Name: rs58013264
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.

rs58013264

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:862060 (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=0.185390 (49071/264690, TOPMED)
C=0.182177 (25339/139090, GnomAD)
C=0.14579 (4090/28054, 14KJPN) (+ 14 more)
C=0.15280 (2561/16760, 8.3KJPN)
C=0.17303 (2890/16702, ALFA)
C=0.1928 (1235/6404, 1000G_30x)
C=0.1895 (949/5008, 1000G)
C=0.1157 (446/3854, ALSPAC)
C=0.1170 (434/3708, TWINSUK)
C=0.1505 (441/2930, KOREAN)
C=0.1643 (301/1832, Korea1K)
C=0.140 (140/998, GoNL)
C=0.107 (64/600, NorthernSweden)
C=0.167 (36/216, Qatari)
C=0.083 (18/216, Vietnamese)
T=0.452 (76/168, SGDP_PRJ)
T=0.40 (8/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC107984850 : 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	16702	T=0.82697	C=0.17303
European	Sub	12214	T=0.85639	C=0.14361
African	Sub	2864	T=0.7081	C=0.2919
African Others	Sub	108	T=0.657	C=0.343
African American	Sub	2756	T=0.7101	C=0.2899
Asian	Sub	108	T=0.861	C=0.139
East Asian	Sub	84	T=0.86	C=0.14
Other Asian	Sub	24	T=0.88	C=0.12
Latin American 1	Sub	146	T=0.767	C=0.233
Latin American 2	Sub	610	T=0.825	C=0.175
South Asian	Sub	94	T=0.88	C=0.12
Other	Sub	666	T=0.800	C=0.200

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=0.814610	C=0.185390
gnomAD - Genomes	Global	Study-wide	139090	T=0.817823	C=0.182177
gnomAD - Genomes	European	Sub	75494	T=0.86448	C=0.13552
gnomAD - Genomes	African	Sub	41424	T=0.71154	C=0.28846
gnomAD - Genomes	American	Sub	13594	T=0.84331	C=0.15669
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.8974	C=0.1026
gnomAD - Genomes	East Asian	Sub	3126	T=0.8912	C=0.1088
gnomAD - Genomes	Other	Sub	2130	T=0.8366	C=0.1634
14KJPN	JAPANESE	Study-wide	28054	T=0.85421	C=0.14579
8.3KJPN	JAPANESE	Study-wide	16760	T=0.84720	C=0.15280
Allele Frequency Aggregator	Total	Global	16702	T=0.82697	C=0.17303
Allele Frequency Aggregator	European	Sub	12214	T=0.85639	C=0.14361
Allele Frequency Aggregator	African	Sub	2864	T=0.7081	C=0.2919
Allele Frequency Aggregator	Other	Sub	666	T=0.800	C=0.200
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.825	C=0.175
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.767	C=0.233
Allele Frequency Aggregator	Asian	Sub	108	T=0.861	C=0.139
Allele Frequency Aggregator	South Asian	Sub	94	T=0.88	C=0.12
1000Genomes_30x	Global	Study-wide	6404	T=0.8072	C=0.1928
1000Genomes_30x	African	Sub	1786	T=0.6932	C=0.3068
1000Genomes_30x	Europe	Sub	1266	T=0.8815	C=0.1185
1000Genomes_30x	South Asian	Sub	1202	T=0.8020	C=0.1980
1000Genomes_30x	East Asian	Sub	1170	T=0.8803	C=0.1197
1000Genomes_30x	American	Sub	980	T=0.838	C=0.162
1000Genomes	Global	Study-wide	5008	T=0.8105	C=0.1895
1000Genomes	African	Sub	1322	T=0.6914	C=0.3086
1000Genomes	East Asian	Sub	1008	T=0.8810	C=0.1190
1000Genomes	Europe	Sub	1006	T=0.8787	C=0.1213
1000Genomes	South Asian	Sub	978	T=0.806	C=0.194
1000Genomes	American	Sub	694	T=0.843	C=0.157
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8843	C=0.1157
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8830	C=0.1170
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.8495	C=0.1505
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8357	C=0.1643
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.860	C=0.140
Northern Sweden	ACPOP	Study-wide	600	T=0.893	C=0.107
Qatari	Global	Study-wide	216	T=0.833	C=0.167
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.917	C=0.083
SGDP_PRJ	Global	Study-wide	168	T=0.452	C=0.548
Siberian	Global	Study-wide	20	T=0.40	C=0.60

