Name: rs149220464
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.

rs149220464

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:120551541 (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: T=0.037421 (9905/264690, TOPMED)
T=0.043583 (6091/139756, GnomAD)
T=0.00007 (2/28258, 14KJPN) (+ 14 more)
T=0.05043 (934/18520, ALFA)
T=0.00012 (2/16760, 8.3KJPN)
T=0.0395 (253/6404, 1000G_30x)
T=0.0411 (206/5008, 1000G)
T=0.0656 (294/4480, Estonian)
T=0.0602 (232/3854, ALSPAC)
T=0.0583 (216/3708, TWINSUK)
T=0.0007 (2/2922, KOREAN)
T=0.0005 (1/1832, Korea1K)
T=0.054 (54/998, GoNL)
T=0.050 (30/600, NorthernSweden)
T=0.074 (16/216, Qatari)
T=0.05 (2/40, GENOME_DK)
C=0.47 (17/36, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RNF10 : 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	18520	C=0.94957	T=0.05043
European	Sub	14152	C=0.94036	T=0.05964
African	Sub	2898	C=0.9879	T=0.0121
African Others	Sub	114	C=1.000	T=0.000
African American	Sub	2784	C=0.9874	T=0.0126
Asian	Sub	112	C=0.991	T=0.009
East Asian	Sub	86	C=0.99	T=0.01
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	146	C=0.945	T=0.055
Latin American 2	Sub	610	C=0.970	T=0.030
South Asian	Sub	98	C=0.87	T=0.13
Other	Sub	504	C=0.970	T=0.030

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=0.962579	T=0.037421
gnomAD - Genomes	Global	Study-wide	139756	C=0.956417	T=0.043583
gnomAD - Genomes	European	Sub	75720	C=0.93623	T=0.06377
gnomAD - Genomes	African	Sub	41868	C=0.98918	T=0.01082
gnomAD - Genomes	American	Sub	13588	C=0.96129	T=0.03871
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	C=0.9418	T=0.0582
gnomAD - Genomes	East Asian	Sub	3126	C=0.9974	T=0.0026
gnomAD - Genomes	Other	Sub	2138	C=0.9616	T=0.0384
14KJPN	JAPANESE	Study-wide	28258	C=0.99993	T=0.00007
Allele Frequency Aggregator	Total	Global	18520	C=0.94957	T=0.05043
Allele Frequency Aggregator	European	Sub	14152	C=0.94036	T=0.05964
Allele Frequency Aggregator	African	Sub	2898	C=0.9879	T=0.0121
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.970	T=0.030
Allele Frequency Aggregator	Other	Sub	504	C=0.970	T=0.030
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.945	T=0.055
Allele Frequency Aggregator	Asian	Sub	112	C=0.991	T=0.009
Allele Frequency Aggregator	South Asian	Sub	98	C=0.87	T=0.13
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99988	T=0.00012
1000Genomes_30x	Global	Study-wide	6404	C=0.9605	T=0.0395
1000Genomes_30x	African	Sub	1786	C=0.9989	T=0.0011
1000Genomes_30x	Europe	Sub	1266	C=0.9384	T=0.0616
1000Genomes_30x	South Asian	Sub	1202	C=0.8985	T=0.1015
1000Genomes_30x	East Asian	Sub	1170	C=0.9906	T=0.0094
1000Genomes_30x	American	Sub	980	C=0.959	T=0.041
1000Genomes	Global	Study-wide	5008	C=0.9589	T=0.0411
1000Genomes	African	Sub	1322	C=0.9985	T=0.0015
1000Genomes	East Asian	Sub	1008	C=0.9901	T=0.0099
1000Genomes	Europe	Sub	1006	C=0.9394	T=0.0606
1000Genomes	South Asian	Sub	978	C=0.896	T=0.104
1000Genomes	American	Sub	694	C=0.955	T=0.045
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9344	T=0.0656
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9398	T=0.0602
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9417	T=0.0583
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9993	T=0.0007
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9995	T=0.0005
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.946	T=0.054
Northern Sweden	ACPOP	Study-wide	600	C=0.950	T=0.050
Qatari	Global	Study-wide	216	C=0.926	T=0.074
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05
SGDP_PRJ	Global	Study-wide	36	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 12	NC_000012.12:g.120551541C>T
GRCh37.p13 chr 12	NC_000012.11:g.120989344C>T

