Name: rs3809337
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.

rs3809337

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:24763994 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.455091 (120458/264690, TOPMED)
C=0.450876 (63138/140034, GnomAD)
T=0.43520 (12298/28258, 14KJPN) (+ 15 more)
C=0.43531 (9933/22818, ALFA)
T=0.44171 (7403/16760, 8.3KJPN)
C=0.4494 (2878/6404, 1000G_30x)
C=0.4485 (2246/5008, 1000G)
C=0.3828 (1715/4480, Estonian)
C=0.4928 (1444/2930, KOREAN)
C=0.4815 (910/1890, HapMap)
C=0.416 (415/998, GoNL)
C=0.393 (236/600, NorthernSweden)
T=0.427 (228/534, MGP)
C=0.295 (124/420, SGDP_PRJ)
T=0.440 (95/216, Qatari)
C=0.311 (66/212, Vietnamese)
C=0.20 (10/50, Siberian)
C=0.47 (19/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RNF17 : 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	22818	C=0.43531	T=0.56469
European	Sub	16610	C=0.41824	T=0.58176
African	Sub	4114	C=0.4876	T=0.5124
African Others	Sub	148	C=0.459	T=0.541
African American	Sub	3966	C=0.4887	T=0.5113
Asian	Sub	124	C=0.387	T=0.613
East Asian	Sub	96	C=0.42	T=0.58
Other Asian	Sub	28	C=0.29	T=0.71
Latin American 1	Sub	168	C=0.458	T=0.542
Latin American 2	Sub	670	C=0.548	T=0.452
South Asian	Sub	98	C=0.44	T=0.56
Other	Sub	1034	C=0.4304	T=0.5696

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.455091	T=0.544909
gnomAD - Genomes	Global	Study-wide	140034	C=0.450876	T=0.549124
gnomAD - Genomes	European	Sub	75844	C=0.42220	T=0.57780
gnomAD - Genomes	African	Sub	41948	C=0.48808	T=0.51192
gnomAD - Genomes	American	Sub	13644	C=0.49707	T=0.50293
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.4846	T=0.5154
gnomAD - Genomes	East Asian	Sub	3126	C=0.4235	T=0.5765
gnomAD - Genomes	Other	Sub	2150	C=0.4312	T=0.5688
14KJPN	JAPANESE	Study-wide	28258	C=0.56480	T=0.43520
Allele Frequency Aggregator	Total	Global	22818	C=0.43531	T=0.56469
Allele Frequency Aggregator	European	Sub	16610	C=0.41824	T=0.58176
Allele Frequency Aggregator	African	Sub	4114	C=0.4876	T=0.5124
Allele Frequency Aggregator	Other	Sub	1034	C=0.4304	T=0.5696
Allele Frequency Aggregator	Latin American 2	Sub	670	C=0.548	T=0.452
Allele Frequency Aggregator	Latin American 1	Sub	168	C=0.458	T=0.542
Allele Frequency Aggregator	Asian	Sub	124	C=0.387	T=0.613
Allele Frequency Aggregator	South Asian	Sub	98	C=0.44	T=0.56
8.3KJPN	JAPANESE	Study-wide	16760	C=0.55829	T=0.44171
1000Genomes_30x	Global	Study-wide	6404	C=0.4494	T=0.5506
1000Genomes_30x	African	Sub	1786	C=0.4905	T=0.5095
1000Genomes_30x	Europe	Sub	1266	C=0.4052	T=0.5948
1000Genomes_30x	South Asian	Sub	1202	C=0.4426	T=0.5574
1000Genomes_30x	East Asian	Sub	1170	C=0.4026	T=0.5974
1000Genomes_30x	American	Sub	980	C=0.496	T=0.504
1000Genomes	Global	Study-wide	5008	C=0.4485	T=0.5515
1000Genomes	African	Sub	1322	C=0.5030	T=0.4970
1000Genomes	East Asian	Sub	1008	C=0.4028	T=0.5972
1000Genomes	Europe	Sub	1006	C=0.4085	T=0.5915
1000Genomes	South Asian	Sub	978	C=0.433	T=0.567
1000Genomes	American	Sub	694	C=0.491	T=0.509
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.3828	T=0.6172
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.4928	T=0.5072
HapMap	Global	Study-wide	1890	C=0.4815	T=0.5185
HapMap	American	Sub	768	C=0.438	T=0.562
HapMap	African	Sub	692	C=0.529	T=0.471
HapMap	Asian	Sub	254	C=0.531	T=0.469
HapMap	Europe	Sub	176	C=0.415	T=0.585
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.416	T=0.584
Northern Sweden	ACPOP	Study-wide	600	C=0.393	T=0.607
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.573	T=0.427
SGDP_PRJ	Global	Study-wide	420	C=0.295	T=0.705
Qatari	Global	Study-wide	216	C=0.560	T=0.440
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.311	T=0.689
Siberian	Global	Study-wide	50	C=0.20	T=0.80
The Danish reference pan genome	Danish	Study-wide	40	C=0.47	T=0.53

