Name: rs10849759
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.

rs10849759

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:120556685 (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=0.252499 (66834/264690, TOPMED)
A=0.256553 (35882/139862, GnomAD)
T=0.48945 (13829/28254, 14KJPN) (+ 18 more)
A=0.28332 (5352/18890, ALFA)
T=0.48473 (8124/16760, 8.3KJPN)
A=0.2601 (1666/6404, 1000G_30x)
A=0.2666 (1335/5008, 1000G)
A=0.3141 (1407/4480, Estonian)
A=0.3191 (1230/3854, ALSPAC)
A=0.3274 (1214/3708, TWINSUK)
A=0.4894 (1433/2928, KOREAN)
A=0.4836 (886/1832, Korea1K)
A=0.317 (316/998, GoNL)
A=0.320 (192/600, NorthernSweden)
T=0.380 (108/284, SGDP_PRJ)
A=0.183 (42/230, HapMap)
A=0.273 (59/216, Qatari)
T=0.410 (86/210, Vietnamese)
A=0.38 (15/40, GENOME_DK)
T=0.46 (11/24, Siberian)
A=0.17 (2/12, Ancient Sardinia)

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	18890	T=0.71668	A=0.28332
European	Sub	14286	T=0.68543	A=0.31457
African	Sub	2946	T=0.8887	A=0.1113
African Others	Sub	114	T=0.974	A=0.026
African American	Sub	2832	T=0.8852	A=0.1148
Asian	Sub	112	T=0.482	A=0.518
East Asian	Sub	86	T=0.50	A=0.50
Other Asian	Sub	26	T=0.42	A=0.58
Latin American 1	Sub	146	T=0.767	A=0.233
Latin American 2	Sub	610	T=0.651	A=0.349
South Asian	Sub	98	T=0.84	A=0.16
Other	Sub	692	T=0.698	A=0.302

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=0.747501	A=0.252499
gnomAD - Genomes	Global	Study-wide	139862	T=0.743447	A=0.256553
gnomAD - Genomes	European	Sub	75746	T=0.68171	A=0.31829
gnomAD - Genomes	African	Sub	41924	T=0.87890	A=0.12110
gnomAD - Genomes	American	Sub	13608	T=0.72443	A=0.27557
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.7665	A=0.2335
gnomAD - Genomes	East Asian	Sub	3118	T=0.4929	A=0.5071
gnomAD - Genomes	Other	Sub	2142	T=0.7250	A=0.2750
14KJPN	JAPANESE	Study-wide	28254	T=0.48945	A=0.51055
Allele Frequency Aggregator	Total	Global	18890	T=0.71668	A=0.28332
Allele Frequency Aggregator	European	Sub	14286	T=0.68543	A=0.31457
Allele Frequency Aggregator	African	Sub	2946	T=0.8887	A=0.1113
Allele Frequency Aggregator	Other	Sub	692	T=0.698	A=0.302
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.651	A=0.349
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.767	A=0.233
Allele Frequency Aggregator	Asian	Sub	112	T=0.482	A=0.518
Allele Frequency Aggregator	South Asian	Sub	98	T=0.84	A=0.16
8.3KJPN	JAPANESE	Study-wide	16760	T=0.48473	A=0.51527
1000Genomes_30x	Global	Study-wide	6404	T=0.7399	A=0.2601
1000Genomes_30x	African	Sub	1786	T=0.9166	A=0.0834
1000Genomes_30x	Europe	Sub	1266	T=0.7196	A=0.2804
1000Genomes_30x	South Asian	Sub	1202	T=0.7271	A=0.2729
1000Genomes_30x	East Asian	Sub	1170	T=0.5068	A=0.4932
1000Genomes_30x	American	Sub	980	T=0.738	A=0.262
1000Genomes	Global	Study-wide	5008	T=0.7334	A=0.2666
1000Genomes	African	Sub	1322	T=0.9123	A=0.0877
1000Genomes	East Asian	Sub	1008	T=0.5079	A=0.4921
1000Genomes	Europe	Sub	1006	T=0.7207	A=0.2793
1000Genomes	South Asian	Sub	978	T=0.731	A=0.269
1000Genomes	American	Sub	694	T=0.742	A=0.258
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.6859	A=0.3141
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.6809	A=0.3191
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.6726	A=0.3274
KOREAN population from KRGDB	KOREAN	Study-wide	2928	T=0.5106	A=0.4894
Korean Genome Project	KOREAN	Study-wide	1832	T=0.5164	A=0.4836
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.683	A=0.317
Northern Sweden	ACPOP	Study-wide	600	T=0.680	A=0.320
SGDP_PRJ	Global	Study-wide	284	T=0.380	A=0.620
HapMap	Global	Study-wide	230	T=0.817	A=0.183
HapMap	American	Sub	120	T=0.708	A=0.292
HapMap	African	Sub	110	T=0.936	A=0.064
Qatari	Global	Study-wide	216	T=0.727	A=0.273
A Vietnamese Genetic Variation Database	Global	Study-wide	210	T=0.410	A=0.590
The Danish reference pan genome	Danish	Study-wide	40	T=0.62	A=0.38
Siberian	Global	Study-wide	24	T=0.46	A=0.54
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	12	T=0.83	A=0.17

