Name: rs115505908
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.

rs115505908

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:24754178 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.042427 (11230/264690, TOPMED)
A=0.041102 (5600/136246, GnomAD)
A=0.00998 (282/28258, 14KJPN) (+ 11 more)
A=0.00351 (63/17938, ALFA)
A=0.00943 (158/16760, 8.3KJPN)
A=0.0156 (60/3854, ALSPAC)
A=0.0148 (55/3708, TWINSUK)
A=0.0116 (34/2922, KOREAN)
A=0.0104 (19/1832, Korea1K)
A=0.012 (7/600, NorthernSweden)
A=0.069 (15/216, Qatari)
A=0.05 (2/40, GENOME_DK)
T=0.50 (18/36, SGDP_PRJ)
A=0.50 (18/36, SGDP_PRJ)

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	17929	T=0.99649	A=0.00351
European	Sub	13981	T=0.99671	A=0.00329
African	Sub	2370	T=0.9962	A=0.0038
African Others	Sub	88	T=1.00	A=0.00
African American	Sub	2282	T=0.9961	A=0.0039
Asian	Sub	108	T=1.000	A=0.000
East Asian	Sub	82	T=1.00	A=0.00
Other Asian	Sub	26	T=1.00	A=0.00
Latin American 1	Sub	136	T=1.000	A=0.000
Latin American 2	Sub	592	T=1.000	A=0.000
South Asian	Sub	94	T=1.00	A=0.00
Other	Sub	648	T=0.988	A=0.012

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=0.957573	A=0.042427
gnomAD - Genomes	Global	Study-wide	136246	T=0.958898	A=0.041102
gnomAD - Genomes	European	Sub	73884	T=0.98113	A=0.01887
gnomAD - Genomes	African	Sub	40644	T=0.90628	A=0.09372
gnomAD - Genomes	American	Sub	13300	T=0.97955	A=0.02045
gnomAD - Genomes	Ashkenazi Jewish	Sub	3248	T=0.9880	A=0.0120
gnomAD - Genomes	East Asian	Sub	3088	T=0.9916	A=0.0084
gnomAD - Genomes	Other	Sub	2082	T=0.9712	A=0.0288
14KJPN	JAPANESE	Study-wide	28258	T=0.99002	A=0.00998
Allele Frequency Aggregator	Total	Global	17938	T=0.99599	A=0.00351
Allele Frequency Aggregator	European	Sub	13990	T=0.99607	A=0.00329
Allele Frequency Aggregator	African	Sub	2370	T=0.9962	A=0.0038
Allele Frequency Aggregator	Other	Sub	648	T=0.988	A=0.012
Allele Frequency Aggregator	Latin American 2	Sub	592	T=1.000	A=0.000
Allele Frequency Aggregator	Latin American 1	Sub	136	T=1.000	A=0.000
Allele Frequency Aggregator	Asian	Sub	108	T=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	94	T=1.00	A=0.00
8.3KJPN	JAPANESE	Study-wide	16760	T=0.99057	A=0.00943
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9844	A=0.0156
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9852	A=0.0148
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9884	A=0.0116
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9896	A=0.0104
Northern Sweden	ACPOP	Study-wide	600	T=0.988	A=0.012
Qatari	Global	Study-wide	216	T=0.931	A=0.069
The Danish reference pan genome	Danish	Study-wide	40	T=0.95	A=0.05
SGDP_PRJ	Global	Study-wide	36	T=0.50	A=0.50

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.24754178T>A
GRCh37.p13 chr 13	NC_000013.10:g.25328316T>A

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.-279+135… XM_011535152.3:c.-279+1352T>A	N/A	Intron Variant
RNF17 transcript variant X3	XM_011535155.3:c.-278-266… XM_011535155.3:c.-278-2661T>A	N/A	Intron Variant
RNF17 transcript variant X2	XM_011535156.3:c.-279+135… XM_011535156.3:c.-279+1352T>A	N/A	Intron Variant
RNF17 transcript variant X4	XM_011535157.3:c.-279+135… XM_011535157.3:c.-279+1352T>A	N/A	Intron Variant
RNF17 transcript variant X7	XM_011535158.3:c.-279+135… XM_011535158.3:c.-279+1352T>A	N/A	Intron Variant
RNF17 transcript variant X8	XM_011535159.3:c.-279+135… XM_011535159.3:c.-279+1352T>A	N/A	Intron Variant
RNF17 transcript variant X9	XM_011535160.3:c.-279+135… XM_011535160.3:c.-279+1352T>A	N/A	Intron Variant
RNF17 transcript variant X15	XM_047430486.1:c.-278-266… XM_047430486.1:c.-278-2661T>A	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	T=	A
GRCh38.p14 chr 13	NC_000013.11:g.24754178=	NC_000013.11:g.24754178T>A
GRCh37.p13 chr 13	NC_000013.10:g.25328316=	NC_000013.10:g.25328316T>A
RNF17 transcript variant X1	XM_011535152.3:c.-279+1352=	XM_011535152.3:c.-279+1352T>A
RNF17 transcript variant X3	XM_011535155.3:c.-278-2661=	XM_011535155.3:c.-278-2661T>A
RNF17 transcript variant X2	XM_011535156.3:c.-279+1352=	XM_011535156.3:c.-279+1352T>A
RNF17 transcript variant X4	XM_011535157.3:c.-279+1352=	XM_011535157.3:c.-279+1352T>A
RNF17 transcript variant X7	XM_011535158.3:c.-279+1352=	XM_011535158.3:c.-279+1352T>A
RNF17 transcript variant X8	XM_011535159.3:c.-279+1352=	XM_011535159.3:c.-279+1352T>A
RNF17 transcript variant X9	XM_011535160.3:c.-279+1352=	XM_011535160.3:c.-279+1352T>A
RNF17 transcript variant X15	XM_047430486.1:c.-278-2661=	XM_047430486.1:c.-278-2661T>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#.

