Name: rs9578965
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.

rs9578965

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:26132028 (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>A / C>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.022887 (6058/264690, TOPMED)
A=0.00438 (116/26508, ALFA)
A=0.0173 (111/6404, 1000G_30x) (+ 5 more)
A=0.0174 (87/5008, 1000G)
A=0.0266 (40/1504, HapMap)
A=0.009 (2/216, Qatari)
C=0.5 (5/10, SGDP_PRJ)
A=0.5 (5/10, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RNF6 : 500B Downstream 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	26508	C=0.99562	A=0.00438, G=0.00000
European	Sub	20268	C=0.99965	A=0.00035, G=0.00000
African	Sub	3942	C=0.9734	A=0.0266, G=0.0000
African Others	Sub	132	C=0.962	A=0.038, G=0.000
African American	Sub	3810	C=0.9738	A=0.0262, G=0.0000
Asian	Sub	128	C=1.000	A=0.000, G=0.000
East Asian	Sub	100	C=1.00	A=0.00, G=0.00
Other Asian	Sub	28	C=1.00	A=0.00, G=0.00
Latin American 1	Sub	162	C=1.000	A=0.000, G=0.000
Latin American 2	Sub	698	C=0.997	A=0.003, G=0.000
South Asian	Sub	114	C=1.000	A=0.000, G=0.000
Other	Sub	1196	C=0.9983	A=0.0017, G=0.0000

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	C=0.977113	A=0.022887
Allele Frequency Aggregator	Total	Global	26508	C=0.99562	A=0.00438, G=0.00000
Allele Frequency Aggregator	European	Sub	20268	C=0.99965	A=0.00035, G=0.00000
Allele Frequency Aggregator	African	Sub	3942	C=0.9734	A=0.0266, G=0.0000
Allele Frequency Aggregator	Other	Sub	1196	C=0.9983	A=0.0017, G=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	698	C=0.997	A=0.003, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	162	C=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	Asian	Sub	128	C=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	South Asian	Sub	114	C=1.000	A=0.000, G=0.000
1000Genomes_30x	Global	Study-wide	6404	C=0.9827	A=0.0173
1000Genomes_30x	African	Sub	1786	C=0.9390	A=0.0610
1000Genomes_30x	Europe	Sub	1266	C=1.0000	A=0.0000
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	A=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	C=0.998	A=0.002
1000Genomes	Global	Study-wide	5008	C=0.9826	A=0.0174
1000Genomes	African	Sub	1322	C=0.9357	A=0.0643
1000Genomes	East Asian	Sub	1008	C=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	C=1.0000	A=0.0000
1000Genomes	South Asian	Sub	978	C=1.000	A=0.000
1000Genomes	American	Sub	694	C=0.997	A=0.003
HapMap	Global	Study-wide	1504	C=0.9734	A=0.0266
HapMap	African	Sub	678	C=0.948	A=0.052
HapMap	American	Sub	656	C=0.994	A=0.006
HapMap	Asian	Sub	170	C=0.994	A=0.006
Qatari	Global	Study-wide	216	C=0.991	A=0.009
SGDP_PRJ	Global	Study-wide	10	C=0.5	A=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 13	NC_000013.11:g.26132028C>A
GRCh38.p14 chr 13	NC_000013.11:g.26132028C>G
GRCh37.p13 chr 13	NC_000013.10:g.26706166C>A
GRCh37.p13 chr 13	NC_000013.10:g.26706166C>G
RNF6 RefSeqGene	NG_017042.2:g.95344G>T
RNF6 RefSeqGene	NG_017042.2:g.95344G>C
ATP8A2P3 pseudogene	NG_032522.2:g.22248G>T
ATP8A2P3 pseudogene	NG_032522.2:g.22248G>C

