Name: rs2013191
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.

rs2013191

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:21953359 (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: G>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.120737 (31958/264690, TOPMED)
G=0.25186 (5597/22223, 14KJPN)
G=0.14087 (2609/18520, ALFA) (+ 11 more)
G=0.25212 (3238/12843, 8.3KJPN)
G=0.1494 (718/4805, 1000G_30x)
G=0.1494 (564/3775, 1000G)
G=0.1699 (630/3708, TWINSUK)
G=0.2642 (774/2930, KOREAN)
G=0.1762 (509/2889, ALSPAC)
G=0.048 (24/498, SGDP_PRJ)
G=0.102 (11/108, Qatari)
G=0.10 (5/48, Vietnamese)
G=0.12 (5/40, GENOME_DK)
G=0.07 (3/40, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SMS : 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	G=0.14087	A=0.85913
European	Sub	14152	G=0.16174	A=0.83826
African	Sub	2898	G=0.0335	A=0.9665
African Others	Sub	114	G=0.009	A=0.991
African American	Sub	2784	G=0.0345	A=0.9655
Asian	Sub	112	G=0.179	A=0.821
East Asian	Sub	86	G=0.20	A=0.80
Other Asian	Sub	26	G=0.12	A=0.88
Latin American 1	Sub	146	G=0.110	A=0.890
Latin American 2	Sub	610	G=0.151	A=0.849
South Asian	Sub	98	G=0.26	A=0.74
Other	Sub	504	G=0.139	A=0.861

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	G=0.120737	A=0.879263
14KJPN	JAPANESE	Study-wide	22223	G=0.25186	A=0.74814
Allele Frequency Aggregator	Total	Global	18520	G=0.14087	A=0.85913
Allele Frequency Aggregator	European	Sub	14152	G=0.16174	A=0.83826
Allele Frequency Aggregator	African	Sub	2898	G=0.0335	A=0.9665
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.151	A=0.849
Allele Frequency Aggregator	Other	Sub	504	G=0.139	A=0.861
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.110	A=0.890
Allele Frequency Aggregator	Asian	Sub	112	G=0.179	A=0.821
Allele Frequency Aggregator	South Asian	Sub	98	G=0.26	A=0.74
8.3KJPN	JAPANESE	Study-wide	12843	G=0.25212	A=0.74788
1000Genomes_30x	Global	Study-wide	4805	G=0.1494	A=0.8506
1000Genomes_30x	African	Sub	1328	G=0.0128	A=0.9872
1000Genomes_30x	Europe	Sub	961	G=0.207	A=0.793
1000Genomes_30x	South Asian	Sub	883	G=0.257	A=0.743
1000Genomes_30x	East Asian	Sub	878	G=0.192	A=0.808
1000Genomes_30x	American	Sub	755	G=0.140	A=0.860
1000Genomes	Global	Study-wide	3775	G=0.1494	A=0.8506
1000Genomes	African	Sub	1003	G=0.0120	A=0.9880
1000Genomes	Europe	Sub	766	G=0.196	A=0.804
1000Genomes	East Asian	Sub	764	G=0.185	A=0.815
1000Genomes	South Asian	Sub	718	G=0.259	A=0.741
1000Genomes	American	Sub	524	G=0.143	A=0.857
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.1699	A=0.8301
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.2642	A=0.7358, T=0.0000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	2889	G=0.1762	A=0.8238
SGDP_PRJ	Global	Study-wide	498	G=0.048	A=0.952
Qatari	Global	Study-wide	108	G=0.102	A=0.898
A Vietnamese Genetic Variation Database	Global	Study-wide	48	G=0.10	A=0.90
The Danish reference pan genome	Danish	Study-wide	40	G=0.12	A=0.88
Siberian	Global	Study-wide	40	G=0.07	A=0.93

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.21953359G>A
GRCh38.p14 chr X	NC_000023.11:g.21953359G>T
GRCh37.p13 chr X	NC_000023.10:g.21971477G>A
GRCh37.p13 chr X	NC_000023.10:g.21971477G>T
SMS RefSeqGene	NG_009228.1:g.17636G>A
SMS RefSeqGene	NG_009228.1:g.17636G>T

