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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.

rs8064

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:20651106 (GRCh38.p13) 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
C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.141316 (37405/264690, TOPMED)
G=0.145171 (20362/140262, GnomAD)
G=0.17042 (3420/20068, ALFA) (+ 14 more)
G=0.11957 (2004/16760, 8.3KJPN)
G=0.1150 (576/5008, 1000G)
G=0.2027 (908/4480, Estonian)
G=0.2045 (788/3854, ALSPAC)
G=0.1955 (725/3708, TWINSUK)
G=0.1198 (351/2930, KOREAN)
G=0.1258 (202/1606, HapMap)
G=0.213 (213/998, GoNL)
G=0.187 (112/600, NorthernSweden)
G=0.231 (50/216, Qatari)
G=0.152 (32/210, Vietnamese)
C=0.453 (58/128, SGDP_PRJ)
G=0.10 (4/40, GENOME_DK)
C=0.33 (8/24, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PINK1-AS : Non Coding Transcript Variant
PINK1 : 3 Prime UTR Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.20651106C>G
GRCh37.p13 chr 1 NC_000001.10:g.20977599C>G
PINK1 RefSeqGene NG_008164.1:g.22652C>G
DDOST RefSeqGene NG_032064.1:g.15439G>C
Gene: PINK1, PTEN induced kinase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PINK1 transcript NM_032409.3:c.*415= N/A 3 Prime UTR Variant
Gene: PINK1-AS, PINK1 antisense RNA (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PINK1-AS transcript NR_046507.1:n.1088G>C N/A Non Coding Transcript 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.

Allele: G (allele ID: 278658 )
ClinVar Accession Disease Names Clinical Significance
RCV000261476.1 Parkinson Disease, Recessive Likely-Benign
RCV000331316.1 Congenital disorder of glycosylation Likely-Benign
RCV001098431.1 Parkinson disease 6, autosomal recessive early-onset Benign

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 20068 C=0.82958 G=0.17042
European Sub 15436 C=0.80098 G=0.19902
African Sub 2946 C=0.9674 G=0.0326
African Others Sub 114 C=1.000 G=0.000
African American Sub 2832 C=0.9661 G=0.0339
Asian Sub 112 C=0.857 G=0.143
East Asian Sub 86 C=0.84 G=0.16
Other Asian Sub 26 C=0.92 G=0.08
Latin American 1 Sub 146 C=0.788 G=0.212
Latin American 2 Sub 610 C=0.833 G=0.167
South Asian Sub 98 C=0.92 G=0.08
Other Sub 720 C=0.868 G=0.132


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 C=0.858684 G=0.141316
gnomAD - Genomes Global Study-wide 140262 C=0.854829 G=0.145171
gnomAD - Genomes European Sub 75924 C=0.80077 G=0.19923
gnomAD - Genomes African Sub 42070 C=0.96330 G=0.03670
gnomAD - Genomes American Sub 13664 C=0.85451 G=0.14549
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.7326 G=0.2674
gnomAD - Genomes East Asian Sub 3126 C=0.8493 G=0.1507
gnomAD - Genomes Other Sub 2154 C=0.8403 G=0.1597
8.3KJPN JAPANESE Study-wide 16760 C=0.88043 G=0.11957
1000Genomes Global Study-wide 5008 C=0.8850 G=0.1150
1000Genomes African Sub 1322 C=0.9939 G=0.0061
1000Genomes East Asian Sub 1008 C=0.8730 G=0.1270
1000Genomes Europe Sub 1006 C=0.8062 G=0.1938
1000Genomes South Asian Sub 978 C=0.858 G=0.142
1000Genomes American Sub 694 C=0.847 G=0.153
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.7973 G=0.2027
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7955 G=0.2045
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8045 G=0.1955
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.8802 G=0.1198
HapMap Global Study-wide 1606 C=0.8742 G=0.1258
HapMap American Sub 770 C=0.848 G=0.152
HapMap African Sub 406 C=0.948 G=0.052
HapMap Asian Sub 254 C=0.886 G=0.114
HapMap Europe Sub 176 C=0.801 G=0.199
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.787 G=0.213
Northern Sweden ACPOP Study-wide 600 C=0.813 G=0.187
Qatari Global Study-wide 216 C=0.769 G=0.231
A Vietnamese Genetic Variation Database Global Study-wide 210 C=0.848 G=0.152
SGDP_PRJ Global Study-wide 128 C=0.453 G=0.547
The Danish reference pan genome Danish Study-wide 40 C=0.90 G=0.10
Siberian Global Study-wide 24 C=0.33 G=0.67
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 C= G
GRCh38.p13 chr 1 NC_000001.11:g.20651106= NC_000001.11:g.20651106C>G
GRCh37.p13 chr 1 NC_000001.10:g.20977599= NC_000001.10:g.20977599C>G
PINK1 RefSeqGene NG_008164.1:g.22652= NG_008164.1:g.22652C>G
PINK1 transcript NM_032409.3:c.*415= NM_032409.3:c.*415C>G
PINK1 transcript NM_032409.2:c.*415= NM_032409.2:c.*415C>G
DDOST RefSeqGene NG_032064.1:g.15439= NG_032064.1:g.15439G>C
PINK1-AS transcript NR_046507.1:n.1088= NR_046507.1:n.1088G>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#.

