Name: rs58881863
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.

rs58881863

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:162988754 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.059307 (15698/264690, TOPMED)
C=0.055717 (7809/140154, GnomAD)
C=0.02597 (734/28258, 14KJPN) (+ 14 more)
C=0.02986 (564/18890, ALFA)
C=0.02542 (426/16760, 8.3KJPN)
C=0.0632 (405/6404, 1000G_30x)
C=0.0615 (308/5008, 1000G)
C=0.0011 (5/4480, Estonian)
C=0.0023 (9/3854, ALSPAC)
C=0.0024 (9/3708, TWINSUK)
C=0.0082 (24/2922, KOREAN)
C=0.0115 (21/1832, Korea1K)
C=0.004 (4/998, GoNL)
C=0.002 (1/600, NorthernSweden)
C=0.056 (12/216, Qatari)
T=0.50 (17/34, SGDP_PRJ)
C=0.50 (17/34, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PACRG : 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	18890	T=0.97014	C=0.02986
European	Sub	14286	T=0.99790	C=0.00210
African	Sub	2946	T=0.8367	C=0.1633
African Others	Sub	114	T=0.851	C=0.149
African American	Sub	2832	T=0.8362	C=0.1638
Asian	Sub	112	T=0.991	C=0.009
East Asian	Sub	86	T=0.99	C=0.01
Other Asian	Sub	26	T=1.00	C=0.00
Latin American 1	Sub	146	T=0.966	C=0.034
Latin American 2	Sub	610	T=0.984	C=0.016
South Asian	Sub	98	T=0.99	C=0.01
Other	Sub	692	T=0.948	C=0.052

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	T=0.940693	C=0.059307
gnomAD - Genomes	Global	Study-wide	140154	T=0.944283	C=0.055717
gnomAD - Genomes	European	Sub	75912	T=0.99723	C=0.00277
gnomAD - Genomes	African	Sub	41996	T=0.83015	C=0.16985
gnomAD - Genomes	American	Sub	13646	T=0.97772	C=0.02228
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=0.9952	C=0.0048
gnomAD - Genomes	East Asian	Sub	3132	T=0.9860	C=0.0140
gnomAD - Genomes	Other	Sub	2150	T=0.9526	C=0.0474
14KJPN	JAPANESE	Study-wide	28258	T=0.97403	C=0.02597
Allele Frequency Aggregator	Total	Global	18890	T=0.97014	C=0.02986
Allele Frequency Aggregator	European	Sub	14286	T=0.99790	C=0.00210
Allele Frequency Aggregator	African	Sub	2946	T=0.8367	C=0.1633
Allele Frequency Aggregator	Other	Sub	692	T=0.948	C=0.052
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.984	C=0.016
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.966	C=0.034
Allele Frequency Aggregator	Asian	Sub	112	T=0.991	C=0.009
Allele Frequency Aggregator	South Asian	Sub	98	T=0.99	C=0.01
8.3KJPN	JAPANESE	Study-wide	16760	T=0.97458	C=0.02542
1000Genomes_30x	Global	Study-wide	6404	T=0.9368	C=0.0632
1000Genomes_30x	African	Sub	1786	T=0.8057	C=0.1943
1000Genomes_30x	Europe	Sub	1266	T=0.9945	C=0.0055
1000Genomes_30x	South Asian	Sub	1202	T=0.9992	C=0.0008
1000Genomes_30x	East Asian	Sub	1170	T=0.9744	C=0.0256
1000Genomes_30x	American	Sub	980	T=0.980	C=0.020
1000Genomes	Global	Study-wide	5008	T=0.9385	C=0.0615
1000Genomes	African	Sub	1322	T=0.8033	C=0.1967
1000Genomes	East Asian	Sub	1008	T=0.9712	C=0.0288
1000Genomes	Europe	Sub	1006	T=0.9940	C=0.0060
1000Genomes	South Asian	Sub	978	T=0.999	C=0.001
1000Genomes	American	Sub	694	T=0.983	C=0.017
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9989	C=0.0011
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9977	C=0.0023
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9976	C=0.0024
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9918	C=0.0082
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9885	C=0.0115
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.996	C=0.004
Northern Sweden	ACPOP	Study-wide	600	T=0.998	C=0.002
Qatari	Global	Study-wide	216	T=0.944	C=0.056
SGDP_PRJ	Global	Study-wide	34	T=0.50	C=0.50

