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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.

rs4709533

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:161506736 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.210034 (55594/264690, TOPMED)
G=0.199380 (27908/139974, GnomAD)
G=0.23335 (6594/28258, 14KJPN) (+ 17 more)
G=0.21120 (5421/25668, ALFA)
G=0.22989 (3853/16760, 8.3KJPN)
G=0.2406 (1541/6404, 1000G_30x)
G=0.2372 (1188/5008, 1000G)
G=0.2071 (928/4480, Estonian)
G=0.2032 (783/3854, ALSPAC)
G=0.1828 (678/3708, TWINSUK)
G=0.2923 (856/2928, KOREAN)
G=0.1770 (331/1870, HapMap)
G=0.2757 (505/1832, Korea1K)
G=0.196 (196/998, GoNL)
G=0.233 (140/600, NorthernSweden)
G=0.176 (92/522, SGDP_PRJ)
G=0.134 (29/216, Qatari)
G=0.319 (67/210, Vietnamese)
G=0.27 (14/52, Siberian)
G=0.20 (8/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRKN : 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 25668 G=0.21120 A=0.78880
European Sub 17388 G=0.19744 A=0.80256
African Sub 3620 G=0.1677 A=0.8323
African Others Sub 126 G=0.167 A=0.833
African American Sub 3494 G=0.1677 A=0.8323
Asian Sub 158 G=0.348 A=0.652
East Asian Sub 100 G=0.34 A=0.66
Other Asian Sub 58 G=0.36 A=0.64
Latin American 1 Sub 292 G=0.171 A=0.829
Latin American 2 Sub 2758 G=0.3405 A=0.6595
South Asian Sub 110 G=0.200 A=0.800
Other Sub 1342 G=0.2347 A=0.7653


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=0.210034 A=0.789966
gnomAD - Genomes Global Study-wide 139974 G=0.199380 A=0.800620
gnomAD - Genomes European Sub 75836 G=0.19566 A=0.80434
gnomAD - Genomes African Sub 41926 G=0.16985 A=0.83015
gnomAD - Genomes American Sub 13614 G=0.31504 A=0.68496
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.0632 A=0.9368
gnomAD - Genomes East Asian Sub 3122 G=0.3174 A=0.6826
gnomAD - Genomes Other Sub 2154 G=0.2131 A=0.7869
14KJPN JAPANESE Study-wide 28258 G=0.23335 A=0.76665
Allele Frequency Aggregator Total Global 25668 G=0.21120 A=0.78880
Allele Frequency Aggregator European Sub 17388 G=0.19744 A=0.80256
Allele Frequency Aggregator African Sub 3620 G=0.1677 A=0.8323
Allele Frequency Aggregator Latin American 2 Sub 2758 G=0.3405 A=0.6595
Allele Frequency Aggregator Other Sub 1342 G=0.2347 A=0.7653
Allele Frequency Aggregator Latin American 1 Sub 292 G=0.171 A=0.829
Allele Frequency Aggregator Asian Sub 158 G=0.348 A=0.652
Allele Frequency Aggregator South Asian Sub 110 G=0.200 A=0.800
8.3KJPN JAPANESE Study-wide 16760 G=0.22989 A=0.77011
1000Genomes_30x Global Study-wide 6404 G=0.2406 A=0.7594
1000Genomes_30x African Sub 1786 G=0.1719 A=0.8281
1000Genomes_30x Europe Sub 1266 G=0.1959 A=0.8041
1000Genomes_30x South Asian Sub 1202 G=0.2496 A=0.7504
1000Genomes_30x East Asian Sub 1170 G=0.3316 A=0.6684
1000Genomes_30x American Sub 980 G=0.304 A=0.696
1000Genomes Global Study-wide 5008 G=0.2372 A=0.7628
1000Genomes African Sub 1322 G=0.1672 A=0.8328
1000Genomes East Asian Sub 1008 G=0.3264 A=0.6736
1000Genomes Europe Sub 1006 G=0.1948 A=0.8052
1000Genomes South Asian Sub 978 G=0.237 A=0.763
1000Genomes American Sub 694 G=0.303 A=0.697
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.2071 A=0.7929
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.2032 A=0.7968
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.1828 A=0.8172
KOREAN population from KRGDB KOREAN Study-wide 2928 G=0.2923 A=0.7077, C=0.0000
HapMap Global Study-wide 1870 G=0.1770 A=0.8230
HapMap American Sub 758 G=0.220 A=0.780
HapMap African Sub 690 G=0.122 A=0.878
HapMap Asian Sub 248 G=0.210 A=0.790
HapMap Europe Sub 174 G=0.161 A=0.839
Korean Genome Project KOREAN Study-wide 1832 G=0.2757 A=0.7243
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.196 A=0.804
Northern Sweden ACPOP Study-wide 600 G=0.233 A=0.767
SGDP_PRJ Global Study-wide 522 G=0.176 A=0.824
Qatari Global Study-wide 216 G=0.134 A=0.866
A Vietnamese Genetic Variation Database Global Study-wide 210 G=0.319 A=0.681
Siberian Global Study-wide 52 G=0.27 A=0.73
The Danish reference pan genome Danish Study-wide 40 G=0.20 A=0.80
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 6 NC_000006.12:g.161506736G>A
GRCh38.p14 chr 6 NC_000006.12:g.161506736G>C
GRCh37.p13 chr 6 NC_000006.11:g.161927768G>A
GRCh37.p13 chr 6 NC_000006.11:g.161927768G>C
PRKN RefSeqGene NG_008289.2:g.1226067C>T
PRKN RefSeqGene NG_008289.2:g.1226067C>G
Gene: PRKN, parkin RBR E3 ubiquitin protein ligase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRKN transcript variant 1 NM_004562.3:c.1083+42118C…

