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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs142059155

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:89739867 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.033704 (8921/264690, TOPMED)
A=0.033098 (4627/139796, GnomAD)
A=0.04499 (2205/49010, ALFA) (+ 16 more)
A=0.00050 (14/28258, 14KJPN)
A=0.00048 (8/16760, 8.3KJPN)
A=0.0206 (132/6404, 1000G_30x)
A=0.0192 (96/5008, 1000G)
A=0.0301 (135/4480, Estonian)
A=0.0475 (183/3854, ALSPAC)
A=0.0558 (207/3708, TWINSUK)
A=0.0003 (1/2922, KOREAN)
A=0.040 (40/998, GoNL)
A=0.038 (23/600, NorthernSweden)
A=0.023 (5/216, Qatari)
A=0.05 (2/40, GENOME_DK)
G=0.50 (9/18, SGDP_PRJ)
A=0.50 (9/18, SGDP_PRJ)
G=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SNCA : Intron Variant
LOC124900856 : Non Coding Transcript 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 49010 G=0.95501 A=0.04499
European Sub 40702 G=0.95172 A=0.04828
African Sub 2970 G=0.9946 A=0.0054
African Others Sub 114 G=1.000 A=0.000
African American Sub 2856 G=0.9944 A=0.0056
Asian Sub 158 G=1.000 A=0.000
East Asian Sub 130 G=1.000 A=0.000
Other Asian Sub 28 G=1.00 A=0.00
Latin American 1 Sub 154 G=0.942 A=0.058
Latin American 2 Sub 616 G=0.971 A=0.029
South Asian Sub 98 G=0.99 A=0.01
Other Sub 4312 G=0.9545 A=0.0455


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 G=0.966296 A=0.033704
gnomAD - Genomes Global Study-wide 139796 G=0.966902 A=0.033098
gnomAD - Genomes European Sub 75672 G=0.95618 A=0.04382
gnomAD - Genomes African Sub 41928 G=0.99106 A=0.00894
gnomAD - Genomes American Sub 13598 G=0.95330 A=0.04670
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.9370 A=0.0630
gnomAD - Genomes East Asian Sub 3128 G=0.9994 A=0.0006
gnomAD - Genomes Other Sub 2150 G=0.9581 A=0.0419
Allele Frequency Aggregator Total Global 49010 G=0.95501 A=0.04499
Allele Frequency Aggregator European Sub 40702 G=0.95172 A=0.04828
Allele Frequency Aggregator Other Sub 4312 G=0.9545 A=0.0455
Allele Frequency Aggregator African Sub 2970 G=0.9946 A=0.0054
Allele Frequency Aggregator Latin American 2 Sub 616 G=0.971 A=0.029
Allele Frequency Aggregator Asian Sub 158 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 154 G=0.942 A=0.058
Allele Frequency Aggregator South Asian Sub 98 G=0.99 A=0.01
14KJPN JAPANESE Study-wide 28258 G=0.99950 A=0.00050
8.3KJPN JAPANESE Study-wide 16760 G=0.99952 A=0.00048
1000Genomes_30x Global Study-wide 6404 G=0.9792 A=0.0206, T=0.0002
1000Genomes_30x African Sub 1786 G=0.9961 A=0.0039, T=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9518 A=0.0482, T=0.0000
1000Genomes_30x South Asian Sub 1202 G=0.9809 A=0.0183, T=0.0008
1000Genomes_30x East Asian Sub 1170 G=0.9991 A=0.0009, T=0.0000
1000Genomes_30x American Sub 980 G=0.958 A=0.042, T=0.000
1000Genomes Global Study-wide 5008 G=0.9808 A=0.0192
1000Genomes African Sub 1322 G=0.9955 A=0.0045
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9533 A=0.0467
1000Genomes South Asian Sub 978 G=0.984 A=0.016
1000Genomes American Sub 694 G=0.961 A=0.039
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9699 A=0.0301
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9525 A=0.0475
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9442 A=0.0558
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9997 A=0.0003
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.960 A=0.040
Northern Sweden ACPOP Study-wide 600 G=0.962 A=0.038
Qatari Global Study-wide 216 G=0.977 A=0.023
The Danish reference pan genome Danish Study-wide 40 G=0.95 A=0.05
SGDP_PRJ Global Study-wide 18 G=0.50 A=0.50
Siberian Global Study-wide 4 G=0.5 A=0.5
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.89739867G>A
GRCh38.p14 chr 4 NC_000004.12:g.89739867G>T
GRCh37.p13 chr 4 NC_000004.11:g.90661018G>A
GRCh37.p13 chr 4 NC_000004.11:g.90661018G>T
SNCA RefSeqGene NG_011851.1:g.103430C>T
SNCA RefSeqGene NG_011851.1:g.103430C>A
Gene: SNCA, synuclein alpha (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SNCA transcript variant 1 NM_000345.4:c.307-10590C>T N/A Intron Variant
SNCA transcript variant 2 NM_001146054.2:c.307-1059…

