Name: rs9364650
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.

rs9364650

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:162307224 (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>C / A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.090083 (23844/264690, TOPMED)
C=0.075820 (10611/139950, GnomAD)
A=0.49788 (14068/28256, 14KJPN) (+ 15 more)
A=0.49845 (8353/16758, 8.3KJPN)
C=0.06981 (1166/16702, ALFA)
C=0.1766 (1131/6404, 1000G_30x)
C=0.1845 (924/5008, 1000G)
C=0.0743 (333/4480, Estonian)
C=0.0607 (234/3854, ALSPAC)
C=0.0456 (169/3708, TWINSUK)
C=0.4669 (1368/2930, KOREAN)
C=0.4711 (863/1832, Korea1K)
C=0.036 (36/998, GoNL)
C=0.107 (64/598, NorthernSweden)
C=0.069 (15/216, Qatari)
A=0.471 (99/210, Vietnamese)
A=0.385 (77/200, SGDP_PRJ)
A=0.45 (9/20, 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	16702	A=0.93019	C=0.06981
European	Sub	12214	A=0.93860	C=0.06140
African	Sub	2864	A=0.9455	C=0.0545
African Others	Sub	108	A=0.963	C=0.037
African American	Sub	2756	A=0.9448	C=0.0552
Asian	Sub	108	A=0.528	C=0.472
East Asian	Sub	84	A=0.49	C=0.51
Other Asian	Sub	24	A=0.67	C=0.33
Latin American 1	Sub	146	A=0.911	C=0.089
Latin American 2	Sub	610	A=0.805	C=0.195
South Asian	Sub	94	A=0.85	C=0.15
Other	Sub	666	A=0.905	C=0.095

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
TopMed	Global	Study-wide	264690	A=0.909917	C=0.090083
gnomAD - Genomes	Global	Study-wide	139950	A=0.924180	C=0.075820
gnomAD - Genomes	European	Sub	75820	A=0.94111	C=0.05889
gnomAD - Genomes	African	Sub	41944	A=0.94500	C=0.05500
gnomAD - Genomes	American	Sub	13616	A=0.86714	C=0.13286
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.9401	C=0.0599
gnomAD - Genomes	East Asian	Sub	3096	A=0.4842	C=0.5158
gnomAD - Genomes	Other	Sub	2150	A=0.8912	C=0.1088
14KJPN	JAPANESE	Study-wide	28256	A=0.49788	C=0.50212
8.3KJPN	JAPANESE	Study-wide	16758	A=0.49845	C=0.50155
Allele Frequency Aggregator	Total	Global	16702	A=0.93019	C=0.06981
Allele Frequency Aggregator	European	Sub	12214	A=0.93860	C=0.06140
Allele Frequency Aggregator	African	Sub	2864	A=0.9455	C=0.0545
Allele Frequency Aggregator	Other	Sub	666	A=0.905	C=0.095
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.805	C=0.195
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.911	C=0.089
Allele Frequency Aggregator	Asian	Sub	108	A=0.528	C=0.472
Allele Frequency Aggregator	South Asian	Sub	94	A=0.85	C=0.15
1000Genomes_30x	Global	Study-wide	6404	A=0.8234	C=0.1766
1000Genomes_30x	African	Sub	1786	A=0.9602	C=0.0398
1000Genomes_30x	Europe	Sub	1266	A=0.9281	C=0.0719
1000Genomes_30x	South Asian	Sub	1202	A=0.8028	C=0.1972
1000Genomes_30x	East Asian	Sub	1170	A=0.5060	C=0.4940
1000Genomes_30x	American	Sub	980	A=0.843	C=0.157
1000Genomes	Global	Study-wide	5008	A=0.8155	C=0.1845
1000Genomes	African	Sub	1322	A=0.9569	C=0.0431
1000Genomes	East Asian	Sub	1008	A=0.5149	C=0.4851
1000Genomes	Europe	Sub	1006	A=0.9254	C=0.0746
1000Genomes	South Asian	Sub	978	A=0.806	C=0.194
1000Genomes	American	Sub	694	A=0.837	C=0.163
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9257	C=0.0743
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9393	C=0.0607
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9544	C=0.0456
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.5331	C=0.4669, G=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	A=0.5289	C=0.4711
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.964	C=0.036
Northern Sweden	ACPOP	Study-wide	598	A=0.893	C=0.107
Qatari	Global	Study-wide	216	A=0.931	C=0.069
A Vietnamese Genetic Variation Database	Global	Study-wide	210	A=0.471	C=0.529
SGDP_PRJ	Global	Study-wide	200	A=0.385	C=0.615
Siberian	Global	Study-wide	20	A=0.45	C=0.55

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.162307224A>C
GRCh38.p14 chr 6	NC_000006.12:g.162307224A>G
GRCh37.p13 chr 6	NC_000006.11:g.162728256A>C
GRCh37.p13 chr 6	NC_000006.11:g.162728256A>G
PRKN RefSeqGene	NG_008289.2:g.425579T>G
PRKN RefSeqGene	NG_008289.2:g.425579T>C