Gene: RNF6, ring finger protein 6 (minus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
RNF6 transcript variant 2	NM_183045.1:c.	N/A	Downstream Transcript Variant
RNF6 transcript variant 1	NM_005977.4:c.	N/A	N/A
RNF6 transcript variant 4	NM_183043.3:c.	N/A	N/A
RNF6 transcript variant 3	NM_183044.3:c.	N/A	N/A
RNF6 transcript variant X13	XM_011535178.3:c.	N/A	Downstream Transcript Variant
RNF6 transcript variant X14	XM_047430498.1:c.	N/A	Downstream Transcript Variant
RNF6 transcript variant X15	XM_047430499.1:c.	N/A	Downstream Transcript Variant
RNF6 transcript variant X16	XM_047430500.1:c.	N/A	Downstream Transcript Variant
RNF6 transcript variant X1	XM_005266485.4:c.	N/A	N/A
RNF6 transcript variant X3	XM_005266486.3:c.	N/A	N/A
RNF6 transcript variant X2	XM_011535177.4:c.	N/A	N/A
RNF6 transcript variant X6	XM_017020685.3:c.	N/A	N/A
RNF6 transcript variant X7	XM_017020686.2:c.	N/A	N/A
RNF6 transcript variant X12	XM_017020687.2:c.	N/A	N/A
RNF6 transcript variant X4	XM_024449390.2:c.	N/A	N/A
RNF6 transcript variant X9	XM_024449391.2:c.	N/A	N/A
RNF6 transcript variant X11	XM_024449392.2:c.	N/A	N/A
RNF6 transcript variant X5	XM_047430494.1:c.	N/A	N/A
RNF6 transcript variant X8	XM_047430495.1:c.	N/A	N/A
RNF6 transcript variant X10	XM_047430496.1:c.	N/A	N/A

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=	A	G
GRCh38.p14 chr 13	NC_000013.11:g.26132028=	NC_000013.11:g.26132028C>A	NC_000013.11:g.26132028C>G
GRCh37.p13 chr 13	NC_000013.10:g.26706166=	NC_000013.10:g.26706166C>A	NC_000013.10:g.26706166C>G
RNF6 RefSeqGene	NG_017042.2:g.95344=	NG_017042.2:g.95344G>T	NG_017042.2:g.95344G>C
ATP8A2P3 pseudogene	NG_032522.2:g.22248=	NG_032522.2:g.22248G>T	NG_032522.2:g.22248G>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#.

