:c.306+3536A>T	NM_001375285.1:c.306+3536A>G
SNCA transcript variant 6	NM_001375286.1:c.306+3536=	NM_001375286.1:c.306+3536A>T	NM_001375286.1:c.306+3536A>G
SNCA transcript variant 7	NM_001375287.1:c.306+3536=	NM_001375287.1:c.306+3536A>T	NM_001375287.1:c.306+3536A>G
SNCA transcript variant 8	NM_001375288.1:c.306+3536=	NM_001375288.1:c.306+3536A>T	NM_001375288.1:c.306+3536A>G
SNCA transcript variant 4	NM_007308.2:c.306+3536=	NM_007308.2:c.306+3536A>T	NM_007308.2:c.306+3536A>G
SNCA transcript variant 4	NM_007308.3:c.306+3536=	NM_007308.3:c.306+3536A>T	NM_007308.3:c.306+3536A>G
SNCA transcript variant X1	XM_005263182.1:c.306+3536=	XM_005263182.1:c.306+3536A>T	XM_005263182.1:c.306+3536A>G
SNCA transcript variant X2	XM_005263183.1:c.264+3536=	XM_005263183.1:c.264+3536A>T	XM_005263183.1:c.264+3536A>G
SNCA transcript variant X3	XM_005263184.1:c.264+3536=	XM_005263184.1:c.264+3536A>T	XM_005263184.1:c.264+3536A>G
SNCA transcript variant X4	XM_005263185.1:c.264+3536=	XM_005263185.1:c.264+3536A>T	XM_005263185.1:c.264+3536A>G
SNCA transcript variant X5	XM_005263186.1:c.264+3536=	XM_005263186.1:c.264+3536A>T	XM_005263186.1:c.264+3536A>G
SNCA transcript variant X6	XM_005263187.1:c.306+3536=	XM_005263187.1:c.306+3536A>T	XM_005263187.1:c.306+3536A>G
SNCA transcript variant X7	XM_005263188.1:c.306+3536=	XM_005263188.1:c.306+3536A>T	XM_005263188.1:c.306+3536A>G
SNCA transcript variant X8	XM_005263189.1:c.306+3536=	XM_005263189.1:c.306+3536A>T	XM_005263189.1:c.306+3536A>G
SNCA transcript variant X1	XM_011532203.2:c.306+3536=	XM_011532203.2:c.306+3536A>T	XM_011532203.2:c.306+3536A>G
SNCA transcript variant X2	XM_011532204.4:c.306+3536=	XM_011532204.4:c.306+3536A>T	XM_011532204.4:c.306+3536A>G
SNCA transcript variant X3	XM_011532205.3:c.306+3536=	XM_011532205.3:c.306+3536A>T	XM_011532205.3:c.306+3536A>G
SNCA transcript variant X4	XM_011532206.2:c.306+3536=	XM_011532206.2:c.306+3536A>T	XM_011532206.2:c.306+3536A>G
SNCA transcript variant X5	XM_011532207.2:c.306+3536=	XM_011532207.2:c.306+3536A>T	XM_011532207.2:c.306+3536A>G
SNCA transcript variant X6	XM_047416097.1:c.306+3536=	XM_047416097.1:c.306+3536A>T	XM_047416097.1:c.306+3536A>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#.

