Name: rs17081170
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.

rs17081170

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:24790223 (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: G=0.146927 (38890/264690, TOPMED)
G=0.06069 (931/15340, ALFA)
G=0.1045 (669/6404, 1000G_30x) (+ 10 more)
G=0.1040 (521/5008, 1000G)
G=0.1183 (530/4480, Estonian)
G=0.155 (155/998, GoNL)
G=0.132 (79/600, NorthernSweden)
G=0.106 (35/330, HapMap)
G=0.287 (62/216, Qatari)
C=0.426 (46/108, SGDP_PRJ)
G=0.15 (6/40, GENOME_DK)
C=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)

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	15340	C=0.93931	A=0.00000, G=0.06069
European	Sub	11966	C=0.92621	A=0.00000, G=0.07379
African	Sub	2048	C=0.9902	A=0.0000, G=0.0098
African Others	Sub	78	C=0.96	A=0.00, G=0.04
African American	Sub	1970	C=0.9914	A=0.0000, G=0.0086
Asian	Sub	112	C=1.000	A=0.000, G=0.000
East Asian	Sub	86	C=1.00	A=0.00, G=0.00
Other Asian	Sub	26	C=1.00	A=0.00, G=0.00
Latin American 1	Sub	110	C=1.000	A=0.000, G=0.000
Latin American 2	Sub	472	C=1.000	A=0.000, G=0.000
South Asian	Sub	84	C=1.00	A=0.00, G=0.00
Other	Sub	548	C=0.949	A=0.000, G=0.051

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=0.853073	G=0.146927
Allele Frequency Aggregator	Total	Global	15340	C=0.93931	A=0.00000, G=0.06069
Allele Frequency Aggregator	European	Sub	11966	C=0.92621	A=0.00000, G=0.07379
Allele Frequency Aggregator	African	Sub	2048	C=0.9902	A=0.0000, G=0.0098
Allele Frequency Aggregator	Other	Sub	548	C=0.949	A=0.000, G=0.051
Allele Frequency Aggregator	Latin American 2	Sub	472	C=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	110	C=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	South Asian	Sub	84	C=1.00	A=0.00, G=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.8955	G=0.1045
1000Genomes_30x	African	Sub	1786	C=0.8522	G=0.1478
1000Genomes_30x	Europe	Sub	1266	C=0.8428	G=0.1572
1000Genomes_30x	South Asian	Sub	1202	C=0.9160	G=0.0840
1000Genomes_30x	East Asian	Sub	1170	C=0.9991	G=0.0009
1000Genomes_30x	American	Sub	980	C=0.894	G=0.106
1000Genomes	Global	Study-wide	5008	C=0.8960	G=0.1040
1000Genomes	African	Sub	1322	C=0.8495	G=0.1505
1000Genomes	East Asian	Sub	1008	C=0.9990	G=0.0010
1000Genomes	Europe	Sub	1006	C=0.8400	G=0.1600
1000Genomes	South Asian	Sub	978	C=0.911	G=0.089
1000Genomes	American	Sub	694	C=0.895	G=0.105
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8817	G=0.1183
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.845	G=0.155
Northern Sweden	ACPOP	Study-wide	600	C=0.868	G=0.132
HapMap	Global	Study-wide	330	C=0.894	G=0.106
HapMap	African	Sub	120	C=0.883	G=0.117
HapMap	American	Sub	120	C=0.825	G=0.175
HapMap	Asian	Sub	90	C=1.00	G=0.00
Qatari	Global	Study-wide	216	C=0.713	G=0.287
SGDP_PRJ	Global	Study-wide	108	C=0.426	G=0.574
The Danish reference pan genome	Danish	Study-wide	40	C=0.85	G=0.15
Siberian	Global	Study-wide	2	C=0.5	G=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.24790223C>A
GRCh38.p14 chr 13	NC_000013.11:g.24790223C>G
GRCh37.p13 chr 13	NC_000013.10:g.25364361C>A
GRCh37.p13 chr 13	NC_000013.10:g.25364361C>G

