Name: rs4638424
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.

rs4638424

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:26166602 (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: C=0.283785 (75115/264690, TOPMED)
C=0.274436 (38426/140018, GnomAD)
C=0.20139 (5691/28258, 14KJPN) (+ 17 more)
C=0.25079 (6006/23948, ALFA)
C=0.20119 (3372/16760, 8.3KJPN)
C=0.2870 (1838/6404, 1000G_30x)
C=0.2784 (1394/5008, 1000G)
C=0.1783 (799/4480, Estonian)
C=0.2065 (796/3854, ALSPAC)
C=0.1909 (708/3708, TWINSUK)
C=0.2171 (636/2930, KOREAN)
C=0.2014 (369/1832, Korea1K)
C=0.2879 (479/1664, HapMap)
C=0.206 (206/998, GoNL)
C=0.197 (118/600, NorthernSweden)
C=0.181 (93/514, SGDP_PRJ)
C=0.356 (77/216, Qatari)
C=0.213 (46/216, Vietnamese)
C=0.09 (5/54, Siberian)
C=0.17 (7/40, GENOME_DK)

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	23948	C=0.25079	T=0.74921
European	Sub	15668	C=0.20066	T=0.79934
African	Sub	3610	C=0.4019	T=0.5981
African Others	Sub	126	C=0.452	T=0.548
African American	Sub	3484	C=0.4001	T=0.5999
Asian	Sub	160	C=0.212	T=0.787
East Asian	Sub	102	C=0.255	T=0.745
Other Asian	Sub	58	C=0.14	T=0.86
Latin American 1	Sub	292	C=0.288	T=0.712
Latin American 2	Sub	2766	C=0.3171	T=0.6829
South Asian	Sub	110	C=0.191	T=0.809
Other	Sub	1342	C=0.2943	T=0.7057

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=0.283785	T=0.716215
gnomAD - Genomes	Global	Study-wide	140018	C=0.274436	T=0.725564
gnomAD - Genomes	European	Sub	75880	C=0.20995	T=0.79005
gnomAD - Genomes	African	Sub	41904	C=0.39538	T=0.60462
gnomAD - Genomes	American	Sub	13634	C=0.29008	T=0.70992
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.2151	T=0.7849
gnomAD - Genomes	East Asian	Sub	3130	C=0.2099	T=0.7901
gnomAD - Genomes	Other	Sub	2146	C=0.2796	T=0.7204
14KJPN	JAPANESE	Study-wide	28258	C=0.20139	T=0.79861
Allele Frequency Aggregator	Total	Global	23948	C=0.25079	T=0.74921
Allele Frequency Aggregator	European	Sub	15668	C=0.20066	T=0.79934
Allele Frequency Aggregator	African	Sub	3610	C=0.4019	T=0.5981
Allele Frequency Aggregator	Latin American 2	Sub	2766	C=0.3171	T=0.6829
Allele Frequency Aggregator	Other	Sub	1342	C=0.2943	T=0.7057
Allele Frequency Aggregator	Latin American 1	Sub	292	C=0.288	T=0.712
Allele Frequency Aggregator	Asian	Sub	160	C=0.212	T=0.787
Allele Frequency Aggregator	South Asian	Sub	110	C=0.191	T=0.809
8.3KJPN	JAPANESE	Study-wide	16760	C=0.20119	T=0.79881
1000Genomes_30x	Global	Study-wide	6404	C=0.2870	T=0.7130
1000Genomes_30x	African	Sub	1786	C=0.4244	T=0.5756
1000Genomes_30x	Europe	Sub	1266	C=0.2204	T=0.7796
1000Genomes_30x	South Asian	Sub	1202	C=0.1772	T=0.8228
1000Genomes_30x	East Asian	Sub	1170	C=0.2333	T=0.7667
1000Genomes_30x	American	Sub	980	C=0.321	T=0.679
1000Genomes	Global	Study-wide	5008	C=0.2784	T=0.7216
1000Genomes	African	Sub	1322	C=0.4213	T=0.5787
1000Genomes	East Asian	Sub	1008	C=0.2242	T=0.7758
1000Genomes	Europe	Sub	1006	C=0.2197	T=0.7803
1000Genomes	South Asian	Sub	978	C=0.180	T=0.820
1000Genomes	American	Sub	694	C=0.308	T=0.692
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.1783	T=0.8217
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.2065	T=0.7935
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.1909	T=0.8091
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.2171	G=0.0000, T=0.7829
Korean Genome Project	KOREAN	Study-wide	1832	C=0.2014	T=0.7986
HapMap	Global	Study-wide	1664	C=0.2879	T=0.7121
HapMap	American	Sub	770	C=0.279	T=0.721
HapMap	African	Sub	464	C=0.377	T=0.623
HapMap	Asian	Sub	254	C=0.213	T=0.787
HapMap	Europe	Sub	176	C=0.199	T=0.801
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.206	T=0.794
Northern Sweden	ACPOP	Study-wide	600	C=0.197	T=0.803
SGDP_PRJ	Global	Study-wide	514	C=0.181	T=0.819
Qatari	Global	Study-wide	216	C=0.356	T=0.644
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.213	T=0.787
Siberian	Global	Study-wide	54	C=0.09	T=0.91
The Danish reference pan genome	Danish	Study-wide	40	C=0.17	T=0.82

