Name: rs57858801
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.

rs57858801

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:46093248 (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 / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.495844 (131245/264690, TOPMED)
T=0.499115 (69340/138926, GnomAD)
A=0.45771 (9677/21142, 14KJPN) (+ 11 more)
A=0.46683 (8389/17970, ALFA)
A=0.47456 (7948/16748, 8.3KJPN)
T=0.4739 (3035/6404, 1000G_30x)
T=0.4694 (2351/5008, 1000G)
A=0.4831 (1862/3854, ALSPAC)
A=0.4916 (1823/3708, TWINSUK)
A=0.4512 (1321/2928, KOREAN)
A=0.4509 (826/1832, Korea1K)
A=0.470 (469/998, GoNL)
T=0.293 (122/416, SGDP_PRJ)
T=0.361 (78/216, Qatari)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	17970	T=0.53317	A=0.46683, C=0.00000
European	Sub	13802	T=0.54920	A=0.45080, C=0.00000
African	Sub	2512	T=0.4526	A=0.5474, C=0.0000
African Others	Sub	102	T=0.480	A=0.520, C=0.000
African American	Sub	2410	T=0.4515	A=0.5485, C=0.0000
Asian	Sub	112	T=0.438	A=0.562, C=0.000
East Asian	Sub	86	T=0.45	A=0.55, C=0.00
Other Asian	Sub	26	T=0.38	A=0.62, C=0.00
Latin American 1	Sub	146	T=0.534	A=0.466, C=0.000
Latin American 2	Sub	610	T=0.616	A=0.384, C=0.000
South Asian	Sub	98	T=0.34	A=0.66, C=0.00
Other	Sub	690	T=0.475	A=0.525, C=0.000

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=0.495844	A=0.504156
gnomAD - Genomes	Global	Study-wide	138926	T=0.499115	A=0.500885
gnomAD - Genomes	European	Sub	75400	T=0.53037	A=0.46963
gnomAD - Genomes	African	Sub	41464	T=0.43537	A=0.56463
gnomAD - Genomes	American	Sub	13530	T=0.53592	A=0.46408
gnomAD - Genomes	Ashkenazi Jewish	Sub	3312	T=0.4278	A=0.5722
gnomAD - Genomes	East Asian	Sub	3076	T=0.5098	A=0.4902
gnomAD - Genomes	Other	Sub	2144	T=0.4953	A=0.5047
14KJPN	JAPANESE	Study-wide	21142	T=0.54229	A=0.45771
Allele Frequency Aggregator	Total	Global	17970	T=0.53317	A=0.46683, C=0.00000
Allele Frequency Aggregator	European	Sub	13802	T=0.54920	A=0.45080, C=0.00000
Allele Frequency Aggregator	African	Sub	2512	T=0.4526	A=0.5474, C=0.0000
Allele Frequency Aggregator	Other	Sub	690	T=0.475	A=0.525, C=0.000
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.616	A=0.384, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.534	A=0.466, C=0.000
Allele Frequency Aggregator	Asian	Sub	112	T=0.438	A=0.562, C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=0.34	A=0.66, C=0.00
8.3KJPN	JAPANESE	Study-wide	16748	T=0.52544	A=0.47456
1000Genomes_30x	Global	Study-wide	6404	T=0.4739	A=0.5261
1000Genomes_30x	African	Sub	1786	T=0.4250	A=0.5750
1000Genomes_30x	Europe	Sub	1266	T=0.5387	A=0.4613
1000Genomes_30x	South Asian	Sub	1202	T=0.3686	A=0.6314
1000Genomes_30x	East Asian	Sub	1170	T=0.5222	A=0.4778
1000Genomes_30x	American	Sub	980	T=0.551	A=0.449
1000Genomes	Global	Study-wide	5008	T=0.4694	A=0.5306
1000Genomes	African	Sub	1322	T=0.4198	A=0.5802
1000Genomes	East Asian	Sub	1008	T=0.5308	A=0.4692
1000Genomes	Europe	Sub	1006	T=0.5308	A=0.4692
1000Genomes	South Asian	Sub	978	T=0.361	A=0.639
1000Genomes	American	Sub	694	T=0.539	A=0.461
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5169	A=0.4831
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5084	A=0.4916
KOREAN population from KRGDB	KOREAN	Study-wide	2928	T=0.5488	A=0.4512
Korean Genome Project	KOREAN	Study-wide	1832	T=0.5491	A=0.4509
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.530	A=0.470
SGDP_PRJ	Global	Study-wide	416	T=0.293	A=0.707
Qatari	Global	Study-wide	216	T=0.361	A=0.639