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.120556685T>A
GRCh37.p13 chr 12	NC_000012.11:g.120994488T>A

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

Molecule type	Change	Amino acid[Codon]	SO Term
RNF10 transcript variant 2	NM_001330474.2:c.646-597T… NM_001330474.2:c.646-597T>A	N/A	Intron Variant
RNF10 transcript variant 1	NM_014868.5:c.646-597T>A	N/A	Intron Variant
RNF10 transcript variant X1	XM_005254013.3:c.496-597T… XM_005254013.3:c.496-597T>A	N/A	Intron Variant
RNF10 transcript variant X2	XM_017020282.2:c.496-597T… XM_017020282.2:c.496-597T>A	N/A	Intron Variant
RNF10 transcript variant X5	XM_017020283.3:c.646-597T… XM_017020283.3:c.646-597T>A	N/A	Intron Variant
RNF10 transcript variant X3	XM_047429937.1:c.646-597T… XM_047429937.1:c.646-597T>A	N/A	Intron Variant
RNF10 transcript variant X4	XM_047429938.1:c.646-597T… XM_047429938.1:c.646-597T>A	N/A	Intron Variant
RNF10 transcript variant X6	XM_047429939.1:c.646-597T… XM_047429939.1:c.646-597T>A	N/A	Intron Variant
RNF10 transcript variant X7	XM_047429940.1:c.646-597T… XM_047429940.1:c.646-597T>A	N/A	Intron Variant
RNF10 transcript variant X8	XM_047429941.1:c.646-597T… XM_047429941.1:c.646-597T>A	N/A	Intron Variant
RNF10 transcript variant X9	XM_047429942.1:c.646-597T… XM_047429942.1:c.646-597T>A	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=	A
GRCh38.p14 chr 12	NC_000012.12:g.120556685=	NC_000012.12:g.120556685T>A
GRCh37.p13 chr 12	NC_000012.11:g.120994488=	NC_000012.11:g.120994488T>A
RNF10 transcript variant 2	NM_001330474.2:c.646-597=	NM_001330474.2:c.646-597T>A
RNF10 transcript variant 1	NM_014868.4:c.646-597=	NM_014868.4:c.646-597T>A
RNF10 transcript variant 1	NM_014868.5:c.646-597=	NM_014868.5:c.646-597T>A
RNF10 transcript variant X1	XM_005254010.1:c.721-597=	XM_005254010.1:c.721-597T>A
RNF10 transcript variant X2	XM_005254011.1:c.646-597=	XM_005254011.1:c.646-597T>A
RNF10 transcript variant X3	XM_005254012.1:c.646-597=	XM_005254012.1:c.646-597T>A
RNF10 transcript variant X2	XM_005254013.1:c.496-597=	XM_005254013.1:c.496-597T>A
RNF10 transcript variant X1	XM_005254013.3:c.496-597=	XM_005254013.3:c.496-597T>A
RNF10 transcript variant X5	XM_005254014.1:c.646-597=	XM_005254014.1:c.646-597T>A
RNF10 transcript variant X2	XM_017020282.2:c.496-597=	XM_017020282.2:c.496-597T>A
RNF10 transcript variant X5	XM_017020283.3:c.646-597=	XM_017020283.3:c.646-597T>A
RNF10 transcript variant X3	XM_047429937.1:c.646-597=	XM_047429937.1:c.646-597T>A
RNF10 transcript variant X4	XM_047429938.1:c.646-597=	XM_047429938.1:c.646-597T>A
RNF10 transcript variant X6	XM_047429939.1:c.646-597=	XM_047429939.1:c.646-597T>A
RNF10 transcript variant X7	XM_047429940.1:c.646-597=	XM_047429940.1:c.646-597T>A
RNF10 transcript variant X8	XM_047429941.1:c.646-597=	XM_047429941.1:c.646-597T>A
RNF10 transcript variant X9	XM_047429942.1:c.646-597=	XM_047429942.1:c.646-597T>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#.