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

Molecule type	Change	Amino acid[Codon]	SO Term
RNF17 transcript variant 2	NM_001184993.2:c.935+451C… NM_001184993.2:c.935+451C>A	N/A	Intron Variant
RNF17 transcript variant 1	NM_031277.3:c.935+451C>A	N/A	Intron Variant
RNF17 transcript variant X5	XM_006719846.4:c.995+451C… XM_006719846.4:c.995+451C>A	N/A	Intron Variant
RNF17 transcript variant X6	XM_006719849.3:c.935+451C… XM_006719849.3:c.935+451C>A	N/A	Intron Variant
RNF17 transcript variant X1	XM_011535152.3:c.1016+451… XM_011535152.3:c.1016+451C>A	N/A	Intron Variant
RNF17 transcript variant X3	XM_011535155.3:c.1016+451… XM_011535155.3:c.1016+451C>A	N/A	Intron Variant
RNF17 transcript variant X2	XM_011535156.3:c.1016+451… XM_011535156.3:c.1016+451C>A	N/A	Intron Variant
RNF17 transcript variant X4	XM_011535157.3:c.1016+451… XM_011535157.3:c.1016+451C>A	N/A	Intron Variant
RNF17 transcript variant X7	XM_011535158.3:c.1016+451… XM_011535158.3:c.1016+451C>A	N/A	Intron Variant
RNF17 transcript variant X8	XM_011535159.3:c.1016+451… XM_011535159.3:c.1016+451C>A	N/A	Intron Variant
RNF17 transcript variant X9	XM_011535160.3:c.1016+451… XM_011535160.3:c.1016+451C>A	N/A	Intron Variant
RNF17 transcript variant X12	XM_011535162.2:c.413+451C… XM_011535162.2:c.413+451C>A	N/A	Intron Variant
RNF17 transcript variant X10	XM_017020676.2:c.752+451C… XM_017020676.2:c.752+451C>A	N/A	Intron Variant
RNF17 transcript variant X15	XM_047430486.1:c.1016+451… XM_047430486.1:c.1016+451C>A	N/A	Intron Variant
RNF17 transcript variant X11	XM_047430488.1:c.512+451C… XM_047430488.1:c.512+451C>A	N/A	Intron 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

