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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.

rs4413589

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:161655695 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.411202 (108841/264690, TOPMED)
G=0.425736 (59638/140082, GnomAD)
G=0.38151 (30024/78698, PAGE_STUDY) (+ 16 more)
G=0.22298 (6301/28258, 14KJPN)
G=0.42494 (8350/19650, ALFA)
G=0.22607 (3789/16760, 8.3KJPN)
G=0.3869 (2478/6404, 1000G_30x)
G=0.3846 (1926/5008, 1000G)
G=0.4350 (1949/4480, Estonian)
G=0.4006 (1544/3854, ALSPAC)
G=0.4002 (1484/3708, TWINSUK)
G=0.2683 (786/2930, KOREAN)
G=0.373 (372/998, GoNL)
G=0.412 (247/600, NorthernSweden)
A=0.352 (117/332, SGDP_PRJ)
G=0.384 (83/216, Qatari)
G=0.335 (71/212, Vietnamese)
G=0.38 (15/40, GENOME_DK)
A=0.44 (16/36, Siberian)
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 19650 A=0.57506 G=0.42494
European Sub 14364 A=0.58194 G=0.41806
African Sub 3380 A=0.4956 G=0.5044
African Others Sub 114 A=0.412 G=0.588
African American Sub 3266 A=0.4985 G=0.5015
Asian Sub 146 A=0.658 G=0.342
East Asian Sub 120 A=0.658 G=0.342
Other Asian Sub 26 A=0.65 G=0.35
Latin American 1 Sub 146 A=0.596 G=0.404
Latin American 2 Sub 610 A=0.782 G=0.218
South Asian Sub 104 A=0.712 G=0.288
Other Sub 900 A=0.591 G=0.409


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 A=0.588798 G=0.411202
gnomAD - Genomes Global Study-wide 140082 A=0.574264 G=0.425736
gnomAD - Genomes European Sub 75892 A=0.58689 G=0.41311
gnomAD - Genomes African Sub 41944 A=0.49106 G=0.50894
gnomAD - Genomes American Sub 13644 A=0.71966 G=0.28034
gnomAD - Genomes Ashkenazi Jewish Sub 3318 A=0.6224 G=0.3776
gnomAD - Genomes East Asian Sub 3130 A=0.6827 G=0.3173
gnomAD - Genomes Other Sub 2154 A=0.5970 G=0.4030
The PAGE Study Global Study-wide 78698 A=0.61849 G=0.38151
The PAGE Study AfricanAmerican Sub 32512 A=0.49336 G=0.50664
The PAGE Study Mexican Sub 10810 A=0.78372 G=0.21628
The PAGE Study Asian Sub 8318 A=0.7459 G=0.2541
The PAGE Study PuertoRican Sub 7918 A=0.6412 G=0.3588
The PAGE Study NativeHawaiian Sub 4534 A=0.7278 G=0.2722
The PAGE Study Cuban Sub 4230 A=0.6123 G=0.3877
The PAGE Study Dominican Sub 3828 A=0.5836 G=0.4164
The PAGE Study CentralAmerican Sub 2450 A=0.7518 G=0.2482
The PAGE Study SouthAmerican Sub 1982 A=0.7654 G=0.2346
The PAGE Study NativeAmerican Sub 1260 A=0.6563 G=0.3437
The PAGE Study SouthAsian Sub 856 A=0.667 G=0.333
14KJPN JAPANESE Study-wide 28258 A=0.77702 G=0.22298
Allele Frequency Aggregator Total Global 19650 A=0.57506 G=0.42494
Allele Frequency Aggregator European Sub 14364 A=0.58194 G=0.41806
Allele Frequency Aggregator African Sub 3380 A=0.4956 G=0.5044
Allele Frequency Aggregator Other Sub 900 A=0.591 G=0.409
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.782 G=0.218
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.596 G=0.404
Allele Frequency Aggregator Asian Sub 146 A=0.658 G=0.342
Allele Frequency Aggregator South Asian Sub 104 A=0.712 G=0.288
8.3KJPN JAPANESE Study-wide 16760 A=0.77393 G=0.22607
1000Genomes_30x Global Study-wide 6404 A=0.6131 G=0.3869
1000Genomes_30x African Sub 1786 A=0.4882 G=0.5118
1000Genomes_30x Europe Sub 1266 A=0.6169 G=0.3831
1000Genomes_30x South Asian Sub 1202 A=0.6389 G=0.3611
1000Genomes_30x East Asian Sub 1170 A=0.6735 G=0.3265
1000Genomes_30x American Sub 980 A=0.732 G=0.268
1000Genomes Global Study-wide 5008 A=0.6154 G=0.3846
1000Genomes African Sub 1322 A=0.4917 G=0.5083
1000Genomes East Asian Sub 1008 A=0.6736 G=0.3264
1000Genomes Europe Sub 1006 A=0.6153 G=0.3847
1000Genomes South Asian Sub 978 A=0.645 G=0.355
1000Genomes American Sub 694 A=0.725 G=0.275
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.5650 G=0.4350
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.5994 G=0.4006
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.5998 G=0.4002
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.7317 G=0.2683, T=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.627 G=0.373
Northern Sweden ACPOP Study-wide 600 A=0.588 G=0.412
SGDP_PRJ Global Study-wide 332 A=0.352 G=0.648
Qatari Global Study-wide 216 A=0.616 G=0.384
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.665 G=0.335
The Danish reference pan genome Danish Study-wide 40 A=0.62 G=0.38
Siberian Global Study-wide 36 A=0.44 G=0.56
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.161655695A>G
GRCh38.p14 chr 6 NC_000006.12:g.161655695A>T
GRCh37.p13 chr 6 NC_000006.11:g.162076727A>G
GRCh37.p13 chr 6 NC_000006.11:g.162076727A>T
PRKN RefSeqGene NG_008289.2:g.1077108T>C
PRKN RefSeqGene NG_008289.2:g.1077108T>A
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.872-86279T>C N/A Intron Variant
PRKN transcript variant 2 NM_013987.3:c.788-86279T>C N/A Intron Variant
PRKN transcript variant 3 NM_013988.3:c.425-86279T>C N/A Intron Variant
PRKN transcript variant X2 XM_011535863.2:c.869-8627…

