Name: rs78148447
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.

rs78148447

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:161974289 (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: C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.01100 (204/18538, ALFA)
T=0.0078 (50/6404, 1000G_30x)
T=0.0078 (39/5008, 1000G) (+ 10 more)
T=0.0411 (184/4480, Estonian)
T=0.0265 (102/3854, ALSPAC)
T=0.0291 (108/3708, TWINSUK)
T=0.030 (30/998, GoNL)
T=0.030 (18/600, NorthernSweden)
T=0.05 (2/40, GENOME_DK)
C=0.50 (6/12, SGDP_PRJ)
T=0.50 (6/12, SGDP_PRJ)
C=0.5 (3/6, Siberian)
T=0.5 (3/6, 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	18538	C=0.98900	G=0.00000, T=0.01100
European	Sub	13710	C=0.98600	G=0.00000, T=0.01400
African	Sub	2946	C=1.0000	G=0.0000, T=0.0000
African Others	Sub	114	C=1.000	G=0.000, T=0.000
African American	Sub	2832	C=1.0000	G=0.0000, T=0.0000
Asian	Sub	116	C=1.000	G=0.000, T=0.000
East Asian	Sub	88	C=1.00	G=0.00, T=0.00
Other Asian	Sub	28	C=1.00	G=0.00, T=0.00
Latin American 1	Sub	146	C=1.000	G=0.000, T=0.000
Latin American 2	Sub	590	C=1.000	G=0.000, T=0.000
South Asian	Sub	96	C=1.00	G=0.00, T=0.00
Other	Sub	934	C=0.987	G=0.000, T=0.013

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
Allele Frequency Aggregator	Total	Global	18538	C=0.98900	G=0.00000, T=0.01100
Allele Frequency Aggregator	European	Sub	13710	C=0.98600	G=0.00000, T=0.01400
Allele Frequency Aggregator	African	Sub	2946	C=1.0000	G=0.0000, T=0.0000
Allele Frequency Aggregator	Other	Sub	934	C=0.987	G=0.000, T=0.013
Allele Frequency Aggregator	Latin American 2	Sub	590	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	116	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	96	C=1.00	G=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.9922	T=0.0078
1000Genomes_30x	African	Sub	1786	C=0.9989	T=0.0011
1000Genomes_30x	Europe	Sub	1266	C=0.9731	T=0.0269
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	T=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.986	T=0.014
1000Genomes	Global	Study-wide	5008	C=0.9922	T=0.0078
1000Genomes	African	Sub	1322	C=0.9992	T=0.0008
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.9732	T=0.0268
1000Genomes	South Asian	Sub	978	C=1.000	T=0.000
1000Genomes	American	Sub	694	C=0.984	T=0.016
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9589	T=0.0411
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9735	T=0.0265
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9709	T=0.0291
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.970	T=0.030
Northern Sweden	ACPOP	Study-wide	600	C=0.970	T=0.030
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05
SGDP_PRJ	Global	Study-wide	12	C=0.50	T=0.50
Siberian	Global	Study-wide	6	C=0.5	T=0.5