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 1	NC_000001.11:g.862060T>C
GRCh37.p13 chr 1	NC_000001.10:g.797440T>C

Gene: LOC107984850, uncharacterized LOC107984850 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107984850 transcript variant X1	XR_001737607.3:n.	N/A	Intron Variant
LOC107984850 transcript variant X2	XR_001737608.3:n.	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 1	NC_000001.11:g.862060=	NC_000001.11:g.862060T>C
GRCh37.p13 chr 1	NC_000001.10:g.797440=	NC_000001.10:g.797440T>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#.

51 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss85267206	Dec 14, 2007 (129)
2	BCMHGSC_JDW	ss87156101	Mar 23, 2008 (130)
3	ILLUMINA-UK	ss118438417	Dec 01, 2009 (131)
4	1000GENOMES	ss218190487	Jul 14, 2010 (132)
5	1000GENOMES	ss230395505	Jul 14, 2010 (132)
6	1000GENOMES	ss238115025	Jul 15, 2010 (132)
7	GMI	ss275680959	May 04, 2012 (137)
8	PJP	ss290493828	May 09, 2011 (134)
9	ILLUMINA	ss482406722	May 04, 2012 (137)
10	ILLUMINA	ss534766438	Sep 08, 2015 (146)
11	TISHKOFF	ss553710659	Apr 25, 2013 (138)
12	ILLUMINA	ss781868030	Sep 08, 2015 (146)
13	ILLUMINA	ss835547330	Sep 08, 2015 (146)
14	EVA-GONL	ss974769597	Aug 21, 2014 (142)
15	1000GENOMES	ss1289340224	Aug 21, 2014 (142)
16	DDI	ss1425684940	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1599378546	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1642372579	Apr 01, 2015 (144)
19	WEILL_CORNELL_DGM	ss1917960770	Feb 12, 2016 (147)
20	JJLAB	ss2019498488	Sep 14, 2016 (149)
21	USC_VALOUEV	ss2147484465	Dec 20, 2016 (150)
22	SYSTEMSBIOZJU	ss2624264822	Nov 08, 2017 (151)
23	GRF	ss2697374847	Nov 08, 2017 (151)
24	GNOMAD	ss2750641556	Nov 08, 2017 (151)
25	SWEGEN	ss2986149469	Nov 08, 2017 (151)
26	BIOINF_KMB_FNS_UNIBA	ss3023513722	Nov 08, 2017 (151)
27	CSHL	ss3343272686	Nov 08, 2017 (151)
28	EVA_DECODE	ss3685992486	Jul 12, 2019 (153)
29	ACPOP	ss3726716517	Jul 12, 2019 (153)
30	EVA	ss3745721191	Jul 12, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3798743861	Jul 12, 2019 (153)
32	EVA	ss3825981514	Apr 25, 2020 (154)
33	EVA	ss3836378465	Apr 25, 2020 (154)
34	EVA	ss3841782468	Apr 25, 2020 (154)
35	SGDP_PRJ	ss3847996138	Apr 25, 2020 (154)
36	KRGDB	ss3892836383	Apr 25, 2020 (154)
37	KOGIC	ss3943630087	Apr 25, 2020 (154)
38	TOPMED	ss4436439797	Apr 25, 2021 (155)
39	TOMMO_GENOMICS	ss5142053288	Apr 25, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5240864314	Oct 12, 2022 (156)
41	EVA	ss5314585880	Oct 12, 2022 (156)
42	EVA	ss5316184605	Oct 12, 2022 (156)
43	HUGCELL_USP	ss5442112630	Oct 12, 2022 (156)
44	1000G_HIGH_COVERAGE	ss5512489310	Oct 12, 2022 (156)
45	SANFORD_IMAGENETICS	ss5624749944	Oct 12, 2022 (156)
46	TOMMO_GENOMICS	ss5666192884	Oct 12, 2022 (156)
47	YY_MCH	ss5800243994	Oct 12, 2022 (156)
48	EVA	ss5831418707	Oct 12, 2022 (156)
49	EVA	ss5848748907	Oct 12, 2022 (156)
50	EVA	ss5906705253	Oct 12, 2022 (156)
51	EVA	ss5936583037	Oct 12, 2022 (156)
52	1000Genomes	NC_000001.10 - 797440	Oct 11, 2018 (152)
53	1000Genomes_30x	NC_000001.11 - 862060	Oct 12, 2022 (156)
54	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 797440	Oct 11, 2018 (152)
55	gnomAD - Genomes	NC_000001.11 - 862060	Apr 25, 2021 (155)
56	Genome of the Netherlands Release 5	NC_000001.10 - 797440	Apr 25, 2020 (154)
57	KOREAN population from KRGDB	NC_000001.10 - 797440	Apr 25, 2020 (154)
58	Korean Genome Project	NC_000001.11 - 862060	Apr 25, 2020 (154)
59	Northern Sweden	NC_000001.10 - 797440	Jul 12, 2019 (153)
60	Qatari	NC_000001.10 - 797440	Apr 25, 2020 (154)
61	SGDP_PRJ	NC_000001.10 - 797440	Apr 25, 2020 (154)
62	Siberian	NC_000001.10 - 797440	Apr 25, 2020 (154)
63	8.3KJPN	NC_000001.10 - 797440	Apr 25, 2021 (155)
64	14KJPN	NC_000001.11 - 862060	Oct 12, 2022 (156)
65	TopMed	NC_000001.11 - 862060	Apr 25, 2021 (155)
66	UK 10K study - Twins	NC_000001.10 - 797440	Oct 11, 2018 (152)
67	A Vietnamese Genetic Variation Database	NC_000001.10 - 797440	Jul 12, 2019 (153)
68	ALFA	NC_000001.11 - 862060	Apr 25, 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).