NM_001146054.2:c.307-10590C>T

 		N/A Intron Variant
SNCA transcript variant 3 NM_001146055.2:c.307-1059…

NM_001146055.2:c.307-10590C>T

 		N/A Intron Variant
SNCA transcript variant 5 NM_001375285.1:c.307-1059…

NM_001375285.1:c.307-10590C>T

 		N/A Intron Variant
SNCA transcript variant 6 NM_001375286.1:c.307-1059…

NM_001375286.1:c.307-10590C>T

 		N/A Intron Variant
SNCA transcript variant 7 NM_001375287.1:c.307-1059…

NM_001375287.1:c.307-10590C>T

 		N/A Intron Variant
SNCA transcript variant 8 NM_001375288.1:c.307-1059…

NM_001375288.1:c.307-10590C>T

 		N/A Intron Variant
SNCA transcript variant 9 NM_001375290.1:c.163-1059…

NM_001375290.1:c.163-10590C>T

 		N/A Intron Variant
SNCA transcript variant 4 NM_007308.3:c.307-13207C>T N/A Intron 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. N/A Genic Downstream Transcript Variant
SNCA transcript variant X2 XM_011532204.4:c. N/A Genic Downstream Transcript Variant
SNCA transcript variant X3 XM_011532205.3:c. N/A Genic Downstream Transcript Variant
SNCA transcript variant X4 XM_011532206.2:c. N/A Genic Downstream Transcript Variant
SNCA transcript variant X5 XM_011532207.2:c. N/A Genic Downstream Transcript Variant
SNCA transcript variant X6 XM_047416097.1:c. N/A Genic Downstream Transcript Variant
Gene: LOC124900856, uncharacterized LOC124900856 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124900856 transcript variant X1 XR_007058472.1:n.1403G>A N/A Non Coding Transcript Variant
LOC124900856 transcript variant X1 XR_007058472.1:n.1403G>T N/A Non Coding Transcript Variant
LOC124900856 transcript variant X2 XR_007058473.1:n. 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 G= A T
GRCh38.p14 chr 4 NC_000004.12:g.89739867= NC_000004.12:g.89739867G>A NC_000004.12:g.89739867G>T
GRCh37.p13 chr 4 NC_000004.11:g.90661018= NC_000004.11:g.90661018G>A NC_000004.11:g.90661018G>T
SNCA RefSeqGene NG_011851.1:g.103430= NG_011851.1:g.103430C>T NG_011851.1:g.103430C>A
LOC124900856 transcript variant X1 XR_007058472.1:n.1403= XR_007058472.1:n.1403G>A XR_007058472.1:n.1403G>T
SNCA transcript variant 1 NM_000345.3:c.307-10590= NM_000345.3:c.307-10590C>T NM_000345.3:c.307-10590C>A
SNCA transcript variant 1 NM_000345.4:c.307-10590= NM_000345.4:c.307-10590C>T NM_000345.4:c.307-10590C>A