NM_004562.3:c.1083+42118C>T

N/A Intron Variant
PRKN transcript variant 2 NM_013987.3:c.999+42118C>T N/A Intron Variant
PRKN transcript variant 3 NM_013988.3:c.636+42118C>T N/A Intron Variant
PRKN transcript variant X2 XM_011535863.2:c.1080+421…

XM_011535863.2:c.1080+42118C>T

N/A Intron Variant
PRKN transcript variant X1 XM_017010908.2:c.1197+421…

XM_017010908.2:c.1197+42118C>T

N/A Intron Variant
PRKN transcript variant X3 XM_024446449.2:c.846+4211…

XM_024446449.2:c.846+42118C>T

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 C
GRCh38.p14 chr 6 NC_000006.12:g.161506736= NC_000006.12:g.161506736G>A NC_000006.12:g.161506736G>C
GRCh37.p13 chr 6 NC_000006.11:g.161927768= NC_000006.11:g.161927768G>A NC_000006.11:g.161927768G>C
PRKN RefSeqGene NG_008289.2:g.1226067= NG_008289.2:g.1226067C>T NG_008289.2:g.1226067C>G
PRKN transcript variant 1 NM_004562.2:c.1083+42118= NM_004562.2:c.1083+42118C>T NM_004562.2:c.1083+42118C>G
PRKN transcript variant 1 NM_004562.3:c.1083+42118= NM_004562.3:c.1083+42118C>T NM_004562.3:c.1083+42118C>G
PRKN transcript variant 2 NM_013987.2:c.999+42118= NM_013987.2:c.999+42118C>T NM_013987.2:c.999+42118C>G
PRKN transcript variant 2 NM_013987.3:c.999+42118= NM_013987.3:c.999+42118C>T NM_013987.3:c.999+42118C>G
PRKN transcript variant 3 NM_013988.2:c.636+42118= NM_013988.2:c.636+42118C>T NM_013988.2:c.636+42118C>G
PRKN transcript variant 3 NM_013988.3:c.636+42118= NM_013988.3:c.636+42118C>T NM_013988.3:c.636+42118C>G
PRKN transcript variant X2 XM_011535863.2:c.1080+42118= XM_011535863.2:c.1080+42118C>T XM_011535863.2:c.1080+42118C>G
PRKN transcript variant X1 XM_017010908.2:c.1197+42118= XM_017010908.2:c.1197+42118C>T XM_017010908.2:c.1197+42118C>G
PRKN transcript variant X3 XM_024446449.2:c.846+42118= XM_024446449.2:c.846+42118C>T XM_024446449.2:c.846+42118C>G
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#.