24 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss226081718	Jul 14, 2010 (132)
2	EVA_GENOME_DK	ss1576674701	Apr 01, 2015 (144)
3	EVA_UK10K_ALSPAC	ss1629895045	Apr 01, 2015 (144)
4	EVA_UK10K_TWINSUK	ss1672889078	Apr 01, 2015 (144)
5	WEILL_CORNELL_DGM	ss1933564348	Feb 12, 2016 (147)
6	JJLAB	ss2027536700	Sep 14, 2016 (149)
7	HUMAN_LONGEVITY	ss2194874940	Dec 20, 2016 (150)
8	GRF	ss2700272371	Nov 08, 2017 (151)
9	SWEGEN	ss3010725823	Nov 08, 2017 (151)
10	ACPOP	ss3739585015	Jul 13, 2019 (153)
11	EVA	ss3751239297	Jul 13, 2019 (153)
12	SGDP_PRJ	ss3879599173	Apr 27, 2020 (154)
13	KRGDB	ss3928416730	Apr 27, 2020 (154)
14	KOGIC	ss3973213140	Apr 27, 2020 (154)
15	TOPMED	ss4940030684	Apr 26, 2021 (155)
16	TOMMO_GENOMICS	ss5209189493	Apr 26, 2021 (155)
17	1000G_HIGH_COVERAGE	ss5293106011	Oct 16, 2022 (156)
18	HUGCELL_USP	ss5487531691	Oct 16, 2022 (156)
19	SANFORD_IMAGENETICS	ss5654406900	Oct 16, 2022 (156)
20	TOMMO_GENOMICS	ss5760834374	Oct 16, 2022 (156)
21	YY_MCH	ss5813952814	Oct 16, 2022 (156)
22	EVA	ss5839225655	Oct 16, 2022 (156)
23	EVA	ss5924380421	Oct 16, 2022 (156)
24	EVA	ss5945811703	Oct 16, 2022 (156)
25	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 25328316	Oct 12, 2018 (152)
26	The Danish reference pan genome	NC_000013.10 - 25328316	Apr 27, 2020 (154)
27	gnomAD - Genomes	NC_000013.11 - 24754178	Apr 26, 2021 (155)
28	KOREAN population from KRGDB	NC_000013.10 - 25328316	Apr 27, 2020 (154)
29	Korean Genome Project	NC_000013.11 - 24754178	Apr 27, 2020 (154)
30	Northern Sweden	NC_000013.10 - 25328316	Jul 13, 2019 (153)
31	Qatari	NC_000013.10 - 25328316	Apr 27, 2020 (154)
32	SGDP_PRJ	NC_000013.10 - 25328316	Apr 27, 2020 (154)
33	8.3KJPN	NC_000013.10 - 25328316	Apr 26, 2021 (155)
34	14KJPN	NC_000013.11 - 24754178	Oct 16, 2022 (156)
35	TopMed	NC_000013.11 - 24754178	Apr 26, 2021 (155)
36	UK 10K study - Twins	NC_000013.10 - 25328316	Oct 12, 2018 (152)
37	ALFA	NC_000013.11 - 24754178	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
33515032, 3221356, 35594124, 12869880, 15606278, 31616153, 67158800, 33515032, ss226081718, ss1576674701, ss1629895045, ss1672889078, ss1933564348, ss2027536700, ss2700272371, ss3010725823, ss3739585015, ss3751239297, ss3879599173, ss3928416730, ss5209189493, ss5654406900, ss5839225655, ss5945811703	NC_000013.10:25328315:T:A	NC_000013.11:24754177:T:A	(self)
425579797, 29591141, 94671478, 155576342, 3243622674, ss2194874940, ss3973213140, ss4940030684, ss5293106011, ss5487531691, ss5760834374, ss5813952814, ss5924380421	NC_000013.11:24754177:T:A	NC_000013.11:24754177:T:A	(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 rs115505908

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

rs115505908