Name: rs5933049
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.

rs5933049

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:125970935 (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=0.167483 (44331/264690, TOPMED)
C=0.161001 (16643/103372, GnomAD)
C=0.13327 (8491/63712, ALFA) (+ 16 more)
C=0.14328 (3184/22222, 14KJPN)
C=0.14008 (1799/12843, 8.3KJPN)
C=0.1553 (746/4805, 1000G_30x)
C=0.1542 (582/3775, 1000G)
C=0.1305 (484/3708, TWINSUK)
C=0.1099 (322/2930, KOREAN)
C=0.1353 (391/2889, ALSPAC)
C=0.1593 (330/2072, HGDP_Stanford)
C=0.2084 (393/1886, HapMap)
T=0.170 (19/112, SGDP_PRJ)
C=0.176 (19/108, Qatari)
C=0.19 (9/48, Vietnamese)
C=0.10 (4/40, GENOME_DK)
C=0.0 (0/6, Ancient Sardinia)
T=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)

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	63712	T=0.86673	C=0.13327
European	Sub	50326	T=0.87474	C=0.12526
African	Sub	5120	T=0.7785	C=0.2215
African Others	Sub	182	T=0.742	C=0.258
African American	Sub	4938	T=0.7799	C=0.2201
Asian	Sub	234	T=0.880	C=0.120
East Asian	Sub	162	T=0.889	C=0.111
Other Asian	Sub	72	T=0.86	C=0.14
Latin American 1	Sub	312	T=0.811	C=0.189
Latin American 2	Sub	1368	T=0.8523	C=0.1477
South Asian	Sub	4952	T=0.8893	C=0.1107
Other	Sub	1400	T=0.8457	C=0.1543

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=0.832517	C=0.167483
gnomAD - Genomes	Global	Study-wide	103372	T=0.838999	C=0.161001
gnomAD - Genomes	European	Sub	56876	T=0.87167	C=0.12833
gnomAD - Genomes	African	Sub	30959	T=0.76921	C=0.23079
gnomAD - Genomes	American	Sub	9235	T=0.8440	C=0.1560
gnomAD - Genomes	Ashkenazi Jewish	Sub	2514	T=0.8620	C=0.1380
gnomAD - Genomes	East Asian	Sub	2241	T=0.9264	C=0.0736
gnomAD - Genomes	Other	Sub	1547	T=0.8410	C=0.1590
Allele Frequency Aggregator	Total	Global	63712	T=0.86673	C=0.13327
Allele Frequency Aggregator	European	Sub	50326	T=0.87474	C=0.12526
Allele Frequency Aggregator	African	Sub	5120	T=0.7785	C=0.2215
Allele Frequency Aggregator	South Asian	Sub	4952	T=0.8893	C=0.1107
Allele Frequency Aggregator	Other	Sub	1400	T=0.8457	C=0.1543
Allele Frequency Aggregator	Latin American 2	Sub	1368	T=0.8523	C=0.1477
Allele Frequency Aggregator	Latin American 1	Sub	312	T=0.811	C=0.189
Allele Frequency Aggregator	Asian	Sub	234	T=0.880	C=0.120
14KJPN	JAPANESE	Study-wide	22222	T=0.85672	C=0.14328
8.3KJPN	JAPANESE	Study-wide	12843	T=0.85992	C=0.14008
1000Genomes_30x	Global	Study-wide	4805	T=0.8447	C=0.1553
1000Genomes_30x	African	Sub	1328	T=0.7598	C=0.2402
1000Genomes_30x	Europe	Sub	961	T=0.856	C=0.144
1000Genomes_30x	South Asian	Sub	883	T=0.904	C=0.096
1000Genomes_30x	East Asian	Sub	878	T=0.916	C=0.084
1000Genomes_30x	American	Sub	755	T=0.828	C=0.172
1000Genomes	Global	Study-wide	3775	T=0.8458	C=0.1542
1000Genomes	African	Sub	1003	T=0.7498	C=0.2502
1000Genomes	Europe	Sub	766	T=0.851	C=0.149
1000Genomes	East Asian	Sub	764	T=0.914	C=0.086
1000Genomes	South Asian	Sub	718	T=0.911	C=0.089
1000Genomes	American	Sub	524	T=0.834	C=0.166
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8695	C=0.1305
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.8901	C=0.1099
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	2889	T=0.8647	C=0.1353
HGDP-CEPH-db Supplement 1	Global	Study-wide	2072	T=0.8407	C=0.1593
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	466	T=0.916	C=0.084
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	T=0.891	C=0.109
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	T=0.889	C=0.111
HGDP-CEPH-db Supplement 1	Europe	Sub	318	T=0.808	C=0.192
HGDP-CEPH-db Supplement 1	Africa	Sub	238	T=0.487	C=0.513
HGDP-CEPH-db Supplement 1	America	Sub	216	T=0.917	C=0.083
HGDP-CEPH-db Supplement 1	Oceania	Sub	70	T=0.91	C=0.09
HapMap	Global	Study-wide	1886	T=0.7916	C=0.2084
HapMap	American	Sub	766	T=0.859	C=0.141
HapMap	African	Sub	690	T=0.674	C=0.326
HapMap	Asian	Sub	254	T=0.890	C=0.110
HapMap	Europe	Sub	176	T=0.818	C=0.182
SGDP_PRJ	Global	Study-wide	112	T=0.170	C=0.830
Qatari	Global	Study-wide	108	T=0.824	C=0.176
A Vietnamese Genetic Variation Database	Global	Study-wide	48	T=0.81	C=0.19
The Danish reference pan genome	Danish	Study-wide	40	T=0.90	C=0.10
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	6	T=1.0	C=0.0
Siberian	Global	Study-wide	2	T=0.5	C=0.5