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 10	NC_000010.11:g.46093248T>A
GRCh38.p14 chr 10	NC_000010.11:g.46093248T>C
GRCh37.p13 chr 10 fix patch HG1211_PATCH	NW_003871068.1:g.364363T>A
GRCh37.p13 chr 10 fix patch HG1211_PATCH	NW_003871068.1:g.364363T>C
GRCh37.p13 chr 10	NC_000010.10:g.51502574A>T
GRCh37.p13 chr 10	NC_000010.10:g.51502574A>G

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	C
GRCh38.p14 chr 10	NC_000010.11:g.46093248=	NC_000010.11:g.46093248T>A	NC_000010.11:g.46093248T>C
GRCh37.p13 chr 10 fix patch HG1211_PATCH	NW_003871068.1:g.364363=	NW_003871068.1:g.364363T>A	NW_003871068.1:g.364363T>C
GRCh37.p13 chr 10	NC_000010.10:g.51502574=	NC_000010.10:g.51502574A>T	NC_000010.10:g.51502574A>G
TIMM23B transcript variant X1	XM_003118952.4:c.514+114811=	XM_003118952.4:c.514+114811A>T	XM_003118952.4:c.514+114811A>G
TIMM23B transcript variant X3	XM_005270305.1:c.370+114811=	XM_005270305.1:c.370+114811A>T	XM_005270305.1:c.370+114811A>G

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#.