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.162988754T>C
GRCh37.p13 chr 6	NC_000006.11:g.163409786T>C
PACRG RefSeqGene	NG_011525.1:g.266623T>C

Gene: PACRG, parkin coregulated (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PACRG transcript variant 2	NM_001080378.2:c.292-7339… NM_001080378.2:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant 3	NM_001080379.2:c.292-7339… NM_001080379.2:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant 1	NM_152410.3:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X13	XM_005266825.6:c.292-7339… XM_005266825.6:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X16	XM_005266826.6:c.292-7339… XM_005266826.6:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X10	XM_006715344.5:c.292-7339… XM_006715344.5:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X15	XM_006715345.5:c.292-7339… XM_006715345.5:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X8	XM_011535461.4:c.292-7339… XM_011535461.4:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X6	XM_011535462.4:c.292-7339… XM_011535462.4:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X14	XM_011535466.2:c.292-7339… XM_011535466.2:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X17	XM_011535468.3:c.292-7339… XM_011535468.3:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X18	XM_011535469.3:c.292-7339… XM_011535469.3:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X1	XM_017010275.3:c.292-7339… XM_017010275.3:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X5	XM_017010276.3:c.292-7339… XM_017010276.3:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X2	XM_017010277.3:c.292-7339… XM_017010277.3:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X4	XM_017010278.3:c.292-7339… XM_017010278.3:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X3	XM_017010279.3:c.292-7339… XM_017010279.3:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X7	XM_017010280.3:c.292-7339… XM_017010280.3:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X9	XM_047418208.1:c.292-7339… XM_047418208.1:c.292-73396T>C	N/A	Intron Variant
PACRG transcript variant X11	XM_017010281.3:c.	N/A	Genic Upstream Transcript Variant
PACRG transcript variant X12	XM_017010282.3:c.	N/A	Genic Upstream Transcript Variant
PACRG transcript variant X19	XM_011535471.3:c.	N/A	Genic Downstream Transcript 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	T=	C
GRCh38.p14 chr 6	NC_000006.12:g.162988754=	NC_000006.12:g.162988754T>C
GRCh37.p13 chr 6	NC_000006.11:g.163409786=	NC_000006.11:g.163409786T>C
PACRG RefSeqGene	NG_011525.1:g.266623=	NG_011525.1:g.266623T>C
PACRG transcript variant 2	NM_001080378.1:c.292-73396=	NM_001080378.1:c.292-73396T>C
PACRG transcript variant 2	NM_001080378.2:c.292-73396=	NM_001080378.2:c.292-73396T>C
PACRG transcript variant 3	NM_001080379.1:c.292-73396=	NM_001080379.1:c.292-73396T>C
PACRG transcript variant 3	NM_001080379.2:c.292-73396=	NM_001080379.2:c.292-73396T>C
PACRG transcript variant 1	NM_152410.2:c.292-73396=	NM_152410.2:c.292-73396T>C
PACRG transcript variant 1	NM_152410.3:c.292-73396=	NM_152410.3:c.292-73396T>C
PACRG transcript variant X1	XM_005266824.1:c.292-73396=	XM_005266824.1:c.292-73396T>C
PACRG transcript variant X2	XM_005266825.1:c.292-73396=	XM_005266825.1:c.292-73396T>C
PACRG transcript variant X13	XM_005266825.6:c.292-73396=	XM_005266825.6:c.292-73396T>C
PACRG transcript variant X3	XM_005266826.1:c.292-73396=	XM_005266826.1:c.292-73396T>C
PACRG transcript variant X16	XM_005266826.6:c.292-73396=	XM_005266826.6:c.292-73396T>C
PACRG transcript variant X10	XM_006715344.5:c.292-73396=	XM_006715344.5:c.292-73396T>C
PACRG transcript variant X15	XM_006715345.5:c.292-73396=	XM_006715345.5:c.292-73396T>C
PACRG transcript variant X8	XM_011535461.4:c.292-73396=	XM_011535461.4:c.292-73396T>C
PACRG transcript variant X6	XM_011535462.4:c.292-73396=	XM_011535462.4:c.292-73396T>C
PACRG transcript variant X14	XM_011535466.2:c.292-73396=	XM_011535466.2:c.292-73396T>C
PACRG transcript variant X17	XM_011535468.3:c.292-73396=	XM_011535468.3:c.292-73396T>C
PACRG transcript variant X18	XM_011535469.3:c.292-73396=	XM_011535469.3:c.292-73396T>C
PACRG transcript variant X1	XM_017010275.3:c.292-73396=	XM_017010275.3:c.292-73396T>C
PACRG transcript variant X5	XM_017010276.3:c.292-73396=	XM_017010276.3:c.292-73396T>C
PACRG transcript variant X2	XM_017010277.3:c.292-73396=	XM_017010277.3:c.292-73396T>C
PACRG transcript variant X4	XM_017010278.3:c.292-73396=	XM_017010278.3:c.292-73396T>C
PACRG transcript variant X3	XM_017010279.3:c.292-73396=	XM_017010279.3:c.292-73396T>C
PACRG transcript variant X7	XM_017010280.3:c.292-73396=	XM_017010280.3:c.292-73396T>C
PACRG transcript variant X9	XM_047418208.1:c.292-73396=	XM_047418208.1:c.292-73396T>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#.