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 X	NC_000023.11:g.125970935T>C
GRCh37.p13 chr X	NC_000023.10:g.125104917T>C

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 X	NC_000023.11:g.125970935=	NC_000023.11:g.125970935T>C
GRCh37.p13 chr X	NC_000023.10:g.125104917=	NC_000023.10:g.125104917T>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#.

63 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8212990	Apr 21, 2003 (114)
2	CSHL-HAPMAP	ss20384755	Feb 27, 2004 (120)
3	PERLEGEN	ss46556344	Mar 15, 2006 (126)
4	ILLUMINA	ss66719253	Nov 30, 2006 (127)
5	ILLUMINA	ss67426977	Nov 30, 2006 (127)
6	ILLUMINA	ss67785178	Nov 30, 2006 (127)
7	ILLUMINA	ss70850393	May 24, 2008 (130)
8	ILLUMINA	ss71435609	May 17, 2007 (127)
9	ILLUMINA	ss75652698	Dec 06, 2007 (129)
10	AFFY	ss76821594	Dec 06, 2007 (129)
11	ILLUMINA	ss79211848	Dec 15, 2007 (130)
12	KRIBB_YJKIM	ss84433252	Dec 15, 2007 (130)
13	BGI	ss105763266	Feb 05, 2009 (130)
14	ILLUMINA-UK	ss115652074	Feb 14, 2009 (130)
15	ILLUMINA	ss122486764	Dec 01, 2009 (131)
16	ILLUMINA	ss154344633	Dec 01, 2009 (131)
17	GMI	ss157710409	Dec 01, 2009 (131)
18	ILLUMINA	ss159521122	Dec 01, 2009 (131)
19	ILLUMINA	ss172060778	Jul 04, 2010 (132)
20	ILLUMINA	ss173942910	Jul 04, 2010 (132)
21	BUSHMAN	ss204364142	Jul 04, 2010 (132)
22	GMI	ss283863681	May 04, 2012 (137)
23	1000GENOMES	ss341784854	May 09, 2011 (134)
24	TISHKOFF	ss567035040	Apr 25, 2013 (138)
25	SSMP	ss663009508	Apr 25, 2013 (138)
26	ILLUMINA	ss825542366	Apr 01, 2015 (144)
27	ILLUMINA	ss833032404	Jul 14, 2019 (153)
28	JMKIDD_LAB	ss1083123078	Aug 21, 2014 (142)
29	1000GENOMES	ss1556075517	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1583503097	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1641493095	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1684487128	Apr 01, 2015 (144)
33	WEILL_CORNELL_DGM	ss1939706271	Feb 12, 2016 (147)
34	GENOMED	ss1971432278	Jul 19, 2016 (147)
35	USC_VALOUEV	ss2159231264	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2320193548	Dec 20, 2016 (150)
37	GRF	ss2710348767	Nov 08, 2017 (151)
38	GNOMAD	ss2983162090	Nov 08, 2017 (151)
39	SWEGEN	ss3020589736	Nov 08, 2017 (151)
40	BIOINF_KMB_FNS_UNIBA	ss3029115275	Nov 08, 2017 (151)
41	ILLUMINA	ss3638876035	Oct 12, 2018 (152)
42	ILLUMINA	ss3639437448	Oct 12, 2018 (152)
43	ILLUMINA	ss3639754665	Oct 12, 2018 (152)
44	ILLUMINA	ss3641260954	Oct 12, 2018 (152)
45	ILLUMINA	ss3641558859	Oct 12, 2018 (152)
46	ILLUMINA	ss3643799737	Oct 12, 2018 (152)
47	EVA	ss3770597027	Jul 14, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3823374482	Jul 14, 2019 (153)
49	EVA	ss3836307992	Apr 27, 2020 (154)
50	HGDP	ss3847979215	Apr 27, 2020 (154)
51	SGDP_PRJ	ss3892221224	Apr 27, 2020 (154)
52	KRGDB	ss3942907726	Apr 27, 2020 (154)
53	EVA	ss3985964382	Apr 26, 2021 (155)
54	TOPMED	ss5136630394	Apr 26, 2021 (155)
55	TOMMO_GENOMICS	ss5236183559	Apr 26, 2021 (155)
56	1000G_HIGH_COVERAGE	ss5313860871	Oct 16, 2022 (156)
57	HUGCELL_USP	ss5505278438	Oct 16, 2022 (156)
58	1000G_HIGH_COVERAGE	ss5622909757	Oct 16, 2022 (156)