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.161974289C>G
GRCh38.p14 chr 6	NC_000006.12:g.161974289C>T
GRCh37.p13 chr 6	NC_000006.11:g.162395321C>G
GRCh37.p13 chr 6	NC_000006.11:g.162395321C>T
PRKN RefSeqGene	NG_008289.2:g.758514G>C
PRKN RefSeqGene	NG_008289.2:g.758514G>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.619-872G>C	N/A	Intron Variant
PRKN transcript variant 2	NM_013987.3:c.535-872G>C	N/A	Intron Variant
PRKN transcript variant 3	NM_013988.3:c.172-872G>C	N/A	Intron Variant
PRKN transcript variant X2	XM_011535863.2:c.616-872G… XM_011535863.2:c.616-872G>C	N/A	Intron Variant
PRKN transcript variant X1	XM_017010908.2:c.733-872G… XM_017010908.2:c.733-872G>C	N/A	Intron Variant
PRKN transcript variant X3	XM_024446449.2:c.382-872G… XM_024446449.2:c.382-872G>C	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	C=	G	T
GRCh38.p14 chr 6	NC_000006.12:g.161974289=	NC_000006.12:g.161974289C>G	NC_000006.12:g.161974289C>T
GRCh37.p13 chr 6	NC_000006.11:g.162395321=	NC_000006.11:g.162395321C>G	NC_000006.11:g.162395321C>T
PRKN RefSeqGene	NG_008289.2:g.758514=	NG_008289.2:g.758514G>C	NG_008289.2:g.758514G>A
PRKN transcript variant 1	NM_004562.2:c.619-872=	NM_004562.2:c.619-872G>C	NM_004562.2:c.619-872G>A
PRKN transcript variant 1	NM_004562.3:c.619-872=	NM_004562.3:c.619-872G>C	NM_004562.3:c.619-872G>A
PRKN transcript variant 2	NM_013987.2:c.535-872=	NM_013987.2:c.535-872G>C	NM_013987.2:c.535-872G>A
PRKN transcript variant 2	NM_013987.3:c.535-872=	NM_013987.3:c.535-872G>C	NM_013987.3:c.535-872G>A
PRKN transcript variant 3	NM_013988.2:c.172-872=	NM_013988.2:c.172-872G>C	NM_013988.2:c.172-872G>A
PRKN transcript variant 3	NM_013988.3:c.172-872=	NM_013988.3:c.172-872G>C	NM_013988.3:c.172-872G>A
PARK2 transcript variant X1	XM_005267004.1:c.619-872=	XM_005267004.1:c.619-872G>C	XM_005267004.1:c.619-872G>A
PRKN transcript variant X2	XM_011535863.2:c.616-872=	XM_011535863.2:c.616-872G>C	XM_011535863.2:c.616-872G>A
PRKN transcript variant X1	XM_017010908.2:c.733-872=	XM_017010908.2:c.733-872G>C	XM_017010908.2:c.733-872G>A
PRKN transcript variant X3	XM_024446449.2:c.382-872=	XM_024446449.2:c.382-872G>C	XM_024446449.2:c.382-872G>A

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#.