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.24790223=	NC_000013.11:g.24790223C>A	NC_000013.11:g.24790223C>G
GRCh37.p13 chr 13	NC_000013.10:g.25364361=	NC_000013.10:g.25364361C>A	NC_000013.10:g.25364361C>G
RNF17 transcript variant 2	NM_001184993.1:c.935+451=	NM_001184993.1:c.935+451C>A	NM_001184993.1:c.935+451C>G
RNF17 transcript variant 2	NM_001184993.2:c.935+451=	NM_001184993.2:c.935+451C>A	NM_001184993.2:c.935+451C>G
RNF17 transcript variant 1	NM_031277.2:c.935+451=	NM_031277.2:c.935+451C>A	NM_031277.2:c.935+451C>G
RNF17 transcript variant 1	NM_031277.3:c.935+451=	NM_031277.3:c.935+451C>A	NM_031277.3:c.935+451C>G
RNF17 transcript variant X1	XM_005266472.1:c.995+451=	XM_005266472.1:c.995+451C>A	XM_005266472.1:c.995+451C>G
RNF17 transcript variant X2	XM_005266473.1:c.995+451=	XM_005266473.1:c.995+451C>A	XM_005266473.1:c.995+451C>G
RNF17 transcript variant X3	XM_005266474.1:c.752+451=	XM_005266474.1:c.752+451C>A	XM_005266474.1:c.752+451C>G
RNF17 transcript variant X5	XM_006719846.4:c.995+451=	XM_006719846.4:c.995+451C>A	XM_006719846.4:c.995+451C>G
RNF17 transcript variant X6	XM_006719849.3:c.935+451=	XM_006719849.3:c.935+451C>A	XM_006719849.3:c.935+451C>G
RNF17 transcript variant X1	XM_011535152.3:c.1016+451=	XM_011535152.3:c.1016+451C>A	XM_011535152.3:c.1016+451C>G
RNF17 transcript variant X3	XM_011535155.3:c.1016+451=	XM_011535155.3:c.1016+451C>A	XM_011535155.3:c.1016+451C>G
RNF17 transcript variant X2	XM_011535156.3:c.1016+451=	XM_011535156.3:c.1016+451C>A	XM_011535156.3:c.1016+451C>G
RNF17 transcript variant X4	XM_011535157.3:c.1016+451=	XM_011535157.3:c.1016+451C>A	XM_011535157.3:c.1016+451C>G
RNF17 transcript variant X7	XM_011535158.3:c.1016+451=	XM_011535158.3:c.1016+451C>A	XM_011535158.3:c.1016+451C>G
RNF17 transcript variant X8	XM_011535159.3:c.1016+451=	XM_011535159.3:c.1016+451C>A	XM_011535159.3:c.1016+451C>G
RNF17 transcript variant X9	XM_011535160.3:c.1016+451=	XM_011535160.3:c.1016+451C>A	XM_011535160.3:c.1016+451C>G
RNF17 transcript variant X12	XM_011535162.2:c.413+451=	XM_011535162.2:c.413+451C>A	XM_011535162.2:c.413+451C>G
RNF17 transcript variant X10	XM_017020676.2:c.752+451=	XM_017020676.2:c.752+451C>A	XM_017020676.2:c.752+451C>G
RNF17 transcript variant X15	XM_047430486.1:c.1016+451=	XM_047430486.1:c.1016+451C>A	XM_047430486.1:c.1016+451C>G
RNF17 transcript variant X11	XM_047430488.1:c.512+451=	XM_047430488.1:c.512+451C>A	XM_047430488.1:c.512+451C>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#.