67 SubSNP, 17 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CGAP-GAI ss10009 Sep 19, 2000 (52)
2 PERLEGEN ss24244349 Sep 20, 2004 (123)
3 SI_EXO ss52082698 Oct 15, 2006 (127)
4 AFFY ss76539231 Dec 06, 2007 (129)
5 HGSV ss78122938 Dec 06, 2007 (129)
6 SHGC ss99307725 Feb 05, 2009 (130)
7 BGI ss102725846 Feb 20, 2009 (130)
8 KRIBB_YJKIM ss104807890 Feb 05, 2009 (130)
9 1000GENOMES ss108047462 Jan 22, 2009 (130)
10 ILLUMINA ss152536349 Dec 01, 2009 (131)
11 ILLUMINA ss159102626 Dec 01, 2009 (131)
12 ILLUMINA ss160945719 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss166208866 Jul 04, 2010 (132)
14 ILLUMINA ss168870813 Jul 04, 2010 (132)
15 ILLUMINA ss168873463 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss205390793 Jul 04, 2010 (132)
17 1000GENOMES ss230454941 Jul 14, 2010 (132)
18 1000GENOMES ss238164544 Jul 15, 2010 (132)
19 GMI ss275745631 May 04, 2012 (137)
20 ILLUMINA ss482765721 Sep 08, 2015 (146)
21 ILLUMINA ss536080622 Sep 08, 2015 (146)
22 SSMP ss647627357 Apr 25, 2013 (138)
23 ILLUMINA ss832615422 Aug 21, 2014 (142)
24 ILLUMINA ss833206111 Aug 21, 2014 (142)
25 EVA-GONL ss974926696 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1067721387 Aug 21, 2014 (142)
27 1000GENOMES ss1289959883 Aug 21, 2014 (142)
28 DDI ss1425739061 Apr 01, 2015 (144)
29 EVA_GENOME_DK ss1573929293 Apr 01, 2015 (144)
30 EVA_DECODE ss1584284941 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1599687833 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1642681866 Apr 01, 2015 (144)
33 EVA_SVP ss1712316575 Apr 01, 2015 (144)
34 WEILL_CORNELL_DGM ss1918138476 Feb 12, 2016 (147)
35 GENOMED ss1966701039 Jul 19, 2016 (147)
36 JJLAB ss2019581057 Sep 14, 2016 (149)
37 USC_VALOUEV ss2147584706 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2160570185 Dec 20, 2016 (150)
39 TOPMED ss2322752462 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2624306972 Nov 08, 2017 (151)
41 GRF ss2697489346 Nov 08, 2017 (151)
42 GNOMAD ss2752444839 Nov 08, 2017 (151)
43 SWEGEN ss2986433726 Nov 08, 2017 (151)
44 BIOINF_KMB_FNS_UNIBA ss3023555858 Nov 08, 2017 (151)
45 TOPMED ss3070418218 Nov 08, 2017 (151)
46 CSHL ss3343358158 Nov 08, 2017 (151)
47 ILLUMINA ss3626043746 Oct 11, 2018 (152)
48 ILLUMINA ss3635987625 Oct 11, 2018 (152)
49 ILLUMINA ss3637741807 Oct 11, 2018 (152)
50 ILLUMINA ss3637741808 Oct 11, 2018 (152)
51 OMUKHERJEE_ADBS ss3646226190 Oct 11, 2018 (152)
52 EGCUT_WGS ss3654504134 Jul 12, 2019 (153)
53 EVA_DECODE ss3686306172 Jul 12, 2019 (153)
54 ACPOP ss3726852615 Jul 12, 2019 (153)
55 EVA ss3745917492 Jul 12, 2019 (153)
56 KHV_HUMAN_GENOMES ss3798937225 Jul 12, 2019 (153)
57 EVA ss3825556461 Apr 25, 2020 (154)
58 EVA ss3826060850 Apr 25, 2020 (154)
59 EVA ss3836418624 Apr 25, 2020 (154)
60 EVA ss3841823078 Apr 25, 2020 (154)
61 SGDP_PRJ ss3848365275 Apr 25, 2020 (154)
62 KRGDB ss3893274193 Apr 25, 2020 (154)
63 FSA-LAB ss3983921202 Apr 27, 2021 (155)
64 FSA-LAB ss3983921203 Apr 27, 2021 (155)
65 EVA ss3986009502 Apr 27, 2021 (155)