72 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss16148653	Feb 27, 2004 (120)
2	SC_SNP	ss18509108	Feb 27, 2004 (120)
3	CSHL-HAPMAP	ss19935066	Feb 27, 2004 (120)
4	SSAHASNP	ss20949997	Apr 05, 2004 (121)
5	ABI	ss38897105	Mar 13, 2006 (126)
6	HGSV	ss78833678	Dec 06, 2007 (129)
7	BCMHGSC_JDW	ss89422374	Mar 24, 2008 (129)
8	HUMANGENOME_JCVI	ss97345934	Feb 06, 2009 (130)
9	1000GENOMES	ss112486733	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss119749234	Dec 01, 2009 (131)
11	ENSEMBL	ss133392498	Dec 01, 2009 (131)
12	ENSEMBL	ss137561091	Dec 01, 2009 (131)
13	GMI	ss157973963	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss168746147	Jul 04, 2010 (132)
15	BUSHMAN	ss198771787	Jul 04, 2010 (132)
16	1000GENOMES	ss225996522	Jul 14, 2010 (132)
17	1000GENOMES	ss236113574	Jul 15, 2010 (132)
18	1000GENOMES	ss242636623	Jul 15, 2010 (132)
19	GMI	ss281572821	May 04, 2012 (137)
20	PJP	ss291353292	May 09, 2011 (134)
21	TISHKOFF	ss563447918	Apr 25, 2013 (138)
22	SSMP	ss659032227	Apr 25, 2013 (138)
23	EVA-GONL	ss990029118	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1078822177	Aug 21, 2014 (142)
25	1000GENOMES	ss1346908225	Aug 21, 2014 (142)
26	DDI	ss1427074105	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1576566487	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1629591524	Apr 01, 2015 (144)
29	EVA_DECODE	ss1642138990	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1672585557	Apr 01, 2015 (144)
31	WEILL_CORNELL_DGM	ss1933383883	Feb 12, 2016 (147)
32	JJLAB	ss2027448311	Sep 14, 2016 (149)
33	USC_VALOUEV	ss2155802572	Dec 20, 2016 (150)
34	HUMAN_LONGEVITY	ss2193754041	Dec 20, 2016 (150)
35	SYSTEMSBIOZJU	ss2628206703	Nov 08, 2017 (151)
36	GRF	ss2700162504	Nov 08, 2017 (151)
37	GNOMAD	ss2915943912	Nov 08, 2017 (151)
38	AFFY	ss2984993339	Nov 08, 2017 (151)
39	AFFY	ss2985629516	Nov 08, 2017 (151)
40	SWEGEN	ss3010459256	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3027534807	Nov 08, 2017 (151)
42	CSHL	ss3350280493	Nov 08, 2017 (151)
43	URBANLAB	ss3649935139	Oct 12, 2018 (152)
44	ILLUMINA	ss3653763380	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3677760483	Jul 13, 2019 (153)
46	EVA_DECODE	ss3694604868	Jul 13, 2019 (153)
47	ACPOP	ss3739441806	Jul 13, 2019 (153)
48	EVA	ss3751049151	Jul 13, 2019 (153)
49	PACBIO	ss3787354491	Jul 13, 2019 (153)
50	PACBIO	ss3792433487	Jul 13, 2019 (153)
51	PACBIO	ss3797316637	Jul 13, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3816377468	Jul 13, 2019 (153)
53	EVA	ss3833361056	Apr 27, 2020 (154)
54	EVA	ss3840251418	Apr 27, 2020 (154)
55	EVA	ss3845740364	Apr 27, 2020 (154)
56	SGDP_PRJ	ss3879252958	Apr 27, 2020 (154)
57	KRGDB	ss3928018862	Apr 27, 2020 (154)
58	KOGIC	ss3972876251	Apr 27, 2020 (154)
59	EVA	ss3985619536	Apr 26, 2021 (155)
60	TOPMED	ss4935092996	Apr 26, 2021 (155)
61	TOMMO_GENOMICS	ss5208480454	Apr 26, 2021 (155)
62	1000G_HIGH_COVERAGE	ss5292473526	Oct 16, 2022 (156)
63	HUGCELL_USP	ss5487054454	Oct 16, 2022 (156)
64	EVA	ss5510863354	Oct 16, 2022 (156)
65	1000G_HIGH_COVERAGE	ss5590810824	Oct 16, 2022 (156)
66	SANFORD_IMAGENETICS	ss5654088786	Oct 16, 2022 (156)
67	TOMMO_GENOMICS	ss5758899767	Oct 16, 2022 (156)
68	YY_MCH	ss5813704573	Oct 16, 2022 (156)
69	EVA	ss5838607112	Oct 16, 2022 (156)