Associated ID	History Updated (Build)
rs61768211	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss85267206	NC_000001.8:837302:T:C	NC_000001.11:862059:T:C	(self)
ss87156101, ss118438417, ss275680959, ss290493828, ss482406722	NC_000001.9:787302:T:C	NC_000001.11:862059:T:C	(self)
4991, 505, 625, 13777, 1382, 2700, 13118, 819, 22595, 505, 107, ss218190487, ss230395505, ss238115025, ss534766438, ss553710659, ss781868030, ss835547330, ss974769597, ss1289340224, ss1425684940, ss1599378546, ss1642372579, ss1917960770, ss2019498488, ss2147484465, ss2624264822, ss2697374847, ss2750641556, ss2986149469, ss3343272686, ss3726716517, ss3745721191, ss3825981514, ss3836378465, ss3847996138, ss3892836383, ss5142053288, ss5314585880, ss5316184605, ss5624749944, ss5831418707, ss5936583037	NC_000001.10:797439:T:C	NC_000001.11:862059:T:C	(self)
15245, 71100, 8088, 29988, 46132, 615266579, ss3023513722, ss3685992486, ss3798743861, ss3841782468, ss3943630087, ss4436439797, ss5240864314, ss5442112630, ss5512489310, ss5666192884, ss5800243994, ss5848748907, ss5906705253	NC_000001.11:862059:T:C	NC_000001.11:862059: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 rs58013264

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

rs58013264