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.26166602C>G
GRCh38.p14 chr 13	NC_000013.11:g.26166602C>T
GRCh37.p13 chr 13	NC_000013.10:g.26740739C>G
GRCh37.p13 chr 13	NC_000013.10:g.26740739C>T
RNF6 RefSeqGene	NG_017042.2:g.60770G>C
RNF6 RefSeqGene	NG_017042.2:g.60770G>A

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

Molecule type	Change	Amino acid[Codon]	SO Term
RNF6 transcript variant 2	NM_183045.1:c.409-34151G>C	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.409-3415… XM_011535178.3:c.409-34151G>C	N/A	Intron Variant
RNF6 transcript variant X14	XM_047430498.1:c.409-3415… XM_047430498.1:c.409-34151G>C	N/A	Intron Variant
RNF6 transcript variant X15	XM_047430499.1:c.409-3415… XM_047430499.1:c.409-34151G>C	N/A	Intron Variant
RNF6 transcript variant X16	XM_047430500.1:c.409-3415… XM_047430500.1:c.409-34151G>C	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	C=	G	T
GRCh38.p14 chr 13	NC_000013.11:g.26166602=	NC_000013.11:g.26166602C>G	NC_000013.11:g.26166602C>T
GRCh37.p13 chr 13	NC_000013.10:g.26740739=	NC_000013.10:g.26740739C>G	NC_000013.10:g.26740739C>T
RNF6 RefSeqGene	NG_017042.2:g.60770=	NG_017042.2:g.60770G>C	NG_017042.2:g.60770G>A
RNF6 transcript variant 2	NM_183045.1:c.409-34151=	NM_183045.1:c.409-34151G>C	NM_183045.1:c.409-34151G>A
RNF6 transcript variant X13	XM_011535178.3:c.409-34151=	XM_011535178.3:c.409-34151G>C	XM_011535178.3:c.409-34151G>A
RNF6 transcript variant X14	XM_047430498.1:c.409-34151=	XM_047430498.1:c.409-34151G>C	XM_047430498.1:c.409-34151G>A
RNF6 transcript variant X15	XM_047430499.1:c.409-34151=	XM_047430499.1:c.409-34151G>C	XM_047430499.1:c.409-34151G>A
RNF6 transcript variant X16	XM_047430500.1:c.409-34151=	XM_047430500.1:c.409-34151G>C	XM_047430500.1:c.409-34151G>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#.