70	EVA	ss5850576710	Oct 16, 2022 (156)
71	EVA	ss5906297263	Oct 16, 2022 (156)
72	EVA	ss5945503625	Oct 16, 2022 (156)
73	1000Genomes	NC_000012.11 - 120994488	Oct 12, 2018 (152)
74	1000Genomes_30x	NC_000012.12 - 120556685	Oct 16, 2022 (156)
75	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 120994488	Oct 12, 2018 (152)
76	Genetic variation in the Estonian population	NC_000012.11 - 120994488	Oct 12, 2018 (152)
77	The Danish reference pan genome	NC_000012.11 - 120994488	Apr 27, 2020 (154)
78	gnomAD - Genomes	NC_000012.12 - 120556685	Apr 26, 2021 (155)
79	Genome of the Netherlands Release 5	NC_000012.11 - 120994488	Apr 27, 2020 (154)
80	HapMap	NC_000012.12 - 120556685	Apr 27, 2020 (154)
81	KOREAN population from KRGDB	NC_000012.11 - 120994488	Apr 27, 2020 (154)
82	Korean Genome Project	NC_000012.12 - 120556685	Apr 27, 2020 (154)
83	Northern Sweden	NC_000012.11 - 120994488	Jul 13, 2019 (153)
84	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000012.11 - 120994488	Apr 26, 2021 (155)
85	Qatari	NC_000012.11 - 120994488	Apr 27, 2020 (154)
86	SGDP_PRJ	NC_000012.11 - 120994488	Apr 27, 2020 (154)
87	Siberian	NC_000012.11 - 120994488	Apr 27, 2020 (154)
88	8.3KJPN	NC_000012.11 - 120994488	Apr 26, 2021 (155)
89	14KJPN	NC_000012.12 - 120556685	Oct 16, 2022 (156)
90	TopMed	NC_000012.12 - 120556685	Apr 26, 2021 (155)
91	UK 10K study - Twins	NC_000012.11 - 120994488	Oct 12, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000012.11 - 120994488	Jul 13, 2019 (153)
93	ALFA	NC_000012.12 - 120556685	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
ss78833678	NC_000012.9:119457207:T:A	NC_000012.12:120556684:T:A	(self)
ss89422374, ss112486733, ss119749234, ss168746147, ss198771787, ss281572821, ss291353292, ss1642138990	NC_000012.10:119478870:T:A	NC_000012.12:120556684:T:A	(self)
59728987, 33177312, 23498731, 3154156, 14795496, 35196256, 12726671, 845463, 15425813, 31269938, 8318926, 66449761, 33177312, 7359238, ss225996522, ss236113574, ss242636623, ss563447918, ss659032227, ss990029118, ss1078822177, ss1346908225, ss1427074105, ss1576566487, ss1629591524, ss1672585557, ss1933383883, ss2027448311, ss2155802572, ss2628206703, ss2700162504, ss2915943912, ss2984993339, ss2985629516, ss3010459256, ss3350280493, ss3653763380, ss3677760483, ss3739441806, ss3751049151, ss3787354491, ss3792433487, ss3797316637, ss3833361056, ss3840251418, ss3879252958, ss3928018862, ss3985619536, ss5208480454, ss5510863354, ss5654088786, ss5838607112, ss5945503625	NC_000012.11:120994487:T:A	NC_000012.12:120556684:T:A	(self)
78336759, 421300628, 918679, 29254252, 92736871, 150638653, 3974127691, ss2193754041, ss3027534807, ss3649935139, ss3694604868, ss3816377468, ss3845740364, ss3972876251, ss4935092996, ss5292473526, ss5487054454, ss5590810824, ss5758899767, ss5813704573, ss5850576710, ss5906297263	NC_000012.12:120556684:T:A	NC_000012.12:120556684:T:A	(self)
ss16148653, ss18509108, ss19935066, ss20949997	NT_009775.14:11513229:T:A	NC_000012.12:120556684:T:A	(self)
ss38897105, ss97345934, ss133392498, ss137561091, ss157973963	NT_009775.17:11571017:T:A	NC_000012.12:120556684: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 rs10849759

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

rs10849759