59	SANFORD_IMAGENETICS	ss5665854856	Oct 16, 2022 (156)
60	TOMMO_GENOMICS	ss5798533415	Oct 16, 2022 (156)
61	YY_MCH	ss5819339698	Oct 16, 2022 (156)
62	EVA	ss5857194442	Oct 16, 2022 (156)
63	EVA	ss5978965861	Oct 16, 2022 (156)
64	1000Genomes	NC_000023.10 - 125104917	Oct 12, 2018 (152)
65	1000Genomes_30x	NC_000023.11 - 125970935	Oct 16, 2022 (156)
66	The Avon Longitudinal Study of Parents and Children	NC_000023.10 - 125104917	Oct 12, 2018 (152)
67	The Danish reference pan genome	NC_000023.10 - 125104917	Apr 27, 2020 (154)
68	gnomAD - Genomes	NC_000023.11 - 125970935	Apr 26, 2021 (155)
69	HGDP-CEPH-db Supplement 1	NC_000023.9 - 124932598	Apr 27, 2020 (154)
70	HapMap	NC_000023.11 - 125970935	Apr 27, 2020 (154)
71	KOREAN population from KRGDB	NC_000023.10 - 125104917	Apr 27, 2020 (154)
72	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000023.10 - 125104917	Apr 26, 2021 (155)
73	Qatari	NC_000023.10 - 125104917	Apr 27, 2020 (154)
74	SGDP_PRJ	NC_000023.10 - 125104917	Apr 27, 2020 (154)
75	Siberian	NC_000023.10 - 125104917	Apr 27, 2020 (154)
76	8.3KJPN	NC_000023.10 - 125104917	Apr 26, 2021 (155)
77	14KJPN	NC_000023.11 - 125970935	Oct 16, 2022 (156)
78	TopMed	NC_000023.11 - 125970935	Apr 26, 2021 (155)
79	UK 10K study - Twins	NC_000023.10 - 125104917	Oct 12, 2018 (152)
80	A Vietnamese Genetic Variation Database	NC_000023.10 - 125104917	Jul 14, 2019 (153)
81	ALFA	NC_000023.11 - 125970935	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)
rs58748354	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss3639437448, ss3639754665	NC_000023.8:124830451:T:C	NC_000023.11:125970934:T:C	(self)
657107, ss115652074, ss204364142, ss283863681, ss825542366, ss3643799737, ss3847979215	NC_000023.9:124932597:T:C	NC_000023.11:125970934:T:C	(self)
84034770, 46291117, 9668034, 50085120, 1190309, 21748193, 44238204, 11747618, 94152866, 46291117, 10176729, ss341784854, ss567035040, ss663009508, ss833032404, ss1083123078, ss1556075517, ss1583503097, ss1641493095, ss1684487128, ss1939706271, ss1971432278, ss2159231264, ss2710348767, ss2983162090, ss3020589736, ss3638876035, ss3641260954, ss3641558859, ss3770597027, ss3836307992, ss3892221224, ss3942907726, ss3985964382, ss5236183559, ss5665854856, ss5978965861	NC_000023.10:125104916:T:C	NC_000023.11:125970934:T:C	(self)
110435692, 590833905, 4033184, 132370519, 700236751, 4419318221, ss2320193548, ss3029115275, ss3823374482, ss5136630394, ss5313860871, ss5505278438, ss5622909757, ss5798533415, ss5819339698, ss5857194442	NC_000023.11:125970934:T:C	NC_000023.11:125970934:T:C	(self)
ss20384755	NT_011786.14:683020:T:C	NC_000023.11:125970934:T:C	(self)
ss8212990, ss46556344, ss66719253, ss67426977, ss67785178, ss70850393, ss71435609, ss75652698, ss76821594, ss79211848, ss84433252, ss105763266, ss122486764, ss154344633, ss157710409, ss159521122, ss172060778, ss173942910	NT_011786.16:9372626:T:C	NC_000023.11:125970934: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 rs5933049

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

rs5933049