Name: rs474808
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.

rs474808

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:26150309 (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=0.026355 (6976/264690, TOPMED)
C=0.024597 (3447/140138, GnomAD)
C=0.03737 (2941/78690, PAGE_STUDY) (+ 11 more)
C=0.01427 (539/37766, ALFA)
C=0.0289 (185/6404, 1000G_30x)
C=0.0278 (139/5008, 1000G)
C=0.0010 (4/3854, ALSPAC)
C=0.0011 (4/3708, TWINSUK)
C=0.0572 (79/1380, HapMap)
C=0.001 (1/998, GoNL)
C=0.013 (8/626, Chileans)
C=0.002 (1/600, NorthernSweden)
C=0.032 (7/216, Qatari)
T=0.43 (12/28, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RNF6 : 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	37766	T=0.98573	C=0.01427
European	Sub	25612	T=0.99793	C=0.00207
African	Sub	6042	T=0.9282	C=0.0718
African Others	Sub	192	T=0.917	C=0.083
African American	Sub	5850	T=0.9285	C=0.0715
Asian	Sub	520	T=1.000	C=0.000
East Asian	Sub	422	T=1.000	C=0.000
Other Asian	Sub	98	T=1.00	C=0.00
Latin American 1	Sub	580	T=0.974	C=0.026
Latin American 2	Sub	980	T=0.995	C=0.005
South Asian	Sub	180	T=1.000	C=0.000
Other	Sub	3852	T=0.9917	C=0.0083

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=0.973645	C=0.026355
gnomAD - Genomes	Global	Study-wide	140138	T=0.975403	C=0.024597
gnomAD - Genomes	European	Sub	75920	T=0.99783	C=0.00217
gnomAD - Genomes	African	Sub	41974	T=0.92607	C=0.07393
gnomAD - Genomes	American	Sub	13638	T=0.98951	C=0.01049
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=1.0000	C=0.0000
gnomAD - Genomes	East Asian	Sub	3134	T=1.0000	C=0.0000
gnomAD - Genomes	Other	Sub	2152	T=0.9833	C=0.0167
The PAGE Study	Global	Study-wide	78690	T=0.96263	C=0.03737
The PAGE Study	AfricanAmerican	Sub	32510	T=0.92679	C=0.07321
The PAGE Study	Mexican	Sub	10808	T=0.99380	C=0.00620
The PAGE Study	Asian	Sub	8318	T=1.0000	C=0.0000
The PAGE Study	PuertoRican	Sub	7916	T=0.9739	C=0.0261
The PAGE Study	NativeHawaiian	Sub	4532	T=0.9989	C=0.0011
The PAGE Study	Cuban	Sub	4230	T=0.9870	C=0.0130
The PAGE Study	Dominican	Sub	3828	T=0.9626	C=0.0374
The PAGE Study	CentralAmerican	Sub	2450	T=0.9816	C=0.0184
The PAGE Study	SouthAmerican	Sub	1982	T=0.9894	C=0.0106
The PAGE Study	NativeAmerican	Sub	1260	T=0.9873	C=0.0127
The PAGE Study	SouthAsian	Sub	856	T=0.998	C=0.002
Allele Frequency Aggregator	Total	Global	37766	T=0.98573	C=0.01427
Allele Frequency Aggregator	European	Sub	25612	T=0.99793	C=0.00207
Allele Frequency Aggregator	African	Sub	6042	T=0.9282	C=0.0718
Allele Frequency Aggregator	Other	Sub	3852	T=0.9917	C=0.0083
Allele Frequency Aggregator	Latin American 2	Sub	980	T=0.995	C=0.005
Allele Frequency Aggregator	Latin American 1	Sub	580	T=0.974	C=0.026
Allele Frequency Aggregator	Asian	Sub	520	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	180	T=1.000	C=0.000
1000Genomes_30x	Global	Study-wide	6404	T=0.9711	C=0.0289
1000Genomes_30x	African	Sub	1786	T=0.9065	C=0.0935
1000Genomes_30x	Europe	Sub	1266	T=0.9953	C=0.0047
1000Genomes_30x	South Asian	Sub	1202	T=0.9992	C=0.0008
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	T=0.989	C=0.011
1000Genomes	Global	Study-wide	5008	T=0.9722	C=0.0278
1000Genomes	African	Sub	1322	T=0.9070	C=0.0930
1000Genomes	East Asian	Sub	1008	T=1.0000	C=0.0000
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=0.987	C=0.013
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9990	C=0.0010
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9989	C=0.0011
HapMap	Global	Study-wide	1380	T=0.9428	C=0.0572
HapMap	African	Sub	690	T=0.901	C=0.099
HapMap	American	Sub	424	T=0.979	C=0.021
HapMap	Europe	Sub	176	T=0.989	C=0.011
HapMap	Asian	Sub	90	T=1.00	C=0.00
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.999	C=0.001
Chileans	Chilean	Study-wide	626	T=0.987	C=0.013
Northern Sweden	ACPOP	Study-wide	600	T=0.998	C=0.002
Qatari	Global	Study-wide	216	T=0.968	C=0.032
SGDP_PRJ	Global	Study-wide	28	T=0.43	C=0.57