66 TOPMED ss4441473680 Apr 27, 2021 (155)
67 TOMMO_GENOMICS ss5142835857 Apr 27, 2021 (155)
68 1000Genomes NC_000001.10 - 20977599 Oct 11, 2018 (152)
69 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 20977599 Oct 11, 2018 (152)
70 Genetic variation in the Estonian population NC_000001.10 - 20977599 Oct 11, 2018 (152)
71 The Danish reference pan genome NC_000001.10 - 20977599 Apr 25, 2020 (154)
72 gnomAD - Genomes NC_000001.11 - 20651106 Apr 27, 2021 (155)
73 Genome of the Netherlands Release 5 NC_000001.10 - 20977599 Apr 25, 2020 (154)
74 HapMap NC_000001.11 - 20651106 Apr 25, 2020 (154)
75 KOREAN population from KRGDB NC_000001.10 - 20977599 Apr 25, 2020 (154)
76 Northern Sweden NC_000001.10 - 20977599 Jul 12, 2019 (153)
77 Qatari NC_000001.10 - 20977599 Apr 25, 2020 (154)
78 SGDP_PRJ NC_000001.10 - 20977599 Apr 25, 2020 (154)
79 Siberian NC_000001.10 - 20977599 Apr 25, 2020 (154)
80 8.3KJPN NC_000001.10 - 20977599 Apr 27, 2021 (155)
81 TopMed NC_000001.11 - 20651106 Apr 27, 2021 (155)
82 UK 10K study - Twins NC_000001.10 - 20977599 Oct 11, 2018 (152)
83 A Vietnamese Genetic Variation Database NC_000001.10 - 20977599 Jul 12, 2019 (153)
84 ALFA NC_000001.11 - 20651106 Apr 27, 2021 (155)
85 ClinVar RCV000261476.1 Oct 11, 2018 (152)
86 ClinVar RCV000331316.1 Oct 11, 2018 (152)
87 ClinVar RCV001098431.1 Apr 27, 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)
rs17414512 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78122938 NC_000001.8:20722904:C:G NC_000001.11:20651105:C:G (self)
ss76539231, ss108047462, ss160945719, ss166208866, ss205390793, ss275745631, ss1584284941, ss1712316575 NC_000001.9:20850185:C:G NC_000001.11:20651105:C:G (self)
645173, 340308, 242382, 1418421, 147871, 451587, 137480, 180406, 382255, 101060, 805164, 340308, 73006, ss230454941, ss238164544, ss482765721, ss536080622, ss647627357, ss832615422, ss833206111, ss974926696, ss1067721387, ss1289959883, ss1425739061, ss1573929293, ss1599687833, ss1642681866, ss1918138476, ss1966701039, ss2019581057, ss2147584706, ss2322752462, ss2624306972, ss2697489346, ss2752444839, ss2986433726, ss3343358158, ss3626043746, ss3635987625, ss3637741807, ss3637741808, ss3646226190, ss3654504134, ss3726852615, ss3745917492, ss3825556461, ss3826060850, ss3836418624, ss3848365275, ss3893274193, ss3983921202, ss3983921203, ss3986009502, ss5142835857 NC_000001.10:20977598:C:G NC_000001.11:20651105:C:G (self)
RCV000261476.1, RCV000331316.1, RCV001098431.1, 4477806, 26646, 3192377, 5080015, 9534022663, ss2160570185, ss3023555858, ss3070418218, ss3686306172, ss3798937225, ss3841823078, ss4441473680 NC_000001.11:20651105:C:G NC_000001.11:20651105:C:G (self)
ss52082698 NT_004610.17:3801940:C:G NC_000001.11:20651105:C:G (self)
ss10009, ss24244349, ss99307725, ss102725846, ss104807890, ss152536349, ss159102626, ss168870813, ss168873463 NT_004610.19:7657686:C:G NC_000001.11:20651105:C: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 rs8064

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.post596+ae089ad