42 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss23437807	Sep 20, 2004 (123)
2	1000GENOMES	ss114422810	Jan 25, 2009 (130)
3	COMPLETE_GENOMICS	ss168980656	Jul 04, 2010 (132)
4	COMPLETE_GENOMICS	ss170887154	Jul 04, 2010 (132)
5	1000GENOMES	ss226081853	Jul 14, 2010 (132)
6	1000GENOMES	ss236177930	Jul 15, 2010 (132)
7	TISHKOFF	ss563552208	Apr 25, 2013 (138)
8	SSMP	ss659146503	Apr 25, 2013 (138)
9	EVA-GONL	ss990196150	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1078940030	Aug 21, 2014 (142)
11	1000GENOMES	ss1347505959	Aug 21, 2014 (142)
12	EVA_GENOME_DK	ss1576674894	Apr 01, 2015 (144)
13	EVA_DECODE	ss1642301469	Apr 01, 2015 (144)
14	WEILL_CORNELL_DGM	ss1933564576	Feb 12, 2016 (147)
15	GENOMED	ss1967735379	Jul 19, 2016 (147)
16	JJLAB	ss2027536866	Sep 14, 2016 (149)
17	USC_VALOUEV	ss2155900849	Dec 20, 2016 (150)
18	HUMAN_LONGEVITY	ss2194877019	Dec 20, 2016 (150)
19	GNOMAD	ss2917629960	Nov 08, 2017 (151)
20	SWEGEN	ss3010726246	Nov 08, 2017 (151)
21	BIOINF_KMB_FNS_UNIBA	ss3027583353	Nov 08, 2017 (151)
22	CSHL	ss3350366848	Nov 08, 2017 (151)
23	EGCUT_WGS	ss3677988961	Jul 13, 2019 (153)
24	EVA_DECODE	ss3694931836	Jul 13, 2019 (153)
25	ACPOP	ss3739585230	Jul 13, 2019 (153)
26	EVA	ss3751239615	Jul 13, 2019 (153)
27	PACBIO	ss3787405138	Jul 13, 2019 (153)
28	PACBIO	ss3792478940	Jul 13, 2019 (153)
29	PACBIO	ss3797362648	Jul 13, 2019 (153)
30	KHV_HUMAN_GENOMES	ss3816570510	Jul 13, 2019 (153)
31	EVA	ss3833450011	Apr 27, 2020 (154)
32	SGDP_PRJ	ss3879599649	Apr 27, 2020 (154)
33	TOPMED	ss4940039512	Apr 26, 2021 (155)
34	1000G_HIGH_COVERAGE	ss5293106857	Oct 16, 2022 (156)
35	EVA	ss5409625475	Oct 16, 2022 (156)
36	HUGCELL_USP	ss5487532487	Oct 16, 2022 (156)
37	EVA	ss5510908731	Oct 16, 2022 (156)
38	1000G_HIGH_COVERAGE	ss5591745944	Oct 16, 2022 (156)
39	SANFORD_IMAGENETICS	ss5654407365	Oct 16, 2022 (156)
40	EVA	ss5839226021	Oct 16, 2022 (156)
41	EVA	ss5924381400	Oct 16, 2022 (156)
42	EVA	ss5945812209	Oct 16, 2022 (156)
43	1000Genomes	NC_000013.10 - 25364361	Oct 12, 2018 (152)
44	1000Genomes_30x	NC_000013.11 - 24790223	Oct 16, 2022 (156)
45	Genetic variation in the Estonian population	NC_000013.10 - 25364361	Oct 12, 2018 (152)
46	The Danish reference pan genome	NC_000013.10 - 25364361	Apr 27, 2020 (154)
47	gnomAD - Genomes Submission ignored due to conflicting rows: Row 425587081 (NC_000013.11:24790222:C:A 2/139912) Row 425587082 (NC_000013.11:24790222:C:G 20879/139878)	-	Apr 26, 2021 (155)
48	gnomAD - Genomes Submission ignored due to conflicting rows: Row 425587081 (NC_000013.11:24790222:C:A 2/139912) Row 425587082 (NC_000013.11:24790222:C:G 20879/139878)	-	Apr 26, 2021 (155)
49	Genome of the Netherlands Release 5	NC_000013.10 - 25364361	Apr 27, 2020 (154)
50	HapMap	NC_000013.11 - 24790223	Apr 27, 2020 (154)
51	Northern Sweden	NC_000013.10 - 25364361	Jul 13, 2019 (153)
52	Qatari	NC_000013.10 - 25364361	Apr 27, 2020 (154)
53	SGDP_PRJ	NC_000013.10 - 25364361	Apr 27, 2020 (154)
54	Siberian	NC_000013.10 - 25364361	Apr 27, 2020 (154)
55	TopMed	NC_000013.11 - 24790223	Apr 26, 2021 (155)
56	ALFA	NC_000013.11 - 24790223	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
14095422351	NC_000013.11:24790222:C:A	NC_000013.11:24790222:C:A	(self)
ss114422810, ss168980656, ss170887154, ss1642301469	NC_000013.9:24262360:C:G	NC_000013.11:24790222:C:G	(self)
60349739, 23727209, 3221480, 14953580, 12870095, 15606506, 31616629, 8417203, ss226081853, ss236177930, ss563552208, ss659146503, ss990196150, ss1078940030, ss1347505959, ss1576674894, ss1933564576, ss1967735379, ss2027536866, ss2155900849, ss2917629960, ss3010726246, ss3350366848, ss3677988961, ss3739585230, ss3751239615, ss3787405138, ss3792478940, ss3797362648, ss3833450011, ss3879599649, ss5409625475, ss5510908731, ss5654407365, ss5839226021, ss5945812209	NC_000013.10:25364360:C:G	NC_000013.11:24790222:C:G	(self)
79271879, 948695, 155585170, 14095422351, ss2194877019, ss3027583353, ss3694931836, ss3816570510, ss4940039512, ss5293106857, ss5487532487, ss5591745944, ss5924381400	NC_000013.11:24790222:C:G	NC_000013.11:24790222:C:G	(self)
ss23437807	NT_024524.14:6344360:C:G	NC_000013.11:24790222: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 rs17081170

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

rs17081170