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.26150309T>C
GRCh37.p13 chr 13	NC_000013.10:g.26724447T>C
RNF6 RefSeqGene	NG_017042.2:g.77063A>G
ATP8A2P3 pseudogene	NG_032522.2:g.3967A>G

Gene: RNF6, ring finger protein 6 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RNF6 transcript variant 2	NM_183045.1:c.409-17858A>G	N/A	Intron Variant
RNF6 transcript variant 1	NM_005977.4:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant 4	NM_183043.3:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant 3	NM_183044.3:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant X13	XM_011535178.3:c.409-1785… XM_011535178.3:c.409-17858A>G	N/A	Intron Variant
RNF6 transcript variant X14	XM_047430498.1:c.409-1785… XM_047430498.1:c.409-17858A>G	N/A	Intron Variant
RNF6 transcript variant X15	XM_047430499.1:c.409-1785… XM_047430499.1:c.409-17858A>G	N/A	Intron Variant
RNF6 transcript variant X16	XM_047430500.1:c.409-1785… XM_047430500.1:c.409-17858A>G	N/A	Intron Variant
RNF6 transcript variant X1	XM_005266485.4:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant X3	XM_005266486.3:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant X2	XM_011535177.4:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant X6	XM_017020685.3:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant X7	XM_017020686.2:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant X12	XM_017020687.2:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant X4	XM_024449390.2:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant X9	XM_024449391.2:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant X11	XM_024449392.2:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant X5	XM_047430494.1:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant X8	XM_047430495.1:c.	N/A	Genic Downstream Transcript Variant
RNF6 transcript variant X10	XM_047430496.1: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 13	NC_000013.11:g.26150309=	NC_000013.11:g.26150309T>C
GRCh37.p13 chr 13	NC_000013.10:g.26724447=	NC_000013.10:g.26724447T>C
RNF6 RefSeqGene	NG_017042.2:g.77063=	NG_017042.2:g.77063A>G
ATP8A2P3 pseudogene	NG_032522.2:g.3967=	NG_032522.2:g.3967A>G
RNF6 transcript variant 2	NM_183045.1:c.409-17858=	NM_183045.1:c.409-17858A>G
RNF6 transcript variant X13	XM_011535178.3:c.409-17858=	XM_011535178.3:c.409-17858A>G
RNF6 transcript variant X14	XM_047430498.1:c.409-17858=	XM_047430498.1:c.409-17858A>G
RNF6 transcript variant X15	XM_047430499.1:c.409-17858=	XM_047430499.1:c.409-17858A>G
RNF6 transcript variant X16	XM_047430500.1:c.409-17858=	XM_047430500.1:c.409-17858A>G

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#.