42 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss84550167	Dec 15, 2007 (129)
2	1000GENOMES	ss115434737	Jan 25, 2009 (130)
3	ILLUMINA-UK	ss116806841	Feb 14, 2009 (130)
4	COMPLETE_GENOMICS	ss165153903	Jul 04, 2010 (132)
5	BUSHMAN	ss202714190	Jul 04, 2010 (132)
6	1000GENOMES	ss222807908	Jul 14, 2010 (132)
7	1000GENOMES	ss240772426	Jul 15, 2010 (132)
8	TISHKOFF	ss559683676	Apr 25, 2013 (138)
9	EVA-GONL	ss983752447	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1074224660	Aug 21, 2014 (142)
11	1000GENOMES	ss1323228613	Aug 21, 2014 (142)
12	EVA_DECODE	ss1593328631	Apr 01, 2015 (144)
13	EVA_UK10K_ALSPAC	ss1617213692	Apr 01, 2015 (144)
14	EVA_UK10K_TWINSUK	ss1660207725	Apr 01, 2015 (144)
15	HAMMER_LAB	ss1804782123	Sep 08, 2015 (146)
16	WEILL_CORNELL_DGM	ss1926993774	Feb 12, 2016 (147)
17	HUMAN_LONGEVITY	ss2290365843	Dec 20, 2016 (150)
18	GRF	ss2707998106	Nov 08, 2017 (151)
19	GNOMAD	ss2847811229	Nov 08, 2017 (151)
20	SWEGEN	ss3000332885	Nov 08, 2017 (151)
21	EGCUT_WGS	ss3668272812	Jul 13, 2019 (153)
22	EVA_DECODE	ss3718749570	Jul 13, 2019 (153)
23	ACPOP	ss3734194739	Jul 13, 2019 (153)
24	EVA	ss3765965740	Jul 13, 2019 (153)
25	KHV_HUMAN_GENOMES	ss3809129803	Jul 13, 2019 (153)
26	SGDP_PRJ	ss3866216867	Apr 26, 2020 (154)
27	KRGDB	ss3913210136	Apr 26, 2020 (154)
28	KOGIC	ss3960535918	Apr 26, 2020 (154)
29	TOPMED	ss4729948582	Apr 26, 2021 (155)
30	TOMMO_GENOMICS	ss5180999884	Apr 26, 2021 (155)
31	1000G_HIGH_COVERAGE	ss5271191072	Oct 14, 2022 (156)
32	EVA	ss5370539089	Oct 14, 2022 (156)
33	HUGCELL_USP	ss5468558706	Oct 14, 2022 (156)
34	EVA	ss5508792389	Oct 14, 2022 (156)
35	1000G_HIGH_COVERAGE	ss5558547026	Oct 14, 2022 (156)
36	SANFORD_IMAGENETICS	ss5641974945	Oct 14, 2022 (156)
37	TOMMO_GENOMICS	ss5720191768	Oct 14, 2022 (156)
38	YY_MCH	ss5808166459	Oct 14, 2022 (156)
39	EVA	ss5843319417	Oct 14, 2022 (156)
40	EVA	ss5886923210	Oct 14, 2022 (156)
41	EVA	ss5971069578	Oct 14, 2022 (156)
42	EVA	ss5971069579	Oct 14, 2022 (156)
43	1000Genomes	NC_000006.11 - 163409786	Oct 12, 2018 (152)
44	1000Genomes_30x	NC_000006.12 - 162988754	Oct 14, 2022 (156)
45	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 163409786	Oct 12, 2018 (152)
