Name: rs111815298
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.

rs111815298

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:101544348 (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=0.135302 (35813/264690, TOPMED)
C=0.141850 (19880/140148, GnomAD)
C=0.32688 (9237/28258, 14KJPN) (+ 15 more)
C=0.18338 (3464/18890, ALFA)
C=0.32464 (5441/16760, 8.3KJPN)
C=0.1807 (1157/6404, 1000G_30x)
C=0.1863 (933/5008, 1000G)
C=0.2732 (1224/4480, Estonian)
C=0.1666 (642/3854, ALSPAC)
C=0.1775 (658/3708, TWINSUK)
C=0.3583 (1047/2922, KOREAN)
C=0.152 (152/998, GoNL)
C=0.217 (130/600, NorthernSweden)
C=0.181 (39/216, Qatari)
C=0.356 (77/216, Vietnamese)
T=0.399 (75/188, SGDP_PRJ)
T=0.50 (8/16, Siberian)
C=0.50 (8/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RNF20 : 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	18890	T=0.81662	C=0.18338
European	Sub	14286	T=0.78468	C=0.21532
African	Sub	2946	T=0.9566	C=0.0434
African Others	Sub	114	T=0.974	C=0.026
African American	Sub	2832	T=0.9559	C=0.0441
Asian	Sub	112	T=0.670	C=0.330
East Asian	Sub	86	T=0.64	C=0.36
Other Asian	Sub	26	T=0.77	C=0.23
Latin American 1	Sub	146	T=0.877	C=0.123
Latin American 2	Sub	610	T=0.893	C=0.107
South Asian	Sub	98	T=0.72	C=0.28
Other	Sub	692	T=0.837	C=0.163

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=0.864698	C=0.135302
gnomAD - Genomes	Global	Study-wide	140148	T=0.858150	C=0.141850
gnomAD - Genomes	European	Sub	75884	T=0.81078	C=0.18922
gnomAD - Genomes	African	Sub	42032	T=0.95963	C=0.04037
gnomAD - Genomes	American	Sub	13638	T=0.87293	C=0.12707
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.8084	C=0.1916
gnomAD - Genomes	East Asian	Sub	3120	T=0.6385	C=0.3615
gnomAD - Genomes	Other	Sub	2154	T=0.8482	C=0.1518
14KJPN	JAPANESE	Study-wide	28258	T=0.67312	C=0.32688
Allele Frequency Aggregator	Total	Global	18890	T=0.81662	C=0.18338
Allele Frequency Aggregator	European	Sub	14286	T=0.78468	C=0.21532
Allele Frequency Aggregator	African	Sub	2946	T=0.9566	C=0.0434
Allele Frequency Aggregator	Other	Sub	692	T=0.837	C=0.163
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.893	C=0.107
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.877	C=0.123
Allele Frequency Aggregator	Asian	Sub	112	T=0.670	C=0.330
Allele Frequency Aggregator	South Asian	Sub	98	T=0.72	C=0.28
8.3KJPN	JAPANESE	Study-wide	16760	T=0.67536	C=0.32464
1000Genomes_30x	Global	Study-wide	6404	T=0.8193	C=0.1807
1000Genomes_30x	African	Sub	1786	T=0.9966	C=0.0034
1000Genomes_30x	Europe	Sub	1266	T=0.7978	C=0.2022
1000Genomes_30x	South Asian	Sub	1202	T=0.6864	C=0.3136
1000Genomes_30x	East Asian	Sub	1170	T=0.6333	C=0.3667
1000Genomes_30x	American	Sub	980	T=0.909	C=0.091
1000Genomes	Global	Study-wide	5008	T=0.8137	C=0.1863
1000Genomes	African	Sub	1322	T=0.9962	C=0.0038
1000Genomes	East Asian	Sub	1008	T=0.6419	C=0.3581
1000Genomes	Europe	Sub	1006	T=0.8042	C=0.1958
1000Genomes	South Asian	Sub	978	T=0.684	C=0.316
1000Genomes	American	Sub	694	T=0.912	C=0.088
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.7268	C=0.2732
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8334	C=0.1666
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8225	C=0.1775
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.6417	C=0.3583
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.848	C=0.152
Northern Sweden	ACPOP	Study-wide	600	T=0.783	C=0.217
Qatari	Global	Study-wide	216	T=0.819	C=0.181
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.644	C=0.356
SGDP_PRJ	Global	Study-wide	188	T=0.399	C=0.601
Siberian	Global	Study-wide	16	T=0.50	C=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 9	NC_000009.12:g.101544348T>C
GRCh37.p13 chr 9	NC_000009.11:g.104306630T>C
RNF20 RefSeqGene	NG_047002.1:g.15500T>C