85 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6489154 Feb 20, 2003 (111)
2 SC_SNP ss13075378 Dec 05, 2003 (119)
3 SSAHASNP ss22371547 Apr 05, 2004 (121)
4 ABI ss44714066 Mar 15, 2006 (126)
5 AFFY ss66208274 Dec 02, 2006 (127)
6 AFFY ss76303339 Dec 07, 2007 (129)
7 KRIBB_YJKIM ss82097422 Dec 17, 2007 (131)
8 HGSV ss83118711 Dec 14, 2007 (130)
9 HGSV ss85591849 Dec 14, 2007 (130)
10 BCMHGSC_JDW ss93595671 Mar 24, 2008 (129)
11 HUMANGENOME_JCVI ss98443974 Feb 04, 2009 (130)
12 BGI ss104380870 Dec 01, 2009 (131)
13 1000GENOMES ss111235236 Jan 25, 2009 (130)
14 1000GENOMES ss115417207 Jan 25, 2009 (130)
15 ILLUMINA-UK ss116801241 Feb 14, 2009 (130)
16 ENSEMBL ss133889292 Dec 01, 2009 (131)
17 ENSEMBL ss142475487 Dec 01, 2009 (131)
18 GMI ss157836285 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss162966164 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss165120593 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss167453081 Jul 04, 2010 (132)
22 AFFY ss173190835 Jul 04, 2010 (132)
23 BUSHMAN ss202695521 Jul 04, 2010 (132)
24 BCM-HGSC-SUB ss207368640 Jul 04, 2010 (132)
25 1000GENOMES ss222800448 Jul 14, 2010 (132)
26 1000GENOMES ss233771989 Jul 15, 2010 (132)
27 1000GENOMES ss240768232 Jul 15, 2010 (132)
28 BL ss254789683 May 09, 2011 (134)
29 GMI ss279108676 May 04, 2012 (137)
30 GMI ss285542241 Apr 25, 2013 (138)
31 PJP ss293777269 May 09, 2011 (134)
32 TISHKOFF ss559674943 Apr 25, 2013 (138)
33 SSMP ss654018198 Apr 25, 2013 (138)
34 EVA-GONL ss983739533 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1074214843 Aug 21, 2014 (142)
36 1000GENOMES ss1323182438 Aug 21, 2014 (142)
37 DDI ss1430962649 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1581988143 Apr 01, 2015 (144)
39 EVA_DECODE ss1593315947 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1617188384 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1660182417 Apr 01, 2015 (144)
42 EVA_SVP ss1712917672 Apr 01, 2015 (144)
43 HAMMER_LAB ss1804776199 Sep 08, 2015 (146)
44 WEILL_CORNELL_DGM ss1926981393 Feb 12, 2016 (147)
45 GENOMED ss1970577963 Jul 19, 2016 (147)
46 JJLAB ss2024157345 Sep 14, 2016 (149)
47 USC_VALOUEV ss2152350849 Dec 20, 2016 (150)
48 HUMAN_LONGEVITY ss2290271306 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2626568722 Nov 08, 2017 (151)
50 GRF ss2707990264 Nov 08, 2017 (151)
51 GNOMAD ss2847685529 Nov 08, 2017 (151)
52 SWEGEN ss3000314103 Nov 08, 2017 (151)
53 BIOINF_KMB_FNS_UNIBA ss3025869893 Nov 08, 2017 (151)
54 CSHL ss3347333689 Nov 08, 2017 (151)
55 URBANLAB ss3648517311 Oct 12, 2018 (152)
56 EGCUT_WGS ss3668252651 Jul 13, 2019 (153)
57 EVA_DECODE ss3718725317 Jul 13, 2019 (153)
58 ACPOP ss3734183828 Jul 13, 2019 (153)
59 EVA ss3765950662 Jul 13, 2019 (153)
60 PACBIO ss3785680803 Jul 13, 2019 (153)
61 PACBIO ss3790998537 Jul 13, 2019 (153)
62 PACBIO ss3795878009 Jul 13, 2019 (153)
63 KHV_HUMAN_GENOMES ss3809114431 Jul 13, 2019 (153)
64 EVA ss3830309594 Apr 26, 2020 (154)
65 EVA ss3838639077 Apr 26, 2020 (154)
66 EVA ss3844089276 Apr 26, 2020 (154)
67 SGDP_PRJ ss3866191132 Apr 26, 2020 (154)
68 KRGDB ss3913183486 Apr 26, 2020 (154)
69 KOGIC ss3960512873 Apr 26, 2020 (154)
70 TOPMED ss4729577965 Apr 26, 2021 (155)
71 TOMMO_GENOMICS ss5180947791 Apr 26, 2021 (155)
72 1000G_HIGH_COVERAGE ss5271149610 Oct 13, 2022 (156)
73 EVA ss5370464450 Oct 13, 2022 (156)
74 HUGCELL_USP ss5468521123 Oct 13, 2022 (156)
75 EVA ss5508787679 Oct 13, 2022 (156)
76 1000G_HIGH_COVERAGE ss5558485862 Oct 13, 2022 (156)
77 SANFORD_IMAGENETICS ss5641950701 Oct 13, 2022 (156)
78 TOMMO_GENOMICS ss5720124956 Oct 13, 2022 (156)
79 YY_MCH ss5808155738 Oct 13, 2022 (156)