75 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss11310663	Jul 11, 2003 (126)
2	SC_SNP	ss13260337	Dec 05, 2003 (126)
3	CSHL-HAPMAP	ss16604106	Feb 27, 2004 (126)
4	CSHL-HAPMAP	ss19260856	Feb 27, 2004 (126)
5	SSAHASNP	ss21070045	Apr 05, 2004 (126)
6	AFFY	ss76515960	Dec 06, 2007 (129)
7	HGSV	ss78787042	Dec 06, 2007 (129)
8	BCMHGSC_JDW	ss89546108	Mar 24, 2008 (129)
9	1000GENOMES	ss112629553	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss118394057	Aug 21, 2014 (142)
11	COMPLETE_GENOMICS	ss167746472	Aug 21, 2014 (142)
12	COMPLETE_GENOMICS	ss169012740	Aug 21, 2014 (142)
13	COMPLETE_GENOMICS	ss170901952	Aug 21, 2014 (142)
14	BUSHMAN	ss198990538	Jul 04, 2010 (142)
15	BCM-HGSC-SUB	ss208682651	Aug 21, 2014 (142)
16	1000GENOMES	ss211376660	Jul 14, 2010 (132)
17	1000GENOMES	ss226088174	Jul 14, 2010 (132)
18	1000GENOMES	ss236182250	Jul 15, 2010 (132)
19	1000GENOMES	ss242692040	Jul 15, 2010 (132)
20	BL	ss254867274	May 09, 2011 (134)
21	GMI	ss281645700	May 04, 2012 (137)
22	GMI	ss286671407	Apr 25, 2013 (138)
23	PJP	ss291560585	May 09, 2011 (134)
24	TISHKOFF	ss563559204	Apr 25, 2013 (138)
25	SSMP	ss659154629	Apr 25, 2013 (138)
26	EVA-GONL	ss990207943	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1078948435	Aug 21, 2014 (142)
28	1000GENOMES	ss1347547155	Aug 21, 2014 (142)
29	DDI	ss1427133918	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1576681835	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1629917113	Apr 01, 2015 (144)
32	EVA_DECODE	ss1642312743	Apr 01, 2015 (144)
33	EVA_UK10K_TWINSUK	ss1672911146	Apr 01, 2015 (144)
34	EVA_SVP	ss1713376794	Apr 01, 2015 (144)
35	HAMMER_LAB	ss1807532245	Sep 08, 2015 (146)
36	WEILL_CORNELL_DGM	ss1933576745	Feb 12, 2016 (147)
37	GENOMED	ss1967738359	Jul 19, 2016 (147)
38	JJLAB	ss2027543356	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2155907494	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2194953181	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2628259537	Nov 08, 2017 (151)
42	GRF	ss2700279765	Nov 08, 2017 (151)
43	GNOMAD	ss2917743257	Nov 08, 2017 (151)
44	SWEGEN	ss3010743683	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3027586549	Nov 08, 2017 (151)
46	CSHL	ss3350372310	Nov 08, 2017 (151)
47	URBANLAB	ss3649991587	Oct 12, 2018 (152)
48	EGCUT_WGS	ss3678004775	Jul 13, 2019 (153)
49	EVA_DECODE	ss3694953303	Jul 13, 2019 (153)
50	ACPOP	ss3739595102	Jul 13, 2019 (153)
51	EVA	ss3751252658	Jul 13, 2019 (153)
52	PACBIO	ss3787408563	Jul 13, 2019 (153)
53	PACBIO	ss3792481978	Jul 13, 2019 (153)
54	PACBIO	ss3797365702	Jul 13, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3816583911	Jul 13, 2019 (153)
56	EVA	ss3833456115	Apr 27, 2020 (154)
57	EVA	ss3840304448	Apr 27, 2020 (154)
58	EVA	ss3845789037	Apr 27, 2020 (154)
59	SGDP_PRJ	ss3879622025	Apr 27, 2020 (154)
60	KRGDB	ss3928441250	Apr 27, 2020 (154)
61	KOGIC	ss3973232196	Apr 27, 2020 (154)
62	TOPMED	ss4940382897	Apr 26, 2021 (155)
63	TOMMO_GENOMICS	ss5209236704	Apr 26, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5293143926	Oct 16, 2022 (156)
65	EVA	ss5409690206	Oct 16, 2022 (156)
66	HUGCELL_USP	ss5487565097	Oct 16, 2022 (156)
67	EVA	ss5510912831	Oct 16, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5591799583	Oct 16, 2022 (156)
69	SANFORD_IMAGENETICS	ss5654429309	Oct 16, 2022 (156)
70	TOMMO_GENOMICS	ss5760894469	Oct 16, 2022 (156)