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.24763994C>T
GRCh37.p13 chr 13	NC_000013.10:g.25338132C>T

Gene: RNF17, ring finger protein 17 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RNF17 transcript variant 2	NM_001184993.2:c.	N/A	Genic Upstream Transcript Variant
RNF17 transcript variant 1	NM_031277.3:c.	N/A	Genic Upstream Transcript Variant
RNF17 transcript variant X1	XM_011535152.3:c.28-127C>T	N/A	Intron Variant
RNF17 transcript variant X3	XM_011535155.3:c.28-127C>T	N/A	Intron Variant
RNF17 transcript variant X2	XM_011535156.3:c.28-127C>T	N/A	Intron Variant
RNF17 transcript variant X4	XM_011535157.3:c.28-127C>T	N/A	Intron Variant
RNF17 transcript variant X7	XM_011535158.3:c.28-127C>T	N/A	Intron Variant
RNF17 transcript variant X8	XM_011535159.3:c.28-127C>T	N/A	Intron Variant
RNF17 transcript variant X9	XM_011535160.3:c.28-127C>T	N/A	Intron Variant
RNF17 transcript variant X15	XM_047430486.1:c.28-127C>T	N/A	Intron Variant
RNF17 transcript variant X5	XM_006719846.4:c.	N/A	Genic Upstream Transcript Variant
RNF17 transcript variant X6	XM_006719849.3:c.	N/A	Genic Upstream Transcript Variant
RNF17 transcript variant X12	XM_011535162.2:c.	N/A	Genic Upstream Transcript Variant
RNF17 transcript variant X13	XM_011535163.2:c.	N/A	Genic Upstream Transcript Variant
RNF17 transcript variant X14	XM_011535164.3:c.	N/A	Genic Upstream Transcript Variant
RNF17 transcript variant X10	XM_017020676.2:c.	N/A	Genic Upstream Transcript Variant
RNF17 transcript variant X11	XM_047430488.1:c.	N/A	Genic Upstream 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=	T
GRCh38.p14 chr 13	NC_000013.11:g.24763994=	NC_000013.11:g.24763994C>T
GRCh37.p13 chr 13	NC_000013.10:g.25338132=	NC_000013.10:g.25338132C>T
RNF17 transcript variant X1	XM_011535152.3:c.28-127=	XM_011535152.3:c.28-127C>T
RNF17 transcript variant X3	XM_011535155.3:c.28-127=	XM_011535155.3:c.28-127C>T
RNF17 transcript variant X2	XM_011535156.3:c.28-127=	XM_011535156.3:c.28-127C>T
RNF17 transcript variant X4	XM_011535157.3:c.28-127=	XM_011535157.3:c.28-127C>T
RNF17 transcript variant X7	XM_011535158.3:c.28-127=	XM_011535158.3:c.28-127C>T
RNF17 transcript variant X8	XM_011535159.3:c.28-127=	XM_011535159.3:c.28-127C>T
RNF17 transcript variant X9	XM_011535160.3:c.28-127=	XM_011535160.3:c.28-127C>T
RNF17 transcript variant X15	XM_047430486.1:c.28-127=	XM_047430486.1:c.28-127C>T

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#.