29 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss331793939	May 09, 2011 (134)
2	EVA-GONL	ss980375460	Aug 21, 2014 (142)
3	1000GENOMES	ss1310714011	Aug 21, 2014 (142)
4	EVA_DECODE	ss1589877813	Apr 01, 2015 (144)
5	EVA_UK10K_ALSPAC	ss1610595438	Apr 01, 2015 (144)
6	EVA_UK10K_TWINSUK	ss1653589471	Apr 01, 2015 (144)
7	WEILL_CORNELL_DGM	ss1923619447	Feb 12, 2016 (147)
8	USC_VALOUEV	ss2150524626	Dec 20, 2016 (150)
9	HUMAN_LONGEVITY	ss2264859327	Dec 20, 2016 (150)
10	GNOMAD	ss2812082915	Nov 08, 2017 (151)
11	SWEGEN	ss2995099871	Nov 08, 2017 (151)
12	ILLUMINA	ss3022394125	Nov 08, 2017 (151)
13	ILLUMINA	ss3652880189	Oct 12, 2018 (152)
14	EGCUT_WGS	ss3662987740	Jul 13, 2019 (153)
15	EVA_DECODE	ss3712526285	Jul 13, 2019 (153)
16	ILLUMINA	ss3726151634	Jul 13, 2019 (153)
17	ACPOP	ss3731363755	Jul 13, 2019 (153)
18	SGDP_PRJ	ss3859470932	Apr 26, 2020 (154)
19	TOPMED	ss4622255633	Apr 26, 2021 (155)
20	TOPMED	ss4622255634	Apr 26, 2021 (155)
21	1000G_HIGH_COVERAGE	ss5260054432	Oct 13, 2022 (156)
22	EVA	ss5350547648	Oct 13, 2022 (156)
23	HUGCELL_USP	ss5458722999	Oct 13, 2022 (156)
24	EVA	ss5507613152	Oct 13, 2022 (156)
25	1000G_HIGH_COVERAGE	ss5541586281	Oct 13, 2022 (156)
26	SANFORD_IMAGENETICS	ss5635530505	Oct 13, 2022 (156)
27	EVA	ss5844330676	Oct 13, 2022 (156)
28	EVA	ss5864413959	Oct 13, 2022 (156)
29	EVA	ss5963915397	Oct 13, 2022 (156)
30	1000Genomes	NC_000004.11 - 90739861	Oct 12, 2018 (152)
31	1000Genomes_30x	NC_000004.12 - 89818710	Oct 13, 2022 (156)
32	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 90739861	Oct 12, 2018 (152)
33	Genetic variation in the Estonian population	NC_000004.11 - 90739861	Oct 12, 2018 (152)
34	gnomAD - Genomes	NC_000004.12 - 89818710	Apr 26, 2021 (155)
35	Genome of the Netherlands Release 5	NC_000004.11 - 90739861	Apr 26, 2020 (154)
36	Northern Sweden	NC_000004.11 - 90739861	Jul 13, 2019 (153)
37	Qatari	NC_000004.11 - 90739861	Apr 26, 2020 (154)
38	SGDP_PRJ	NC_000004.11 - 90739861	Apr 26, 2020 (154)
39	Siberian	NC_000004.11 - 90739861	Apr 26, 2020 (154)
40	TopMed Submission ignored due to conflicting rows: Row 459633189 (NC_000004.12:89818709:T:A 1067/264690) Row 459633190 (NC_000004.12:89818709:T:C 2/264690)	-	Apr 26, 2021 (155)
41	TopMed Submission ignored due to conflicting rows: Row 459633189 (NC_000004.12:89818709:T:A 1067/264690) Row 459633190 (NC_000004.12:89818709:T:C 2/264690)	-	Apr 26, 2021 (155)
42	UK 10K study - Twins	NC_000004.11 - 90739861	Oct 12, 2018 (152)
43	ALFA	NC_000004.12 - 89818710	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
ss1589877813	NC_000004.10:90958883:T:A	NC_000004.12:89818709:T:A	(self)
22145853, 12318186, 8725988, 5440584, 4648620, 5661377, 11487912, 3040980, 12318186, ss331793939, ss980375460, ss1310714011, ss1610595438, ss1653589471, ss1923619447, ss2150524626, ss2812082915, ss2995099871, ss3022394125, ss3652880189, ss3662987740, ss3731363755, ss3859470932, ss5350547648, ss5507613152, ss5635530505, ss5844330676, ss5963915397	NC_000004.11:90739860:T:A	NC_000004.12:89818709:T:A	(self)
29112216, 156849219, 13471169641, ss2264859327, ss3712526285, ss3726151634, ss4622255633, ss5260054432, ss5458722999, ss5541586281, ss5864413959	NC_000004.12:89818709:T:A	NC_000004.12:89818709:T:A	(self)
13471169641, ss4622255634	NC_000004.12:89818709:T:C	NC_000004.12:89818709:T:C	(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 rs147165312

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

rs147165312