39 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss233773547	Jul 15, 2010 (132)
2	BL	ss254790930	May 09, 2011 (134)
3	ILLUMINA	ss535479546	Sep 08, 2015 (146)
4	SSMP	ss654020815	Apr 25, 2013 (138)
5	EVA-GONL	ss983743588	Aug 21, 2014 (142)
6	JMKIDD_LAB	ss1074218273	Aug 21, 2014 (142)
7	1000GENOMES	ss1323197519	Aug 21, 2014 (142)
8	EVA_GENOME_DK	ss1581989846	Apr 01, 2015 (144)
9	EVA_DECODE	ss1593319913	Apr 01, 2015 (144)
10	EVA_UK10K_ALSPAC	ss1617196690	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1660190723	Apr 01, 2015 (144)
12	JJLAB	ss2024159462	Sep 14, 2016 (149)
13	USC_VALOUEV	ss2152353235	Dec 20, 2016 (150)
14	HUMAN_LONGEVITY	ss2290301858	Dec 20, 2016 (150)
15	GNOMAD	ss2847725435	Nov 08, 2017 (151)
16	SWEGEN	ss3000320121	Nov 08, 2017 (151)
17	BIOINF_KMB_FNS_UNIBA	ss3025871159	Nov 08, 2017 (151)
18	CSHL	ss3347335568	Nov 08, 2017 (151)
19	ILLUMINA	ss3629709605	Oct 12, 2018 (152)
20	EGCUT_WGS	ss3668258915	Jul 13, 2019 (153)
21	EVA_DECODE	ss3718732933	Jul 13, 2019 (153)
22	ACPOP	ss3734187242	Jul 13, 2019 (153)
23	KHV_HUMAN_GENOMES	ss3809119506	Jul 13, 2019 (153)
24	SGDP_PRJ	ss3866199667	Apr 26, 2020 (154)
25	TOPMED	ss4729693763	Apr 26, 2021 (155)
26	TOPMED	ss4729693764	Apr 26, 2021 (155)
27	EVA	ss5237411607	Apr 26, 2021 (155)
28	1000G_HIGH_COVERAGE	ss5271163098	Oct 14, 2022 (156)
29	EVA	ss5370488772	Oct 14, 2022 (156)
30	HUGCELL_USP	ss5468533529	Oct 14, 2022 (156)
31	1000G_HIGH_COVERAGE	ss5558505415	Oct 14, 2022 (156)
32	SANFORD_IMAGENETICS	ss5624649056	Oct 14, 2022 (156)
33	SANFORD_IMAGENETICS	ss5641958567	Oct 14, 2022 (156)
34	EVA	ss5843308428	Oct 14, 2022 (156)
35	EVA	ss5848122016	Oct 14, 2022 (156)
36	EVA	ss5886891588	Oct 14, 2022 (156)
37	EVA	ss5971039719	Oct 14, 2022 (156)
38	EVA	ss5971039720	Oct 14, 2022 (156)
39	EVA	ss5979810344	Oct 14, 2022 (156)
40	1000Genomes	NC_000006.11 - 162395321	Oct 12, 2018 (152)
41	1000Genomes_30x	NC_000006.12 - 161974289	Oct 14, 2022 (156)
42	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 162395321	Oct 12, 2018 (152)
43	Genetic variation in the Estonian population	NC_000006.11 - 162395321	Oct 12, 2018 (152)
44	The Danish reference pan genome	NC_000006.11 - 162395321	Apr 26, 2020 (154)
45	gnomAD - Genomes Submission ignored due to conflicting rows: Row 247757161 (NC_000006.12:161974288:C:G 3/140214) Row 247757162 (NC_000006.12:161974288:C:T 2972/140202)	-	Apr 26, 2021 (155)
46	gnomAD - Genomes Submission ignored due to conflicting rows: Row 247757161 (NC_000006.12:161974288:C:G 3/140214) Row 247757162 (NC_000006.12:161974288:C:T 2972/140202)	-	Apr 26, 2021 (155)
47	Genome of the Netherlands Release 5	NC_000006.11 - 162395321	Apr 26, 2020 (154)
48	Northern Sweden	NC_000006.11 - 162395321	Jul 13, 2019 (153)
49	SGDP_PRJ	NC_000006.11 - 162395321	Apr 26, 2020 (154)
50	Siberian	NC_000006.11 - 162395321	Apr 26, 2020 (154)
51	TopMed Submission ignored due to conflicting rows: Row 567071321 (NC_000006.12:161974288:C:G 9/264690) Row 567071322 (NC_000006.12:161974288:C:T 5405/264690)	-	Apr 26, 2021 (155)
52	TopMed Submission ignored due to conflicting rows: Row 567071321 (NC_000006.12:161974288:C:G 9/264690) Row 567071322 (NC_000006.12:161974288:C:T 5405/264690)	-	Apr 26, 2021 (155)
53	UK 10K study - Twins	NC_000006.11 - 162395321	Oct 12, 2018 (152)
54	ALFA	NC_000006.12 - 161974289	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
ss2847725435	NC_000006.11:162395320:C:G	NC_000006.12:161974288:C:G	(self)
12831284612, ss4729693763	NC_000006.12:161974288:C:G	NC_000006.12:161974288:C:G	(self)
ss254790930, ss1593319913	NC_000006.10:162315310:C:T	NC_000006.12:161974288:C:T	(self)
35101601, 19577597, 13997163, 8154785, 8712494, 7472107, 18216647, 4869589, 19577597, ss233773547, ss535479546, ss654020815, ss983743588, ss1074218273, ss1323197519, ss1581989846, ss1617196690, ss1660190723, ss2024159462, ss2152353235, ss2847725435, ss3000320121, ss3347335568, ss3629709605, ss3668258915, ss3734187242, ss3866199667, ss5237411607, ss5370488772, ss5624649056, ss5641958567, ss5843308428, ss5848122016, ss5971039719, ss5971039720, ss5979810344	NC_000006.11:162395320:C:T	NC_000006.12:161974288:C:T	(self)
46031350, 12831284612, ss2290301858, ss3025871159, ss3718732933, ss3809119506, ss4729693764, ss5271163098, ss5468533529, ss5558505415, ss5886891588	NC_000006.12:161974288:C:T	NC_000006.12:161974288:C:T	(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 rs78148447

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

rs78148447