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.172-44459T>G	N/A	Intron Variant
PRKN transcript variant 2	NM_013987.3:c.172-44459T>G	N/A	Intron Variant
PRKN transcript variant 3	NM_013988.3:c.171+136086T… NM_013988.3:c.171+136086T>G	N/A	Intron Variant
PRKN transcript variant X2	XM_011535863.2:c.172-4445… XM_011535863.2:c.172-44459T>G	N/A	Intron Variant
PRKN transcript variant X1	XM_017010908.2:c.286-4445… XM_017010908.2:c.286-44459T>G	N/A	Intron Variant
PRKN transcript variant X3	XM_024446449.2:c.-66-4445… XM_024446449.2:c.-66-44459T>G	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	A=	C	G
GRCh38.p14 chr 6	NC_000006.12:g.162307224=	NC_000006.12:g.162307224A>C	NC_000006.12:g.162307224A>G
GRCh37.p13 chr 6	NC_000006.11:g.162728256=	NC_000006.11:g.162728256A>C	NC_000006.11:g.162728256A>G
PRKN RefSeqGene	NG_008289.2:g.425579=	NG_008289.2:g.425579T>G	NG_008289.2:g.425579T>C
PRKN transcript variant 1	NM_004562.2:c.172-44459=	NM_004562.2:c.172-44459T>G	NM_004562.2:c.172-44459T>C
PRKN transcript variant 1	NM_004562.3:c.172-44459=	NM_004562.3:c.172-44459T>G	NM_004562.3:c.172-44459T>C
PRKN transcript variant 2	NM_013987.2:c.172-44459=	NM_013987.2:c.172-44459T>G	NM_013987.2:c.172-44459T>C
PRKN transcript variant 2	NM_013987.3:c.172-44459=	NM_013987.3:c.172-44459T>G	NM_013987.3:c.172-44459T>C
PRKN transcript variant 3	NM_013988.2:c.171+136086=	NM_013988.2:c.171+136086T>G	NM_013988.2:c.171+136086T>C
PRKN transcript variant 3	NM_013988.3:c.171+136086=	NM_013988.3:c.171+136086T>G	NM_013988.3:c.171+136086T>C
PARK2 transcript variant X1	XM_005267004.1:c.172-44459=	XM_005267004.1:c.172-44459T>G	XM_005267004.1:c.172-44459T>C
PRKN transcript variant X2	XM_011535863.2:c.172-44459=	XM_011535863.2:c.172-44459T>G	XM_011535863.2:c.172-44459T>C
PRKN transcript variant X1	XM_017010908.2:c.286-44459=	XM_017010908.2:c.286-44459T>G	XM_017010908.2:c.286-44459T>C
PRKN transcript variant X3	XM_024446449.2:c.-66-44459=	XM_024446449.2:c.-66-44459T>G	XM_024446449.2:c.-66-44459T>C

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#.