Gene: RNF10, ring finger protein 10 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RNF10 transcript variant 2	NM_001330474.2:c.355-958C… NM_001330474.2:c.355-958C>T	N/A	Intron Variant
RNF10 transcript variant 1	NM_014868.5:c.355-958C>T	N/A	Intron Variant
RNF10 transcript variant X1	XM_005254013.3:c.205-958C… XM_005254013.3:c.205-958C>T	N/A	Intron Variant
RNF10 transcript variant X2	XM_017020282.2:c.205-958C… XM_017020282.2:c.205-958C>T	N/A	Intron Variant
RNF10 transcript variant X5	XM_017020283.3:c.355-958C… XM_017020283.3:c.355-958C>T	N/A	Intron Variant
RNF10 transcript variant X3	XM_047429937.1:c.355-958C… XM_047429937.1:c.355-958C>T	N/A	Intron Variant
RNF10 transcript variant X4	XM_047429938.1:c.355-958C… XM_047429938.1:c.355-958C>T	N/A	Intron Variant
RNF10 transcript variant X6	XM_047429939.1:c.355-958C… XM_047429939.1:c.355-958C>T	N/A	Intron Variant
RNF10 transcript variant X7	XM_047429940.1:c.355-958C… XM_047429940.1:c.355-958C>T	N/A	Intron Variant
RNF10 transcript variant X8	XM_047429941.1:c.355-958C… XM_047429941.1:c.355-958C>T	N/A	Intron Variant
RNF10 transcript variant X9	XM_047429942.1:c.355-958C… XM_047429942.1:c.355-958C>T	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	C=	T
GRCh38.p14 chr 12	NC_000012.12:g.120551541=	NC_000012.12:g.120551541C>T
GRCh37.p13 chr 12	NC_000012.11:g.120989344=	NC_000012.11:g.120989344C>T
RNF10 transcript variant 2	NM_001330474.2:c.355-958=	NM_001330474.2:c.355-958C>T
RNF10 transcript variant 1	NM_014868.4:c.355-958=	NM_014868.4:c.355-958C>T
RNF10 transcript variant 1	NM_014868.5:c.355-958=	NM_014868.5:c.355-958C>T
RNF10 transcript variant X1	XM_005254010.1:c.430-958=	XM_005254010.1:c.430-958C>T
RNF10 transcript variant X2	XM_005254011.1:c.355-958=	XM_005254011.1:c.355-958C>T
RNF10 transcript variant X3	XM_005254012.1:c.355-958=	XM_005254012.1:c.355-958C>T
RNF10 transcript variant X2	XM_005254013.1:c.205-958=	XM_005254013.1:c.205-958C>T
RNF10 transcript variant X1	XM_005254013.3:c.205-958=	XM_005254013.3:c.205-958C>T
RNF10 transcript variant X5	XM_005254014.1:c.355-958=	XM_005254014.1:c.355-958C>T
RNF10 transcript variant X2	XM_017020282.2:c.205-958=	XM_017020282.2:c.205-958C>T
RNF10 transcript variant X5	XM_017020283.3:c.355-958=	XM_017020283.3:c.355-958C>T
RNF10 transcript variant X3	XM_047429937.1:c.355-958=	XM_047429937.1:c.355-958C>T
RNF10 transcript variant X4	XM_047429938.1:c.355-958=	XM_047429938.1:c.355-958C>T
RNF10 transcript variant X6	XM_047429939.1:c.355-958=	XM_047429939.1:c.355-958C>T
RNF10 transcript variant X7	XM_047429940.1:c.355-958=	XM_047429940.1:c.355-958C>T
RNF10 transcript variant X8	XM_047429941.1:c.355-958=	XM_047429941.1:c.355-958C>T
RNF10 transcript variant X9	XM_047429942.1:c.355-958=	XM_047429942.1:c.355-958C>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#.