XM_011535863.2:c.869-86279T>C

 		N/A Intron Variant
PRKN transcript variant X1 XM_017010908.2:c.986-8627…

XM_017010908.2:c.986-86279T>C

 		N/A Intron Variant
PRKN transcript variant X3 XM_024446449.2:c.635-8627…

XM_024446449.2:c.635-86279T>C

 		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 A= G T
GRCh38.p14 chr 6 NC_000006.12:g.161655695= NC_000006.12:g.161655695A>G NC_000006.12:g.161655695A>T
GRCh37.p13 chr 6 NC_000006.11:g.162076727= NC_000006.11:g.162076727A>G NC_000006.11:g.162076727A>T
PRKN RefSeqGene NG_008289.2:g.1077108= NG_008289.2:g.1077108T>C NG_008289.2:g.1077108T>A
PRKN transcript variant 1 NM_004562.2:c.872-86279= NM_004562.2:c.872-86279T>C NM_004562.2:c.872-86279T>A
PRKN transcript variant 1 NM_004562.3:c.872-86279= NM_004562.3:c.872-86279T>C NM_004562.3:c.872-86279T>A
PRKN transcript variant 2 NM_013987.2:c.788-86279= NM_013987.2:c.788-86279T>C NM_013987.2:c.788-86279T>A
PRKN transcript variant 2 NM_013987.3:c.788-86279= NM_013987.3:c.788-86279T>C NM_013987.3:c.788-86279T>A
PRKN transcript variant 3 NM_013988.2:c.425-86279= NM_013988.2:c.425-86279T>C NM_013988.2:c.425-86279T>A
PRKN transcript variant 3 NM_013988.3:c.425-86279= NM_013988.3:c.425-86279T>C NM_013988.3:c.425-86279T>A
PARK2 transcript variant X1 XM_005267004.1:c.928+60380= XM_005267004.1:c.928+60380T>C XM_005267004.1:c.928+60380T>A
PRKN transcript variant X2 XM_011535863.2:c.869-86279= XM_011535863.2:c.869-86279T>C XM_011535863.2:c.869-86279T>A
PRKN transcript variant X1 XM_017010908.2:c.986-86279= XM_017010908.2:c.986-86279T>C XM_017010908.2:c.986-86279T>A
PRKN transcript variant X3 XM_024446449.2:c.635-86279= XM_024446449.2:c.635-86279T>C XM_024446449.2:c.635-86279T>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#.