Gene: RNF20, ring finger protein 20 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RNF20 transcript	NM_019592.7:c.629-419T>C	N/A	Intron Variant
RNF20 transcript variant X1	XM_011518862.2:c.629-419T… XM_011518862.2:c.629-419T>C	N/A	Intron Variant
RNF20 transcript variant X2	XM_047423594.1:c.629-419T… XM_047423594.1:c.629-419T>C	N/A	Intron 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 9	NC_000009.12:g.101544348=	NC_000009.12:g.101544348T>C
GRCh37.p13 chr 9	NC_000009.11:g.104306630=	NC_000009.11:g.104306630T>C
RNF20 RefSeqGene	NG_047002.1:g.15500=	NG_047002.1:g.15500T>C
RNF20 transcript	NM_019592.6:c.629-419=	NM_019592.6:c.629-419T>C
RNF20 transcript	NM_019592.7:c.629-419=	NM_019592.7:c.629-419T>C
RNF20 transcript variant X1	XM_011518862.2:c.629-419=	XM_011518862.2:c.629-419T>C
RNF20 transcript variant X2	XM_047423594.1:c.629-419=	XM_047423594.1:c.629-419T>C

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#.

46 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	COMPLETE_GENOMICS	ss164538501	Jul 04, 2010 (132)
2	1000GENOMES	ss234906937	Jul 15, 2010 (132)
3	1000GENOMES	ss241665402	Jul 15, 2010 (132)
4	GMI	ss280336053	May 04, 2012 (137)
5	SSMP	ss656025163	Apr 25, 2013 (138)
6	EVA-GONL	ss986810631	Aug 21, 2014 (142)
7	JMKIDD_LAB	ss1076482353	Aug 21, 2014 (142)
8	1000GENOMES	ss1334824434	Aug 21, 2014 (142)
9	DDI	ss1431911435	Apr 01, 2015 (144)
10	EVA_DECODE	ss1596446927	Apr 01, 2015 (144)
11	EVA_UK10K_ALSPAC	ss1623223072	Apr 01, 2015 (144)
12	EVA_UK10K_TWINSUK	ss1666217105	Apr 01, 2015 (144)
13	WEILL_CORNELL_DGM	ss1930124665	Feb 12, 2016 (147)
14	JJLAB	ss2025780261	Sep 14, 2016 (149)
15	USC_VALOUEV	ss2154009065	Dec 20, 2016 (150)
16	HUMAN_LONGEVITY	ss2313121173	Dec 20, 2016 (150)
17	SYSTEMSBIOZJU	ss2627358372	Nov 08, 2017 (151)
18	GRF	ss2709883315	Nov 08, 2017 (151)
19	GNOMAD	ss2881432844	Nov 08, 2017 (151)
20	SWEGEN	ss3005333415	Nov 08, 2017 (151)
21	BIOINF_KMB_FNS_UNIBA	ss3026670968	Nov 08, 2017 (151)
22	CSHL	ss3348783509	Nov 08, 2017 (151)
23	EGCUT_WGS	ss3672868905	Jul 13, 2019 (153)
24	EVA_DECODE	ss3724438877	Jul 13, 2019 (153)
25	ACPOP	ss3736735290	Jul 13, 2019 (153)
26	EVA	ss3769491930	Jul 13, 2019 (153)
27	KHV_HUMAN_GENOMES	ss3812657535	Jul 13, 2019 (153)
28	EVA	ss3831776540	Apr 26, 2020 (154)
29	EVA	ss3839416441	Apr 26, 2020 (154)
30	EVA	ss3844880439	Apr 26, 2020 (154)
31	SGDP_PRJ	ss3872741065	Apr 26, 2020 (154)
32	KRGDB	ss3920580296	Apr 26, 2020 (154)
33	TOPMED	ss4830121303	Apr 26, 2021 (155)
34	TOMMO_GENOMICS	ss5194584500	Apr 26, 2021 (155)
35	1000G_HIGH_COVERAGE	ss5281626405	Oct 13, 2022 (156)
36	EVA	ss5389240591	Oct 13, 2022 (156)
37	HUGCELL_USP	ss5477546182	Oct 13, 2022 (156)