35 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BL	ss255367432	May 09, 2011 (134)
2	1000GENOMES	ss463163514	Sep 17, 2011 (135)
3	EVA-GONL	ss990029075	Aug 21, 2014 (142)
4	JMKIDD_LAB	ss1078822151	Aug 21, 2014 (142)
5	1000GENOMES	ss1346908070	Aug 21, 2014 (142)
6	EVA_GENOME_DK	ss1576566469	Apr 01, 2015 (144)
7	EVA_UK10K_ALSPAC	ss1629591447	Apr 01, 2015 (144)
8	EVA_DECODE	ss1642138952	Apr 01, 2015 (144)
9	EVA_UK10K_TWINSUK	ss1672585480	Apr 01, 2015 (144)
10	WEILL_CORNELL_DGM	ss1933383835	Feb 12, 2016 (147)
11	JJLAB	ss2027448290	Sep 14, 2016 (149)
12	HUMAN_LONGEVITY	ss2193753733	Dec 20, 2016 (150)
13	GNOMAD	ss2915943373	Nov 08, 2017 (151)
14	SWEGEN	ss3010459154	Nov 08, 2017 (151)
15	CSHL	ss3350280475	Nov 08, 2017 (151)
16	EGCUT_WGS	ss3677760429	Jul 13, 2019 (153)
17	EVA_DECODE	ss3694604803	Jul 13, 2019 (153)
18	ACPOP	ss3739441777	Jul 13, 2019 (153)
19	EVA	ss3751049104	Jul 13, 2019 (153)
20	KHV_HUMAN_GENOMES	ss3816377415	Jul 13, 2019 (153)
21	EVA	ss3833361029	Apr 27, 2020 (154)
22	SGDP_PRJ	ss3879252872	Apr 27, 2020 (154)
23	KRGDB	ss3928018695	Apr 27, 2020 (154)
24	KOGIC	ss3972876132	Apr 27, 2020 (154)
25	TOPMED	ss4935091698	Apr 26, 2021 (155)
26	TOMMO_GENOMICS	ss5208480186	Apr 26, 2021 (155)
27	1000G_HIGH_COVERAGE	ss5292473375	Oct 16, 2022 (156)
28	EVA	ss5408663834	Oct 16, 2022 (156)
29	HUGCELL_USP	ss5487054325	Oct 16, 2022 (156)
30	1000G_HIGH_COVERAGE	ss5590810614	Oct 16, 2022 (156)
31	SANFORD_IMAGENETICS	ss5654088694	Oct 16, 2022 (156)
32	TOMMO_GENOMICS	ss5758899331	Oct 16, 2022 (156)
33	EVA	ss5850576688	Oct 16, 2022 (156)
34	EVA	ss5906297125	Oct 16, 2022 (156)
35	EVA	ss5945503546	Oct 16, 2022 (156)
36	1000Genomes	NC_000012.11 - 120989344	Oct 12, 2018 (152)
37	1000Genomes_30x	NC_000012.12 - 120551541	Oct 16, 2022 (156)
38	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 120989344	Oct 12, 2018 (152)
39	Genetic variation in the Estonian population	NC_000012.11 - 120989344	Oct 12, 2018 (152)
40	The Danish reference pan genome	NC_000012.11 - 120989344	Apr 27, 2020 (154)
41	gnomAD - Genomes	NC_000012.12 - 120551541	Apr 26, 2021 (155)
42	Genome of the Netherlands Release 5	NC_000012.11 - 120989344	Apr 27, 2020 (154)
43	KOREAN population from KRGDB	NC_000012.11 - 120989344	Apr 27, 2020 (154)
44	Korean Genome Project	NC_000012.12 - 120551541	Apr 27, 2020 (154)
45	Northern Sweden	NC_000012.11 - 120989344	Jul 13, 2019 (153)
46	Qatari	NC_000012.11 - 120989344	Apr 27, 2020 (154)
47	SGDP_PRJ	NC_000012.11 - 120989344	Apr 27, 2020 (154)
48	8.3KJPN	NC_000012.11 - 120989344	Apr 26, 2021 (155)
49	14KJPN	NC_000012.12 - 120551541	Oct 16, 2022 (156)
50	TopMed	NC_000012.12 - 120551541	Apr 26, 2021 (155)
51	UK 10K study - Twins	NC_000012.11 - 120989344	Oct 12, 2018 (152)
52	ALFA	NC_000012.12 - 120551541	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
ss255367432, ss1642138952	NC_000012.10:119473726:C:T	NC_000012.12:120551540:C:T	(self)
59728826, 33177231, 23498677, 3154138, 14795460, 35196089, 12726642, 15425765, 31269852, 66449493, 33177231, ss463163514, ss990029075, ss1078822151, ss1346908070, ss1576566469, ss1629591447, ss1672585480, ss1933383835, ss2027448290, ss2915943373, ss3010459154, ss3350280475, ss3677760429, ss3739441777, ss3751049104, ss3833361029, ss3879252872, ss3928018695, ss5208480186, ss5408663834, ss5654088694, ss5945503546	NC_000012.11:120989343:C:T	NC_000012.12:120551540:C:T	(self)
78336549, 421299343, 29254133, 92736435, 150637355, 4428676889, ss2193753733, ss3694604803, ss3816377415, ss3972876132, ss4935091698, ss5292473375, ss5487054325, ss5590810614, ss5758899331, ss5850576688, ss5906297125	NC_000012.12:120551540:C:T	NC_000012.12:120551540: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 rs149220464

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

rs149220464