48 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss84321419	Dec 14, 2007 (129)
2	BCMHGSC_JDW	ss88202026	Mar 23, 2008 (130)
3	BGI	ss102876271	Dec 01, 2009 (131)
4	ENSEMBL	ss131855237	Dec 01, 2009 (131)
5	SNP500CANCER	ss184957347	Jul 04, 2010 (132)
6	BCM-HGSC-SUB	ss207367062	Jul 04, 2010 (132)
7	BL	ss254294389	May 09, 2011 (134)
8	GMI	ss280606170	May 04, 2012 (137)
9	GMI	ss286184740	Apr 25, 2013 (138)
10	1000GENOMES	ss336120240	May 09, 2011 (134)
11	SSMP	ss656687413	Apr 25, 2013 (138)
12	EVA-GONL	ss987464489	Aug 21, 2014 (142)
13	1000GENOMES	ss1337355372	Aug 21, 2014 (142)
14	DDI	ss1426311968	Apr 09, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1624526634	Apr 09, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1667520667	Apr 09, 2015 (144)
17	HAMMER_LAB	ss1806377671	Sep 11, 2015 (146)
18	WEILL_CORNELL_DGM	ss1930822980	Feb 17, 2016 (147)
19	SYSTEMSBIOZJU	ss2627536722	Oct 12, 2018 (152)
20	GRF	ss2698647812	Oct 12, 2018 (152)
21	ILLUMINA	ss2710709644	Oct 12, 2018 (152)
22	GNOMAD	ss2888552583	Oct 12, 2018 (152)
23	SWEGEN	ss3006440392	Oct 12, 2018 (152)
24	CSHL	ss3349109182	Oct 12, 2018 (152)
25	URBANLAB	ss3649356674	Oct 12, 2018 (152)
26	EVA	ss3748077658	Jul 13, 2019 (153)
27	PACBIO	ss3786663376	Jul 13, 2019 (153)
28	PACBIO	ss3791844514	Jul 13, 2019 (153)
29	PACBIO	ss3796726457	Jul 13, 2019 (153)
30	KHV_HUMAN_GENOMES	ss3813424354	Jul 13, 2019 (153)
31	EVA	ss3832110472	Apr 26, 2020 (154)
32	EVA	ss3839591181	Apr 26, 2020 (154)
33	EVA	ss3845056653	Apr 26, 2020 (154)
34	SGDP_PRJ	ss3874159920	Apr 26, 2020 (154)
35	KRGDB	ss3922220145	Apr 26, 2020 (154)
36	KOGIC	ss3967793661	Apr 26, 2020 (154)
37	GNOMAD	ss4217611604	Apr 26, 2021 (155)
38	TOPMED	ss4850980327	Apr 26, 2021 (155)
39	TOMMO_GENOMICS	ss5197544301	Apr 26, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5283876839	Oct 16, 2022 (156)
41	EVA	ss5393330374	Oct 16, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5577728934	Oct 16, 2022 (156)
43	SANFORD_IMAGENETICS	ss5649238177	Oct 16, 2022 (156)
44	TOMMO_GENOMICS	ss5743191001	Oct 16, 2022 (156)
45	YY_MCH	ss5811486499	Oct 16, 2022 (156)
46	EVA	ss5824364317	Oct 16, 2022 (156)
47	EVA	ss5940507310	Oct 16, 2022 (156)
48	EVA	ss5980613990	Oct 16, 2022 (156)
49	1000Genomes	NC_000010.10 - 51502574	Oct 12, 2018 (152)
50	1000Genomes_30x	NC_000010.11 - 46093248	Oct 16, 2022 (156)
51	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 51502574	Oct 12, 2018 (152)
52	gnomAD - Genomes	NC_000010.11 - 46093248	Apr 26, 2021 (155)
53	Genome of the Netherlands Release 5	NC_000010.10 - 51502574	Apr 26, 2020 (154)
54	KOREAN population from KRGDB	NC_000010.10 - 51502574	Apr 26, 2020 (154)
55	Korean Genome Project	NC_000010.11 - 46093248	Apr 26, 2020 (154)
56	Qatari	NC_000010.10 - 51502574	Apr 26, 2020 (154)
57	SGDP_PRJ	NC_000010.10 - 51502574	Apr 26, 2020 (154)
58	8.3KJPN	NC_000010.10 - 51502574	Apr 26, 2021 (155)
59	14KJPN	NC_000010.11 - 46093248	Oct 16, 2022 (156)
60	TopMed	NC_000010.11 - 46093248	Apr 26, 2021 (155)
61	UK 10K study - Twins	NC_000010.10 - 51502574	Oct 12, 2018 (152)
62	ALFA	NC_000010.11 - 46093248	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).

Associated ID	History Updated (Build)
rs61850107	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss84321419	NC_000010.8:51172579:A:T	NC_000010.11:46093247:T:A	(self)
ss88202026, ss207367062, ss254294389, ss280606170, ss286184740	NC_000010.9:51172579:A:T	NC_000010.11:46093247:T:A	(self)
49739385, 27609315, 12309159, 29397539, 12864910, 26176900, 55513608, 27609315, ss336120240, ss656687413, ss987464489, ss1337355372, ss1426311968, ss1624526634, ss1667520667, ss1806377671, ss1930822980, ss2627536722, ss2698647812, ss2710709644, ss2888552583, ss3006440392, ss3349109182, ss3748077658, ss3786663376, ss3791844514, ss3796726457, ss3832110472, ss3839591181, ss3874159920, ss3922220145, ss5197544301, ss5393330374, ss5649238177, ss5824364317, ss5940507310, ss5980613990	NC_000010.10:51502573:A:T	NC_000010.11:46093247:T:A	(self)
65254869, 350931174, 24171662, 77028105, 66525982, 7622336952, ss3649356674, ss3813424354, ss3845056653, ss3967793661, ss4217611604, ss4850980327, ss5283876839, ss5577728934, ss5743191001, ss5811486499	NC_000010.11:46093247:T:A	NC_000010.11:46093247:T:A	(self)
ss102876271, ss131855237, ss184957347	NT_030059.13:2307037:A:T	NC_000010.11:46093247:T:A	(self)
7622336952	NC_000010.11:46093247:T:C	NC_000010.11:46093247: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 rs57858801

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

rs57858801