38	EVA	ss5509791027	Oct 13, 2022 (156)
39	1000G_HIGH_COVERAGE	ss5574409278	Oct 13, 2022 (156)
40	SANFORD_IMAGENETICS	ss5647950845	Oct 13, 2022 (156)
41	TOMMO_GENOMICS	ss5738907326	Oct 13, 2022 (156)
42	YY_MCH	ss5810864626	Oct 13, 2022 (156)
43	EVA	ss5829528598	Oct 13, 2022 (156)
44	EVA	ss5856867565	Oct 13, 2022 (156)
45	EVA	ss5917387497	Oct 13, 2022 (156)
46	EVA	ss5977144214	Oct 13, 2022 (156)
47	1000Genomes	NC_000009.11 - 104306630	Oct 12, 2018 (152)
48	1000Genomes_30x	NC_000009.12 - 101544348	Oct 13, 2022 (156)
49	The Avon Longitudinal Study of Parents and Children	NC_000009.11 - 104306630	Oct 12, 2018 (152)
50	Genetic variation in the Estonian population	NC_000009.11 - 104306630	Oct 12, 2018 (152)
51	gnomAD - Genomes	NC_000009.12 - 101544348	Apr 26, 2021 (155)
52	Genome of the Netherlands Release 5	NC_000009.11 - 104306630	Apr 26, 2020 (154)
53	KOREAN population from KRGDB	NC_000009.11 - 104306630	Apr 26, 2020 (154)
54	Northern Sweden	NC_000009.11 - 104306630	Jul 13, 2019 (153)
55	Qatari	NC_000009.11 - 104306630	Apr 26, 2020 (154)
56	SGDP_PRJ	NC_000009.11 - 104306630	Apr 26, 2020 (154)
57	Siberian	NC_000009.11 - 104306630	Apr 26, 2020 (154)
58	8.3KJPN	NC_000009.11 - 104306630	Apr 26, 2021 (155)
59	14KJPN	NC_000009.12 - 101544348	Oct 13, 2022 (156)
60	TopMed	NC_000009.12 - 101544348	Apr 26, 2021 (155)
61	UK 10K study - Twins	NC_000009.11 - 104306630	Oct 12, 2018 (152)
62	A Vietnamese Genetic Variation Database	NC_000009.11 - 104306630	Jul 13, 2019 (153)
63	ALFA	NC_000009.12 - 101544348	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
ss164538501, ss280336053, ss1596446927	NC_000009.10:103346450:T:C	NC_000009.12:101544347:T:C	(self)
47119415, 26175007, 18607153, 11680381, 27757690, 10020155, 12166595, 24758045, 6525419, 52553807, 26175007, 5813636, ss234906937, ss241665402, ss656025163, ss986810631, ss1076482353, ss1334824434, ss1431911435, ss1623223072, ss1666217105, ss1930124665, ss2025780261, ss2154009065, ss2627358372, ss2709883315, ss2881432844, ss3005333415, ss3348783509, ss3672868905, ss3736735290, ss3769491930, ss3831776540, ss3839416441, ss3872741065, ss3920580296, ss5194584500, ss5389240591, ss5509791027, ss5647950845, ss5829528598, ss5977144214	NC_000009.11:104306629:T:C	NC_000009.12:101544347:T:C	(self)
61935213, 333113673, 72744430, 667498864, 15149166015, ss2313121173, ss3026670968, ss3724438877, ss3812657535, ss3844880439, ss4830121303, ss5281626405, ss5477546182, ss5574409278, ss5738907326, ss5810864626, ss5856867565, ss5917387497	NC_000009.12:101544347:T:C	NC_000009.12:101544347: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 rs111815298

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

rs111815298