44 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss12829156	Dec 05, 2003 (119)
2	HGSV	ss86018999	Dec 16, 2007 (130)
3	BGI	ss104381581	Dec 01, 2009 (131)
4	GMI	ss279111335	May 04, 2012 (137)
5	1000GENOMES	ss333791757	May 09, 2011 (134)
6	SSMP	ss654022592	Apr 25, 2013 (138)
7	EVA-GONL	ss983746528	Aug 21, 2014 (142)
8	JMKIDD_LAB	ss1074220568	Aug 21, 2014 (142)
9	1000GENOMES	ss1323208190	Aug 21, 2014 (142)
10	EVA_DECODE	ss1593322842	Apr 01, 2015 (144)
11	EVA_UK10K_ALSPAC	ss1617202434	Apr 01, 2015 (144)
12	EVA_UK10K_TWINSUK	ss1660196467	Apr 01, 2015 (144)
13	WEILL_CORNELL_DGM	ss1926988265	Feb 12, 2016 (147)
14	JJLAB	ss2024160963	Sep 14, 2016 (149)
15	USC_VALOUEV	ss2152354881	Dec 20, 2016 (150)
16	HUMAN_LONGEVITY	ss2290323649	Dec 20, 2016 (150)
17	SYSTEMSBIOZJU	ss2626570579	Nov 08, 2017 (151)
18	GRF	ss2707994565	Nov 08, 2017 (151)
19	GNOMAD	ss2847754266	Nov 08, 2017 (151)
20	SWEGEN	ss3000324359	Nov 08, 2017 (151)
21	CSHL	ss3347336956	Nov 08, 2017 (151)
22	EGCUT_WGS	ss3668263574	Jul 13, 2019 (153)
23	EVA_DECODE	ss3718738712	Jul 13, 2019 (153)
24	ACPOP	ss3734189678	Jul 13, 2019 (153)
25	EVA	ss3765958859	Jul 13, 2019 (153)
26	KHV_HUMAN_GENOMES	ss3809122912	Jul 13, 2019 (153)
27	EVA	ss3830313426	Apr 26, 2020 (154)
28	SGDP_PRJ	ss3866205716	Apr 26, 2020 (154)
29	KRGDB	ss3913197786	Apr 26, 2020 (154)
30	KOGIC	ss3960525164	Apr 26, 2020 (154)
31	TOPMED	ss4729778953	Apr 26, 2021 (155)
32	TOMMO_GENOMICS	ss5180975703	Apr 26, 2021 (155)
33	1000G_HIGH_COVERAGE	ss5271172453	Oct 14, 2022 (156)
34	EVA	ss5370506362	Oct 14, 2022 (156)
35	HUGCELL_USP	ss5468542199	Oct 14, 2022 (156)
36	1000G_HIGH_COVERAGE	ss5558519599	Oct 14, 2022 (156)
37	SANFORD_IMAGENETICS	ss5641964124	Oct 14, 2022 (156)
38	TOMMO_GENOMICS	ss5720160882	Oct 14, 2022 (156)
39	YY_MCH	ss5808161278	Oct 14, 2022 (156)
40	EVA	ss5843312180	Oct 14, 2022 (156)
41	EVA	ss5855681114	Oct 14, 2022 (156)
42	EVA	ss5886902449	Oct 14, 2022 (156)
43	EVA	ss5971050172	Oct 14, 2022 (156)
44	EVA	ss5971050173	Oct 14, 2022 (156)
45	1000Genomes	NC_000006.11 - 162728256	Oct 12, 2018 (152)
46	1000Genomes_30x	NC_000006.12 - 162307224	Oct 14, 2022 (156)
47	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 162728256	Oct 12, 2018 (152)
48	Genetic variation in the Estonian population	NC_000006.11 - 162728256	Oct 12, 2018 (152)
49	gnomAD - Genomes	NC_000006.12 - 162307224	Apr 26, 2021 (155)
50	Genome of the Netherlands Release 5	NC_000006.11 - 162728256	Apr 26, 2020 (154)
51	KOREAN population from KRGDB	NC_000006.11 - 162728256	Apr 26, 2020 (154)
52	Korean Genome Project	NC_000006.12 - 162307224	Apr 26, 2020 (154)
53	Northern Sweden	NC_000006.11 - 162728256	Jul 13, 2019 (153)
54	Qatari	NC_000006.11 - 162728256	Apr 26, 2020 (154)
55	SGDP_PRJ	NC_000006.11 - 162728256	Apr 26, 2020 (154)
56	Siberian	NC_000006.11 - 162728256	Apr 26, 2020 (154)
57	8.3KJPN	NC_000006.11 - 162728256	Apr 26, 2021 (155)
58	14KJPN	NC_000006.12 - 162307224	Oct 14, 2022 (156)
59	TopMed	NC_000006.12 - 162307224	Apr 26, 2021 (155)
60	UK 10K study - Twins	NC_000006.11 - 162728256	Oct 12, 2018 (152)
61	A Vietnamese Genetic Variation Database	NC_000006.11 - 162728256	Jul 13, 2019 (153)
62	ALFA	NC_000006.12 - 162307224	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).

Associated ID	History Updated (Build)
rs61649273	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss86018999	NC_000006.9:162698666:A:C	NC_000006.12:162307223:A:C	(self)
ss279111335, ss1593322842	NC_000006.10:162648245:A:C	NC_000006.12:162307223:A:C	(self)
35112716, 19583914, 14001822, 8715351, 20375180, 7474543, 9030195, 18222696, 4871235, 38945010, 19583914, 4357761, ss333791757, ss654022592, ss983746528, ss1074220568, ss1323208190, ss1617202434, ss1660196467, ss1926988265, ss2024160963, ss2152354881, ss2626570579, ss2707994565, ss2847754266, ss3000324359, ss3347336956, ss3668263574, ss3734189678, ss3765958859, ss3830313426, ss3866205716, ss3913197786, ss5180975703, ss5370506362, ss5641964124, ss5843312180, ss5971050172, ss5971050173	NC_000006.11:162728255:A:C	NC_000006.12:162307223:A:C	(self)
46045534, 247830171, 16903165, 53997986, 567156511, 11659391574, ss2290323649, ss3718738712, ss3809122912, ss3960525164, ss4729778953, ss5271172453, ss5468542199, ss5558519599, ss5720160882, ss5808161278, ss5855681114, ss5886902449	NC_000006.12:162307223:A:C	NC_000006.12:162307223:A:C	(self)
ss12829156	NT_007422.12:5015596:A:C	NC_000006.12:162307223:A:C	(self)
ss104381581	NT_025741.15:66897712:A:C	NC_000006.12:162307223:A:C	(self)
20375180, ss3913197786	NC_000006.11:162728255:A:G	NC_000006.12:162307223:A:G	(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 rs9364650

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

rs9364650