86 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss4995738	Aug 28, 2002 (107)
2	SC_SNP	ss13259790	Dec 05, 2003 (119)
3	CSHL-HAPMAP	ss16605609	Feb 27, 2004 (120)
4	CSHL-HAPMAP	ss17484089	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss19262314	Feb 27, 2004 (120)
6	SSAHASNP	ss21093266	Apr 05, 2004 (121)
7	PERLEGEN	ss24003815	Sep 20, 2004 (123)
8	ABI	ss43480959	Mar 13, 2006 (126)
9	PERLEGEN	ss69128359	May 17, 2007 (127)
10	ILLUMINA	ss75162500	Dec 06, 2007 (129)
11	BCMHGSC_JDW	ss89537742	Mar 24, 2008 (129)
12	BGI	ss106320214	Feb 04, 2009 (130)
13	1000GENOMES	ss112620520	Jan 25, 2009 (130)
14	1000GENOMES	ss114422480	Jan 25, 2009 (130)
15	ILLUMINA-UK	ss118389956	Feb 14, 2009 (130)
16	KRIBB_YJKIM	ss119464563	Dec 01, 2009 (131)
17	ENSEMBL	ss133486999	Dec 01, 2009 (131)
18	GMI	ss154541006	Dec 01, 2009 (131)
19	ENSEMBL	ss161582592	Dec 01, 2009 (131)
20	COMPLETE_GENOMICS	ss167720234	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss168979984	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss170886877	Jul 04, 2010 (132)
23	ILLUMINA	ss173648735	Jul 04, 2010 (132)
24	BUSHMAN	ss198976868	Jul 04, 2010 (132)
25	BCM-HGSC-SUB	ss208541452	Jul 04, 2010 (132)
26	1000GENOMES	ss226081762	Jul 14, 2010 (132)
27	1000GENOMES	ss236177850	Jul 15, 2010 (132)
28	1000GENOMES	ss242688327	Jul 15, 2010 (132)
29	BL	ss254857410	May 09, 2011 (134)
30	GMI	ss281640584	May 04, 2012 (137)
31	GMI	ss286668997	Apr 25, 2013 (138)
32	PJP	ss291558095	May 09, 2011 (134)
33	ILLUMINA	ss537198307	Sep 08, 2015 (146)
34	TISHKOFF	ss563552108	Apr 25, 2013 (138)
35	SSMP	ss659146385	Apr 25, 2013 (138)
36	EVA-GONL	ss990195974	Aug 21, 2014 (142)
37	JMKIDD_LAB	ss1078939894	Aug 21, 2014 (142)
38	1000GENOMES	ss1347505285	Aug 21, 2014 (142)
39	DDI	ss1427129509	Apr 01, 2015 (144)
40	EVA_GENOME_DK	ss1576674784	Apr 01, 2015 (144)
41	EVA_DECODE	ss1642301259	Apr 01, 2015 (144)
42	EVA_MGP	ss1711352657	Apr 01, 2015 (144)
43	EVA_SVP	ss1713375900	Apr 01, 2015 (144)
44	HAMMER_LAB	ss1807527355	Sep 08, 2015 (146)
45	WEILL_CORNELL_DGM	ss1933564425	Feb 12, 2016 (147)
46	GENOMED	ss1967735321	Jul 19, 2016 (147)
47	JJLAB	ss2027536748	Sep 14, 2016 (149)
48	USC_VALOUEV	ss2155900739	Dec 20, 2016 (150)
49	HUMAN_LONGEVITY	ss2194875521	Dec 20, 2016 (150)
50	SYSTEMSBIOZJU	ss2628255990	Nov 08, 2017 (151)
51	ILLUMINA	ss2635043339	Nov 08, 2017 (151)
52	GRF	ss2700272440	Nov 08, 2017 (151)
53	GNOMAD	ss2917627892	Nov 08, 2017 (151)
54	SWEGEN	ss3010725945	Nov 08, 2017 (151)
55	BIOINF_KMB_FNS_UNIBA	ss3027583287	Nov 08, 2017 (151)
56	CSHL	ss3350366765	Nov 08, 2017 (151)
57	ILLUMINA	ss3627022515	Oct 12, 2018 (152)
58	ILLUMINA	ss3638000416	Oct 12, 2018 (152)
59	ILLUMINA	ss3642991103	Oct 12, 2018 (152)
60	OMUKHERJEE_ADBS	ss3646451712	Oct 12, 2018 (152)
61	EGCUT_WGS	ss3677988614	Jul 13, 2019 (153)
62	EVA_DECODE	ss3694931472	Jul 13, 2019 (153)
63	ACPOP	ss3739585085	Jul 13, 2019 (153)
64	EVA	ss3751239395	Jul 13, 2019 (153)
65	KHV_HUMAN_GENOMES	ss3816570285	Jul 13, 2019 (153)
66	EVA	ss3833449897	Apr 27, 2020 (154)
67	EVA	ss3840300955	Apr 27, 2020 (154)
68	EVA	ss3845785438	Apr 27, 2020 (154)
69	SGDP_PRJ	ss3879599315	Apr 27, 2020 (154)
70	KRGDB	ss3928416891	Apr 27, 2020 (154)
71	EVA	ss4017622875	Apr 26, 2021 (155)
72	TOPMED	ss4940033018	Apr 26, 2021 (155)
73	TOMMO_GENOMICS	ss5209189826	Apr 26, 2021 (155)
74	1000G_HIGH_COVERAGE	ss5293106270	Oct 16, 2022 (156)
75	EVA	ss5409624415	Oct 16, 2022 (156)
76	HUGCELL_USP	ss5487531915	Oct 16, 2022 (156)