69 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss5904453 Feb 20, 2003 (111)
2 PERLEGEN ss24474827 Sep 20, 2004 (123)
3 ABI ss44761845 Mar 14, 2006 (126)
4 HGSV ss84826968 Dec 14, 2007 (130)
5 1000GENOMES ss111237632 Jan 25, 2009 (130)
6 1000GENOMES ss115419300 Jan 25, 2009 (130)
7 ILLUMINA-UK ss116801858 Feb 14, 2009 (130)
8 GMI ss157838171 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss165124463 Jul 04, 2010 (132)
10 COMPLETE_GENOMICS ss167454262 Jul 04, 2010 (132)
11 BCM-HGSC-SUB ss207476476 Jul 04, 2010 (132)
12 1000GENOMES ss222801285 Jul 14, 2010 (132)
13 1000GENOMES ss233772474 Jul 15, 2010 (132)
14 1000GENOMES ss240768653 Jul 15, 2010 (132)
15 GMI ss279109108 May 04, 2012 (137)
16 GMI ss285542469 Apr 25, 2013 (138)
17 TISHKOFF ss559675935 Apr 25, 2013 (138)
18 SSMP ss654019030 Apr 25, 2013 (138)
19 EVA-GONL ss983740817 Aug 21, 2014 (142)
20 1000GENOMES ss1323187146 Aug 21, 2014 (142)
21 DDI ss1430963081 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1581988707 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1617191027 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1660185060 Apr 01, 2015 (144)
25 HAMMER_LAB ss1804776833 Sep 08, 2015 (146)
26 WEILL_CORNELL_DGM ss1926982615 Feb 12, 2016 (147)
27 ILLUMINA ss1958970143 Feb 12, 2016 (147)
28 JJLAB ss2024158071 Sep 14, 2016 (149)
29 USC_VALOUEV ss2152351613 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2290280734 Dec 20, 2016 (150)
31 SYSTEMSBIOZJU ss2626569021 Nov 08, 2017 (151)
32 GRF ss2707991064 Nov 08, 2017 (151)
33 GNOMAD ss2847697949 Nov 08, 2017 (151)
34 AFFY ss2986022471 Nov 08, 2017 (151)
35 SWEGEN ss3000316025 Nov 08, 2017 (151)
36 ILLUMINA ss3022688720 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3025870316 Nov 08, 2017 (151)
38 CSHL ss3347334326 Nov 08, 2017 (151)
39 URBANLAB ss3648517713 Oct 12, 2018 (152)
40 ILLUMINA ss3653214520 Oct 12, 2018 (152)
41 EGCUT_WGS ss3668254704 Jul 13, 2019 (153)
42 EVA_DECODE ss3718727631 Jul 13, 2019 (153)
43 ILLUMINA ss3726404374 Jul 13, 2019 (153)
44 ACPOP ss3734184949 Jul 13, 2019 (153)
45 EVA ss3765952262 Jul 13, 2019 (153)
46 PAGE_CC ss3771338720 Jul 13, 2019 (153)
47 PACBIO ss3785681256 Jul 13, 2019 (153)
48 PACBIO ss3790998953 Jul 13, 2019 (153)
49 PACBIO ss3795878425 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3809116067 Jul 13, 2019 (153)
51 EVA ss3830310233 Apr 26, 2020 (154)
52 EVA ss3838639432 Apr 26, 2020 (154)
53 EVA ss3844089642 Apr 26, 2020 (154)
54 SGDP_PRJ ss3866193829 Apr 26, 2020 (154)
55 KRGDB ss3913186118 Apr 26, 2020 (154)
56 TOPMED ss4729614492 Apr 26, 2021 (155)
57 TOMMO_GENOMICS ss5180952860 Apr 26, 2021 (155)
58 1000G_HIGH_COVERAGE ss5271153770 Oct 14, 2022 (156)
59 EVA ss5370472110 Oct 14, 2022 (156)
60 HUGCELL_USP ss5468524889 Oct 14, 2022 (156)
61 1000G_HIGH_COVERAGE ss5558491849 Oct 14, 2022 (156)
62 SANFORD_IMAGENETICS ss5641953124 Oct 14, 2022 (156)
63 TOMMO_GENOMICS ss5720131461 Oct 14, 2022 (156)
64 YY_MCH ss5808156814 Oct 14, 2022 (156)
65 EVA ss5843304862 Oct 14, 2022 (156)
66 EVA ss5855678651 Oct 14, 2022 (156)
67 EVA ss5886881173 Oct 14, 2022 (156)