40 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss644222	Aug 11, 2000 (83)
2	AFFY	ss76813307	Dec 07, 2007 (129)
3	KRIBB_YJKIM	ss104818418	Feb 04, 2009 (130)
4	ILLUMINA	ss160706345	Dec 01, 2009 (131)
5	1000GENOMES	ss211376631	Jul 14, 2010 (132)
6	1000GENOMES	ss226088097	Jul 14, 2010 (132)
7	1000GENOMES	ss236182193	Jul 15, 2010 (132)
8	ILLUMINA	ss482039675	Sep 08, 2015 (146)
9	TISHKOFF	ss563559108	Apr 25, 2013 (138)
10	EVA-GONL	ss990207787	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1078948326	Aug 21, 2014 (142)
12	1000GENOMES	ss1347546689	Aug 21, 2014 (142)
13	EVA_UK10K_ALSPAC	ss1629916845	Apr 01, 2015 (144)
14	EVA_DECODE	ss1642312579	Apr 01, 2015 (144)
15	EVA_UK10K_TWINSUK	ss1672910878	Apr 01, 2015 (144)
16	HAMMER_LAB	ss1807532167	Sep 08, 2015 (146)
17	WEILL_CORNELL_DGM	ss1933576599	Feb 12, 2016 (147)
18	ILLUMINA	ss1959488287	Feb 12, 2016 (147)
19	HUMAN_LONGEVITY	ss2194952195	Dec 20, 2016 (150)
20	GNOMAD	ss2917741935	Nov 08, 2017 (151)
21	SWEGEN	ss3010743467	Nov 08, 2017 (151)
22	ILLUMINA	ss3021492611	Nov 08, 2017 (151)
23	ILLUMINA	ss3636222880	Oct 12, 2018 (152)
24	ILLUMINA	ss3651877592	Oct 12, 2018 (152)
25	EVA_DECODE	ss3694953029	Jul 13, 2019 (153)
26	ILLUMINA	ss3725379900	Jul 13, 2019 (153)
27	ACPOP	ss3739594971	Jul 13, 2019 (153)
28	PAGE_CC	ss3771735327	Jul 13, 2019 (153)
29	KHV_HUMAN_GENOMES	ss3816583752	Jul 13, 2019 (153)
30	SGDP_PRJ	ss3879621758	Apr 27, 2020 (154)
31	TOPMED	ss4940378815	Apr 26, 2021 (155)
32	1000G_HIGH_COVERAGE	ss5293143459	Oct 16, 2022 (156)
33	EVA	ss5409689482	Oct 16, 2022 (156)
34	HUGCELL_USP	ss5487564693	Oct 16, 2022 (156)
35	EVA	ss5510912771	Oct 16, 2022 (156)
36	1000G_HIGH_COVERAGE	ss5591798973	Oct 16, 2022 (156)
37	SANFORD_IMAGENETICS	ss5654429043	Oct 16, 2022 (156)
38	EVA	ss5839240650	Oct 16, 2022 (156)
39	EVA	ss5924422334	Oct 16, 2022 (156)
40	EVA	ss5945833589	Oct 16, 2022 (156)
41	1000Genomes	NC_000013.10 - 26724447	Oct 12, 2018 (152)
42	1000Genomes_30x	NC_000013.11 - 26150309	Oct 16, 2022 (156)
43	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 26724447	Oct 12, 2018 (152)
44	Chileans	NC_000013.10 - 26724447	Apr 27, 2020 (154)
45	gnomAD - Genomes	NC_000013.11 - 26150309	Apr 26, 2021 (155)
46	Genome of the Netherlands Release 5	NC_000013.10 - 26724447	Apr 27, 2020 (154)
47	HapMap	NC_000013.11 - 26150309	Apr 27, 2020 (154)
48	Northern Sweden	NC_000013.10 - 26724447	Jul 13, 2019 (153)
49	The PAGE Study	NC_000013.11 - 26150309	Jul 13, 2019 (153)
50	Qatari	NC_000013.10 - 26724447	Apr 27, 2020 (154)
51	SGDP_PRJ	NC_000013.10 - 26724447	Apr 27, 2020 (154)
52	TopMed	NC_000013.11 - 26150309	Apr 26, 2021 (155)
53	UK 10K study - Twins	NC_000013.10 - 26724447	Oct 12, 2018 (152)
54	ALFA	NC_000013.11 - 26150309	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
ss211376631, ss1642312579	NC_000013.9:25622446:T:C	NC_000013.11:26150308:T:C	(self)
60392192, 33539211, 115475, 14964854, 12879836, 15618529, 31638738, 33539211, ss226088097, ss236182193, ss482039675, ss563559108, ss990207787, ss1078948326, ss1347546689, ss1629916845, ss1672910878, ss1807532167, ss1933576599, ss1959488287, ss2917741935, ss3010743467, ss3021492611, ss3636222880, ss3651877592, ss3739594971, ss3879621758, ss5409689482, ss5510912771, ss5654429043, ss5839240650, ss5945833589	NC_000013.10:26724446:T:C	NC_000013.11:26150308:T:C	(self)
79324908, 425868354, 950950, 956796, 155924473, 14343506989, ss2194952195, ss3694953029, ss3725379900, ss3771735327, ss3816583752, ss4940378815, ss5293143459, ss5487564693, ss5591798973, ss5924422334	NC_000013.11:26150308:T:C	NC_000013.11:26150308:T:C	(self)
ss644222, ss76813307, ss104818418, ss160706345	NT_024524.14:7704446:T:C	NC_000013.11:26150308: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 rs474808

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

rs474808