77	1000G_HIGH_COVERAGE	ss5591745066	Oct 16, 2022 (156)
78	SANFORD_IMAGENETICS	ss5654407040	Oct 16, 2022 (156)
79	TOMMO_GENOMICS	ss5760834767	Oct 16, 2022 (156)
80	EVA	ss5800182737	Oct 16, 2022 (156)
81	YY_MCH	ss5813952888	Oct 16, 2022 (156)
82	EVA	ss5839225772	Oct 16, 2022 (156)
83	EVA	ss5850648863	Oct 16, 2022 (156)
84	EVA	ss5924380711	Oct 16, 2022 (156)
85	EVA	ss5945811858	Oct 16, 2022 (156)
86	EVA	ss5980779881	Oct 16, 2022 (156)
87	1000Genomes	NC_000013.10 - 25338132	Oct 12, 2018 (152)
88	1000Genomes_30x	NC_000013.11 - 24763994	Oct 16, 2022 (156)
89	Genetic variation in the Estonian population	NC_000013.10 - 25338132	Oct 12, 2018 (152)
90	The Danish reference pan genome	NC_000013.10 - 25338132	Apr 27, 2020 (154)
91	gnomAD - Genomes	NC_000013.11 - 24763994	Apr 26, 2021 (155)
92	Genome of the Netherlands Release 5	NC_000013.10 - 25338132	Apr 27, 2020 (154)
93	HapMap	NC_000013.11 - 24763994	Apr 27, 2020 (154)
94	KOREAN population from KRGDB	NC_000013.10 - 25338132	Apr 27, 2020 (154)
95	Medical Genome Project healthy controls from Spanish population	NC_000013.10 - 25338132	Apr 27, 2020 (154)
96	Northern Sweden	NC_000013.10 - 25338132	Jul 13, 2019 (153)
97	Qatari	NC_000013.10 - 25338132	Apr 27, 2020 (154)
98	SGDP_PRJ	NC_000013.10 - 25338132	Apr 27, 2020 (154)
99	Siberian	NC_000013.10 - 25338132	Apr 27, 2020 (154)
100	8.3KJPN	NC_000013.10 - 25338132	Apr 26, 2021 (155)
101	14KJPN	NC_000013.11 - 24763994	Oct 16, 2022 (156)
102	TopMed	NC_000013.11 - 24763994	Apr 26, 2021 (155)
103	A Vietnamese Genetic Variation Database	NC_000013.10 - 25338132	Jul 13, 2019 (153)
104	ALFA	NC_000013.11 - 24763994	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
ss89537742, ss112620520, ss114422480, ss118389956, ss167720234, ss168979984, ss170886877, ss198976868, ss208541452, ss254857410, ss281640584, ss286668997, ss291558095, ss1642301259, ss1713375900, ss2635043339, ss3642991103	NC_000013.9:24236131:C:T	NC_000013.11:24763993:C:T	(self)
60349034, 23726862, 3221402, 14953404, 35594285, 468417, 12869950, 15606355, 31616295, 8417093, 67159133, 7434486, ss226081762, ss236177850, ss242688327, ss537198307, ss563552108, ss659146385, ss990195974, ss1078939894, ss1347505285, ss1427129509, ss1576674784, ss1711352657, ss1807527355, ss1933564425, ss1967735321, ss2027536748, ss2155900739, ss2628255990, ss2700272440, ss2917627892, ss3010725945, ss3350366765, ss3627022515, ss3638000416, ss3646451712, ss3677988614, ss3739585085, ss3751239395, ss3833449897, ss3840300955, ss3879599315, ss3928416891, ss4017622875, ss5209189826, ss5409624415, ss5654407040, ss5800182737, ss5839225772, ss5945811858, ss5980779881	NC_000013.10:25338131:C:T	NC_000013.11:24763993:C:T	(self)
79271001, 425581756, 948645, 94671871, 155578676, 9577844392, ss2194875521, ss3027583287, ss3694931472, ss3816570285, ss3845785438, ss4940033018, ss5293106270, ss5487531915, ss5591745066, ss5760834767, ss5813952888, ss5850648863, ss5924380711	NC_000013.11:24763993:C:T	NC_000013.11:24763993:C:T	(self)
ss13259790	NT_009799.12:6318131:C:T	NC_000013.11:24763993:C:T	(self)
ss16605609, ss17484089, ss19262314, ss21093266	NT_024524.13:6318131:C:T	NC_000013.11:24763993:C:T	(self)
ss4995738, ss24003815, ss43480959, ss69128359, ss75162500, ss106320214, ss119464563, ss133486999, ss154541006, ss161582592, ss173648735	NT_024524.14:6318131:C:T	NC_000013.11:24763993: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 rs3809337

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

rs3809337