71	YY_MCH	ss5813962799	Oct 16, 2022 (156)
72	EVA	ss5839240837	Oct 16, 2022 (156)
73	EVA	ss5850654001	Oct 16, 2022 (156)
74	EVA	ss5924422815	Oct 16, 2022 (156)
75	EVA	ss5945833863	Oct 16, 2022 (156)
76	1000Genomes	NC_000013.10 - 26740739	Oct 12, 2018 (152)
77	1000Genomes_30x	NC_000013.11 - 26166602	Oct 16, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 26740739	Oct 12, 2018 (152)
79	Genetic variation in the Estonian population	NC_000013.10 - 26740739	Oct 12, 2018 (152)
80	The Danish reference pan genome	NC_000013.10 - 26740739	Apr 27, 2020 (154)
81	gnomAD - Genomes	NC_000013.11 - 26166602	Apr 26, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000013.10 - 26740739	Apr 27, 2020 (154)
83	HapMap	NC_000013.11 - 26166602	Apr 27, 2020 (154)
84	KOREAN population from KRGDB	NC_000013.10 - 26740739	Apr 27, 2020 (154)
85	Korean Genome Project	NC_000013.11 - 26166602	Apr 27, 2020 (154)
86	Northern Sweden	NC_000013.10 - 26740739	Jul 13, 2019 (153)
87	Qatari	NC_000013.10 - 26740739	Apr 27, 2020 (154)
88	SGDP_PRJ	NC_000013.10 - 26740739	Apr 27, 2020 (154)
89	Siberian	NC_000013.10 - 26740739	Apr 27, 2020 (154)
90	8.3KJPN	NC_000013.10 - 26740739	Apr 26, 2021 (155)
91	14KJPN	NC_000013.11 - 26166602	Oct 16, 2022 (156)
92	TopMed	NC_000013.11 - 26166602	Apr 26, 2021 (155)
93	UK 10K study - Twins	NC_000013.10 - 26740739	Oct 12, 2018 (152)
94	A Vietnamese Genetic Variation Database	NC_000013.10 - 26740739	Jul 13, 2019 (153)
95	ALFA	NC_000013.11 - 26166602	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)
rs7491015	Mar 10, 2006 (126)
rs77068209	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
35618644, ss3928441250	NC_000013.10:26740738:C:G	NC_000013.11:26166601:C:G	(self)
ss76515960, ss78787042, ss89546108, ss112629553, ss118394057, ss167746472, ss169012740, ss170901952, ss198990538, ss208682651, ss211376660, ss254867274, ss281645700, ss286671407, ss291560585, ss1642312743, ss1713376794	NC_000013.9:25638738:C:T	NC_000013.11:26166601:C:T	(self)
60392677, 33539519, 23743023, 3225987, 14965007, 35618644, 12879967, 15618675, 31639005, 8423848, 67206011, 33539519, 7440222, ss226088174, ss236182250, ss242692040, ss563559204, ss659154629, ss990207943, ss1078948435, ss1347547155, ss1427133918, ss1576681835, ss1629917113, ss1672911146, ss1807532245, ss1933576745, ss1967738359, ss2027543356, ss2155907494, ss2628259537, ss2700279765, ss2917743257, ss3010743683, ss3350372310, ss3678004775, ss3739595102, ss3751252658, ss3787408563, ss3792481978, ss3797365702, ss3833456115, ss3840304448, ss3879622025, ss3928441250, ss5209236704, ss5409690206, ss5510912831, ss5654429309, ss5839240837, ss5945833863	NC_000013.10:26740738:C:T	NC_000013.11:26166601:C:T	(self)
79325518, 425871634, 950991, 29610197, 94731573, 155928555, 6314487983, ss2194953181, ss3027586549, ss3649991587, ss3694953303, ss3816583911, ss3845789037, ss3973232196, ss4940382897, ss5293143926, ss5487565097, ss5591799583, ss5760894469, ss5813962799, ss5850654001, ss5924422815	NC_000013.11:26166601:C:T	NC_000013.11:26166601:C:T	(self)
ss11310663, ss13260337	NT_009799.12:7720738:C:T	NC_000013.11:26166601:C:T	(self)
ss16604106, ss19260856, ss21070045	NT_024524.13:7720738:C:T	NC_000013.11:26166601: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 rs4638424

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs4638424