SNCA transcript variant 2 NM_001146054.1:c.307-10590= NM_001146054.1:c.307-10590C>T NM_001146054.1:c.307-10590C>A
SNCA transcript variant 2 NM_001146054.2:c.307-10590= NM_001146054.2:c.307-10590C>T NM_001146054.2:c.307-10590C>A
SNCA transcript variant 3 NM_001146055.1:c.307-10590= NM_001146055.1:c.307-10590C>T NM_001146055.1:c.307-10590C>A
SNCA transcript variant 3 NM_001146055.2:c.307-10590= NM_001146055.2:c.307-10590C>T NM_001146055.2:c.307-10590C>A
SNCA transcript variant 5 NM_001375285.1:c.307-10590= NM_001375285.1:c.307-10590C>T NM_001375285.1:c.307-10590C>A
SNCA transcript variant 6 NM_001375286.1:c.307-10590= NM_001375286.1:c.307-10590C>T NM_001375286.1:c.307-10590C>A
SNCA transcript variant 7 NM_001375287.1:c.307-10590= NM_001375287.1:c.307-10590C>T NM_001375287.1:c.307-10590C>A
SNCA transcript variant 8 NM_001375288.1:c.307-10590= NM_001375288.1:c.307-10590C>T NM_001375288.1:c.307-10590C>A
SNCA transcript variant 9 NM_001375290.1:c.163-10590= NM_001375290.1:c.163-10590C>T NM_001375290.1:c.163-10590C>A
SNCA transcript variant 4 NM_007308.2:c.307-13207= NM_007308.2:c.307-13207C>T NM_007308.2:c.307-13207C>A
SNCA transcript variant 4 NM_007308.3:c.307-13207= NM_007308.3:c.307-13207C>T NM_007308.3:c.307-13207C>A
SNCA transcript variant X1 XM_005263182.1:c.307-10590= XM_005263182.1:c.307-10590C>T XM_005263182.1:c.307-10590C>A
SNCA transcript variant X2 XM_005263183.1:c.265-10590= XM_005263183.1:c.265-10590C>T XM_005263183.1:c.265-10590C>A
SNCA transcript variant X3 XM_005263184.1:c.265-10590= XM_005263184.1:c.265-10590C>T XM_005263184.1:c.265-10590C>A
SNCA transcript variant X4 XM_005263185.1:c.265-10590= XM_005263185.1:c.265-10590C>T XM_005263185.1:c.265-10590C>A
SNCA transcript variant X5 XM_005263186.1:c.265-10590= XM_005263186.1:c.265-10590C>T XM_005263186.1:c.265-10590C>A
SNCA transcript variant X6 XM_005263187.1:c.307-13207= XM_005263187.1:c.307-13207C>T XM_005263187.1:c.307-13207C>A
SNCA transcript variant X7 XM_005263188.1:c.307-13207= XM_005263188.1:c.307-13207C>T XM_005263188.1:c.307-13207C>A
SNCA transcript variant X8 XM_005263189.1:c.307-13207= XM_005263189.1:c.307-13207C>T XM_005263189.1:c.307-13207C>A
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#.