39 SubSNP, 9 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss13304090	Dec 05, 2003 (119)
2	ILLUMINA	ss75007207	Dec 07, 2007 (129)
3	HGSV	ss80613752	Dec 14, 2007 (130)
4	1000GENOMES	ss114438032	Jan 25, 2009 (130)
5	ILLUMINA-UK	ss118393929	Feb 14, 2009 (130)
6	KRIBB_YJKIM	ss119596655	Dec 01, 2009 (131)
7	COMPLETE_GENOMICS	ss169012062	Jul 04, 2010 (132)
8	ILLUMINA	ss174871419	Jul 04, 2010 (132)
9	BUSHMAN	ss198990250	Jul 04, 2010 (132)
10	1000GENOMES	ss226088023	Jul 14, 2010 (132)
11	PJP	ss291560537	May 09, 2011 (134)
12	ILLUMINA	ss481211918	May 04, 2012 (137)
13	ILLUMINA	ss483170306	May 04, 2012 (137)
14	ILLUMINA	ss534194250	Sep 08, 2015 (146)
15	ILLUMINA	ss779264266	Sep 08, 2015 (146)
16	ILLUMINA	ss781424726	Sep 08, 2015 (146)
17	ILLUMINA	ss834730964	Sep 08, 2015 (146)
18	JMKIDD_LAB	ss1078948213	Aug 21, 2014 (142)
19	1000GENOMES	ss1347546155	Aug 21, 2014 (142)
20	WEILL_CORNELL_DGM	ss1933576457	Feb 12, 2016 (147)
21	HUMAN_LONGEVITY	ss2194951095	Dec 20, 2016 (150)
22	ILLUMINA	ss2633041113	Nov 08, 2017 (151)
23	GNOMAD	ss2917740535	Nov 08, 2017 (151)
24	ILLUMINA	ss3627025014	Oct 12, 2018 (152)
25	ILLUMINA	ss3631045524	Oct 12, 2018 (152)
26	ILLUMINA	ss3638001003	Oct 12, 2018 (152)
27	ILLUMINA	ss3642991646	Oct 12, 2018 (152)
28	EVA_DECODE	ss3694952732	Jul 13, 2019 (153)
29	EVA	ss3833455958	Apr 27, 2020 (154)
30	SGDP_PRJ	ss3879621464	Apr 27, 2020 (154)
31	TOPMED	ss4940374373	Apr 26, 2021 (155)
32	1000G_HIGH_COVERAGE	ss5293142974	Oct 16, 2022 (156)
33	EVA	ss5409688610	Oct 16, 2022 (156)
34	HUGCELL_USP	ss5487564260	Oct 16, 2022 (156)
35	EVA	ss5510912706	Oct 16, 2022 (156)
36	1000G_HIGH_COVERAGE	ss5591798301	Oct 16, 2022 (156)
37	SANFORD_IMAGENETICS	ss5654428763	Oct 16, 2022 (156)
38	EVA	ss5924421788	Oct 16, 2022 (156)
39	EVA	ss5945833319	Oct 16, 2022 (156)
40	1000Genomes	NC_000013.10 - 26706166	Oct 12, 2018 (152)
41	1000Genomes_30x	NC_000013.11 - 26132028	Oct 16, 2022 (156)
42	gnomAD - Genomes Submission ignored due to conflicting rows: Row 425864562 (NC_000013.11:26132027:C:A 3045/139366) Row 425864563 (NC_000013.11:26132027:C:G 12/139382)	-	Apr 26, 2021 (155)
43	gnomAD - Genomes Submission ignored due to conflicting rows: Row 425864562 (NC_000013.11:26132027:C:A 3045/139366) Row 425864563 (NC_000013.11:26132027:C:G 12/139382)	-	Apr 26, 2021 (155)
44	HapMap	NC_000013.11 - 26132028	Apr 27, 2020 (154)
45	Qatari	NC_000013.10 - 26706166	Apr 27, 2020 (154)
46	SGDP_PRJ	NC_000013.10 - 26706166	Apr 27, 2020 (154)
47	TopMed	NC_000013.11 - 26132028	Apr 26, 2021 (155)
48	ALFA	NC_000013.11 - 26132028	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)
rs57708633	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss80613752, ss114438032, ss118393929, ss169012062, ss198990250, ss291560537, ss483170306, ss3642991646	NC_000013.9:25604165:C:A	NC_000013.11:26132027:C:A	(self)
60391634, 15618387, 31638444, ss226088023, ss481211918, ss534194250, ss779264266, ss781424726, ss834730964, ss1078948213, ss1347546155, ss1933576457, ss2633041113, ss2917740535, ss3627025014, ss3631045524, ss3638001003, ss3833455958, ss3879621464, ss5409688610, ss5510912706, ss5654428763, ss5945833319	NC_000013.10:26706165:C:A	NC_000013.11:26132027:C:A	(self)
79324236, 950939, 155920031, 6783003819, ss2194951095, ss3694952732, ss4940374373, ss5293142974, ss5487564260, ss5591798301, ss5924421788	NC_000013.11:26132027:C:A	NC_000013.11:26132027:C:A	(self)
ss13304090	NT_009799.12:7686165:C:A	NC_000013.11:26132027:C:A	(self)
ss75007207, ss119596655, ss174871419	NT_024524.14:7686165:C:A	NC_000013.11:26132027:C:A	(self)
ss2917740535	NC_000013.10:26706165:C:G	NC_000013.11:26132027:C:G	(self)
6783003819	NC_000013.11:26132027:C:G	NC_000013.11:26132027:C: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 rs9578965

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

rs9578965