80 EVA ss5843303095 Oct 13, 2022 (156)
81 EVA ss5855678096 Oct 13, 2022 (156)
82 EVA ss5886876550 Oct 13, 2022 (156)
83 EVA ss5971024916 Oct 13, 2022 (156)
84 EVA ss5971024917 Oct 13, 2022 (156)
85 EVA ss5980404842 Oct 13, 2022 (156)
86 1000Genomes NC_000006.11 - 161927768 Oct 12, 2018 (152)
87 1000Genomes_30x NC_000006.12 - 161506736 Oct 13, 2022 (156)
88 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 161927768 Oct 12, 2018 (152)
89 Genetic variation in the Estonian population NC_000006.11 - 161927768 Oct 12, 2018 (152)
90 The Danish reference pan genome NC_000006.11 - 161927768 Apr 26, 2020 (154)
91 gnomAD - Genomes NC_000006.12 - 161506736 Apr 26, 2021 (155)
92 Genome of the Netherlands Release 5 NC_000006.11 - 161927768 Apr 26, 2020 (154)
93 HapMap NC_000006.12 - 161506736 Apr 26, 2020 (154)
94 KOREAN population from KRGDB NC_000006.11 - 161927768 Apr 26, 2020 (154)
95 Korean Genome Project NC_000006.12 - 161506736 Apr 26, 2020 (154)
96 Northern Sweden NC_000006.11 - 161927768 Jul 13, 2019 (153)
97 Qatari NC_000006.11 - 161927768 Apr 26, 2020 (154)
98 SGDP_PRJ NC_000006.11 - 161927768 Apr 26, 2020 (154)
99 Siberian NC_000006.11 - 161927768 Apr 26, 2020 (154)
100 8.3KJPN NC_000006.11 - 161927768 Apr 26, 2021 (155)
101 14KJPN NC_000006.12 - 161506736 Oct 13, 2022 (156)
102 TopMed NC_000006.12 - 161506736 Apr 26, 2021 (155)
103 UK 10K study - Twins NC_000006.11 - 161927768 Oct 12, 2018 (152)
104 A Vietnamese Genetic Variation Database NC_000006.11 - 161927768 Jul 13, 2019 (153)
105 ALFA NC_000006.12 - 161506736 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)
rs58056593 May 24, 2008 (130)
rs61715191 Dec 02, 2009 (131)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83118711, ss85591849 NC_000006.9:161898178:G:A NC_000006.12:161506735:G:A (self)
ss66208274, ss76303339, ss93595671, ss111235236, ss115417207, ss116801241, ss162966164, ss165120593, ss167453081, ss173190835, ss202695521, ss207368640, ss254789683, ss279108676, ss285542241, ss293777269, ss1593315947, ss1712917672 NC_000006.10:161847757:G:A NC_000006.12:161506735:G:A (self)
35086037, 19568609, 13990899, 8153082, 8708545, 20360880, 7468693, 9023323, 18208112, 4867203, 38917098, 19568609, 4354376, ss222800448, ss233771989, ss240768232, ss559674943, ss654018198, ss983739533, ss1074214843, ss1323182438, ss1430962649, ss1581988143, ss1617188384, ss1660182417, ss1804776199, ss1926981393, ss1970577963, ss2024157345, ss2152350849, ss2626568722, ss2707990264, ss2847685529, ss3000314103, ss3347333689, ss3668252651, ss3734183828, ss3765950662, ss3785680803, ss3790998537, ss3795878009, ss3830309594, ss3838639077, ss3866191132, ss3913183486, ss5180947791, ss5370464450, ss5508787679, ss5641950701, ss5843303095, ss5971024916, ss5971024917, ss5980404842 NC_000006.11:161927767:G:A NC_000006.12:161506735:G:A (self)
46011797, 247655322, 3299489, 16890874, 53962060, 566955523, 869886547, ss2290271306, ss3025869893, ss3648517311, ss3718725317, ss3809114431, ss3844089276, ss3960512873, ss4729577965, ss5271149610, ss5468521123, ss5558485862, ss5720124956, ss5808155738, ss5855678096, ss5886876550 NC_000006.12:161506735:G:A NC_000006.12:161506735:G:A (self)
ss13075378, ss22371547 NT_007422.12:4215108:G:A NC_000006.12:161506735:G:A (self)
ss6489154, ss44714066, ss82097422, ss98443974, ss104380870, ss133889292, ss142475487, ss157836285 NT_025741.15:66097224:G:A NC_000006.12:161506735:G:A (self)
20360880, ss3913183486 NC_000006.11:161927767:G:C NC_000006.12:161506735:G:C (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 rs4709533

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