68 EVA ss5971029526 Oct 14, 2022 (156)
69 EVA ss5971029527 Oct 14, 2022 (156)
70 1000Genomes NC_000006.11 - 162076727 Oct 12, 2018 (152)
71 1000Genomes_30x NC_000006.12 - 161655695 Oct 14, 2022 (156)
72 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 162076727 Oct 12, 2018 (152)
73 Genetic variation in the Estonian population NC_000006.11 - 162076727 Oct 12, 2018 (152)
74 The Danish reference pan genome NC_000006.11 - 162076727 Apr 26, 2020 (154)
75 gnomAD - Genomes NC_000006.12 - 161655695 Apr 26, 2021 (155)
76 Genome of the Netherlands Release 5 NC_000006.11 - 162076727 Apr 26, 2020 (154)
77 KOREAN population from KRGDB NC_000006.11 - 162076727 Apr 26, 2020 (154)
78 Northern Sweden NC_000006.11 - 162076727 Jul 13, 2019 (153)
79 The PAGE Study NC_000006.12 - 161655695 Jul 13, 2019 (153)
80 Qatari NC_000006.11 - 162076727 Apr 26, 2020 (154)
81 SGDP_PRJ NC_000006.11 - 162076727 Apr 26, 2020 (154)
82 Siberian NC_000006.11 - 162076727 Apr 26, 2020 (154)
83 8.3KJPN NC_000006.11 - 162076727 Apr 26, 2021 (155)
84 14KJPN NC_000006.12 - 161655695 Oct 14, 2022 (156)
85 TopMed NC_000006.12 - 161655695 Apr 26, 2021 (155)
86 UK 10K study - Twins NC_000006.11 - 162076727 Oct 12, 2018 (152)
87 A Vietnamese Genetic Variation Database NC_000006.11 - 162076727 Jul 13, 2019 (153)
88 ALFA NC_000006.12 - 161655695 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)
rs17576195 Oct 08, 2004 (123)
rs57026606 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84826968 NC_000006.9:162047137:A:G NC_000006.12:161655694:A:G (self)
ss111237632, ss115419300, ss116801858, ss165124463, ss167454262, ss207476476, ss279109108, ss285542469 NC_000006.10:161996716:A:G NC_000006.12:161655694:A:G (self)
35090882, 19571478, 13992952, 8153646, 8709809, 20363512, 7469814, 9024545, 18210809, 4867967, 38922167, 19571478, 4355021, ss222801285, ss233772474, ss240768653, ss559675935, ss654019030, ss983740817, ss1323187146, ss1430963081, ss1581988707, ss1617191027, ss1660185060, ss1804776833, ss1926982615, ss1958970143, ss2024158071, ss2152351613, ss2626569021, ss2707991064, ss2847697949, ss2986022471, ss3000316025, ss3022688720, ss3347334326, ss3653214520, ss3668254704, ss3734184949, ss3765952262, ss3785681256, ss3790998953, ss3795878425, ss3830310233, ss3838639432, ss3866193829, ss3913186118, ss5180952860, ss5370472110, ss5641953124, ss5843304862, ss5971029526, ss5971029527 NC_000006.11:162076726:A:G NC_000006.12:161655694:A:G (self)
46017784, 247686491, 560189, 53968565, 566992050, 3532693008, ss2290280734, ss3025870316, ss3648517713, ss3718727631, ss3726404374, ss3771338720, ss3809116067, ss3844089642, ss4729614492, ss5271153770, ss5468524889, ss5558491849, ss5720131461, ss5808156814, ss5855678651, ss5886881173 NC_000006.12:161655694:A:G NC_000006.12:161655694:A:G (self)
ss5904453, ss24474827, ss44761845, ss157838171 NT_025741.15:66246183:A:G NC_000006.12:161655694:A:G (self)
20363512, ss3913186118 NC_000006.11:162076726:A:T NC_000006.12:161655694:A:T (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 rs4413589

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