46	Genetic variation in the Estonian population	NC_000006.11 - 163409786	Oct 12, 2018 (152)
47	gnomAD - Genomes	NC_000006.12 - 162988754	Apr 26, 2021 (155)
48	Genome of the Netherlands Release 5	NC_000006.11 - 163409786	Apr 26, 2020 (154)
49	KOREAN population from KRGDB	NC_000006.11 - 163409786	Apr 26, 2020 (154)
50	Korean Genome Project	NC_000006.12 - 162988754	Apr 26, 2020 (154)
51	Northern Sweden	NC_000006.11 - 163409786	Jul 13, 2019 (153)
52	Qatari	NC_000006.11 - 163409786	Apr 26, 2020 (154)
53	SGDP_PRJ	NC_000006.11 - 163409786	Apr 26, 2020 (154)
54	8.3KJPN	NC_000006.11 - 163409786	Apr 26, 2021 (155)
55	14KJPN	NC_000006.12 - 162988754	Oct 14, 2022 (156)
56	TopMed	NC_000006.12 - 162988754	Apr 26, 2021 (155)
57	UK 10K study - Twins	NC_000006.11 - 163409786	Oct 12, 2018 (152)
58	ALFA	NC_000006.12 - 162988754	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss84550167	NC_000006.9:163380196:T:C	NC_000006.12:162988753:T:C	(self)
ss115434737, ss116806841, ss165153903, ss202714190, ss1593328631	NC_000006.10:163329775:T:C	NC_000006.12:162988753:T:C	(self)
35134003, 19596419, 14011060, 8721161, 20387530, 7479604, 9035704, 18233847, 38969191, 19596419, ss222807908, ss240772426, ss559683676, ss983752447, ss1074224660, ss1323228613, ss1617213692, ss1660207725, ss1804782123, ss1926993774, ss2707998106, ss2847811229, ss3000332885, ss3668272812, ss3734194739, ss3765965740, ss3866216867, ss3913210136, ss5180999884, ss5370539089, ss5508792389, ss5641974945, ss5843319417, ss5971069578, ss5971069579	NC_000006.11:163409785:T:C	NC_000006.12:162988753:T:C	(self)
46072961, 247977001, 16913919, 54028872, 567326140, 3069548435, ss2290365843, ss3718749570, ss3809129803, ss3960535918, ss4729948582, ss5271191072, ss5468558706, ss5558547026, ss5720191768, ss5808166459, ss5886923210	NC_000006.12:162988753:T:C	NC_000006.12:162988753:T:C	(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 rs58881863

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
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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

rs58881863