41 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss331793609 May 09, 2011 (134)
2 ILLUMINA ss536141983 Sep 08, 2015 (146)
3 EVA-GONL ss980374881 Aug 21, 2014 (142)
4 JMKIDD_LAB ss1071733268 Aug 21, 2014 (142)
5 1000GENOMES ss1310712055 Aug 21, 2014 (142)
6 DDI ss1429962083 Apr 01, 2015 (144)
7 EVA_GENOME_DK ss1580660505 Apr 01, 2015 (144)
8 EVA_DECODE ss1589877226 Apr 01, 2015 (144)
9 EVA_UK10K_ALSPAC ss1610594283 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1653588316 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1923618953 Feb 12, 2016 (147)
12 JJLAB ss2022394506 Sep 14, 2016 (149)
13 USC_VALOUEV ss2150524338 Dec 20, 2016 (150)
14 HUMAN_LONGEVITY ss2264854948 Dec 20, 2016 (150)
15 ILLUMINA ss2711010050 Nov 08, 2017 (151)
16 GNOMAD ss2812077176 Nov 08, 2017 (151)
17 SWEGEN ss2995099083 Nov 08, 2017 (151)
18 ILLUMINA ss3629013454 Oct 12, 2018 (152)
19 EGCUT_WGS ss3662986866 Jul 13, 2019 (153)
20 EVA_DECODE ss3712525300 Jul 13, 2019 (153)
21 ACPOP ss3731363321 Jul 13, 2019 (153)
22 ILLUMINA ss3744527722 Jul 13, 2019 (153)
23 PACBIO ss3784785141 Jul 13, 2019 (153)
24 PACBIO ss3790232559 Jul 13, 2019 (153)
25 PACBIO ss3795107934 Jul 13, 2019 (153)
26 KHV_HUMAN_GENOMES ss3805236314 Jul 13, 2019 (153)
27 SGDP_PRJ ss3859469952 Apr 26, 2020 (154)
28 KRGDB ss3905741185 Apr 26, 2020 (154)
29 TOPMED ss4622237474 Apr 26, 2021 (155)
30 TOMMO_GENOMICS ss5166785921 Apr 26, 2021 (155)
31 1000G_HIGH_COVERAGE ss5260052737 Oct 13, 2022 (156)
32 HUGCELL_USP ss5458721274 Oct 13, 2022 (156)
33 1000G_HIGH_COVERAGE ss5541583655 Oct 13, 2022 (156)
34 SANFORD_IMAGENETICS ss5624561301 Oct 13, 2022 (156)
35 SANFORD_IMAGENETICS ss5635529562 Oct 13, 2022 (156)
36 TOMMO_GENOMICS ss5701433949 Oct 13, 2022 (156)
37 EVA ss5844329903 Oct 13, 2022 (156)
38 EVA ss5848017727 Oct 13, 2022 (156)
39 EVA ss5864411937 Oct 13, 2022 (156)
40 EVA ss5963914325 Oct 13, 2022 (156)
41 EVA ss5979707112 Oct 13, 2022 (156)
42 1000Genomes NC_000004.11 - 90661018 Oct 12, 2018 (152)
43 1000Genomes_30x NC_000004.12 - 89739867 Oct 13, 2022 (156)
44 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 90661018 Oct 12, 2018 (152)
45 Genetic variation in the Estonian population NC_000004.11 - 90661018 Oct 12, 2018 (152)
46 The Danish reference pan genome NC_000004.11 - 90661018 Apr 26, 2020 (154)
47 gnomAD - Genomes NC_000004.12 - 89739867 Apr 26, 2021 (155)
48 Genome of the Netherlands Release 5 NC_000004.11 - 90661018 Apr 26, 2020 (154)
49 KOREAN population from KRGDB NC_000004.11 - 90661018 Apr 26, 2020 (154)
50 Northern Sweden NC_000004.11 - 90661018 Jul 13, 2019 (153)
51 Qatari NC_000004.11 - 90661018 Apr 26, 2020 (154)
52 SGDP_PRJ NC_000004.11 - 90661018 Apr 26, 2020 (154)
53 Siberian NC_000004.11 - 90661018 Apr 26, 2020 (154)
54 8.3KJPN NC_000004.11 - 90661018 Apr 26, 2021 (155)
55 14KJPN NC_000004.12 - 89739867 Oct 13, 2022 (156)
56 TopMed NC_000004.12 - 89739867 Apr 26, 2021 (155)
57 UK 10K study - Twins NC_000004.11 - 90661018 Oct 12, 2018 (152)
58 ALFA NC_000004.12 - 89739867 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1589877226 NC_000004.10:90880040:G:A NC_000004.12:89739866:G:A (self)
22143825, 12316897, 8725114, 6825444, 5440010, 12918579, 4648186, 5660883, 11486932, 3040692, 24755228, 12316897, ss331793609, ss536141983, ss980374881, ss1071733268, ss1310712055, ss1429962083, ss1580660505, ss1610594283, ss1653588316, ss1923618953, ss2022394506, ss2150524338, ss2711010050, ss2812077176, ss2995099083, ss3629013454, ss3662986866, ss3731363321, ss3744527722, ss3784785141, ss3790232559, ss3795107934, ss3859469952, ss3905741185, ss5166785921, ss5624561301, ss5635529562, ss5844329903, ss5848017727, ss5963914325, ss5979707112 NC_000004.11:90661017:G:A NC_000004.12:89739866:G:A (self)
29109590, 156834460, 35271053, 459615030, 6896337995, ss2264854948, ss3712525300, ss3805236314, ss4622237474, ss5260052737, ss5458721274, ss5541583655, ss5701433949, ss5864411937 NC_000004.12:89739866:G:A NC_000004.12:89739866:G:A (self)
29109590, ss5541583655 NC_000004.12:89739866:G:T NC_000004.12:89739866:G:T
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 rs142059155

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