Gene: SMS, spermine synthase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SMS transcript variant 2	NM_001258423.2:c.49+12486… NM_001258423.2:c.49+12486G>A	N/A	Intron Variant
SMS transcript variant 1	NM_004595.5:c.49+12486G>A	N/A	Intron Variant
SMS transcript variant X1	XM_011545568.3:c.-54+1199… XM_011545568.3:c.-54+11992G>A	N/A	Intron Variant
SMS transcript variant X2	XM_005274582.3:c.	N/A	Genic Upstream Transcript 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	G=	A	T
GRCh38.p14 chr X	NC_000023.11:g.21953359=	NC_000023.11:g.21953359G>A	NC_000023.11:g.21953359G>T
GRCh37.p13 chr X	NC_000023.10:g.21971477=	NC_000023.10:g.21971477G>A	NC_000023.10:g.21971477G>T
SMS RefSeqGene	NG_009228.1:g.17636=	NG_009228.1:g.17636G>A	NG_009228.1:g.17636G>T
SMS transcript variant 2	NM_001258423.1:c.49+12486=	NM_001258423.1:c.49+12486G>A	NM_001258423.1:c.49+12486G>T
SMS transcript variant 2	NM_001258423.2:c.49+12486=	NM_001258423.2:c.49+12486G>A	NM_001258423.2:c.49+12486G>T
SMS transcript variant 1	NM_004595.4:c.49+12486=	NM_004595.4:c.49+12486G>A	NM_004595.4:c.49+12486G>T
SMS transcript variant 1	NM_004595.5:c.49+12486=	NM_004595.5:c.49+12486G>A	NM_004595.5:c.49+12486G>T
SMS transcript variant X2	XM_005274583.1:c.-146+12486=	XM_005274583.1:c.-146+12486G>A	XM_005274583.1:c.-146+12486G>T
SMS transcript variant X1	XM_011545568.3:c.-54+11992=	XM_011545568.3:c.-54+11992G>A	XM_011545568.3:c.-54+11992G>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#.

53 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2923528	Jan 23, 2001 (92)
2	WI_SSAHASNP	ss6662813	Feb 20, 2003 (117)
3	SC_SNP	ss8175408	Apr 21, 2003 (114)
4	WI_SSAHASNP	ss12030894	Jul 11, 2003 (116)
5	CSHL-HAPMAP	ss18046803	Feb 27, 2004 (120)
6	ABI	ss43602572	Mar 15, 2006 (126)
7	HGSV	ss82736260	Dec 15, 2007 (130)
8	BCMHGSC_JDW	ss94240136	Mar 25, 2008 (129)
9	COMPLETE_GENOMICS	ss163052782	Jul 04, 2010 (132)
10	COMPLETE_GENOMICS	ss164556588	Jul 04, 2010 (132)
11	COMPLETE_GENOMICS	ss166123768	Jul 04, 2010 (132)
12	BUSHMAN	ss204178219	Jul 04, 2010 (132)
13	BCM-HGSC-SUB	ss208904730	Jul 04, 2010 (132)
14	BL	ss255936241	May 09, 2011 (134)
15	GMI	ss283707812	May 04, 2012 (137)
16	GMI	ss287597930	Apr 25, 2013 (138)
17	PJP	ss294531986	May 09, 2011 (134)
18	1000GENOMES	ss341353680	May 09, 2011 (134)
19	TISHKOFF	ss566792233	Apr 25, 2013 (138)
20	SSMP	ss662724348	Apr 25, 2013 (138)
21	JMKIDD_LAB	ss1082823867	Aug 21, 2014 (142)
22	DDI	ss1432012597	Apr 01, 2015 (144)
23	1000GENOMES	ss1553758251	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1583343316	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1640449584	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1683443617	Apr 01, 2015 (144)
27	WEILL_CORNELL_DGM	ss1939196863	Feb 12, 2016 (147)
28	USC_VALOUEV	ss2158975315	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2316141234	Dec 20, 2016 (150)
30	SYSTEMSBIOZJU	ss2629674020	Nov 08, 2017 (151)
31	GRF	ss2710102598	Nov 08, 2017 (151)
32	GNOMAD	ss2977118021	Nov 08, 2017 (151)
33	SWEGEN	ss3019719224	Nov 08, 2017 (151)
34	CSHL	ss3352915393	Nov 08, 2017 (151)
35	EVA	ss3769982723	Jul 13, 2019 (153)
36	PACBIO	ss3788880301	Jul 13, 2019 (153)
37	PACBIO	ss3793743268	Jul 13, 2019 (153)
38	PACBIO	ss3798628417	Jul 13, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3822825883	Jul 13, 2019 (153)
40	EVA	ss3836111419	Apr 27, 2020 (154)
41	EVA	ss3847189131	Apr 27, 2020 (154)
42	SGDP_PRJ	ss3891112973	Apr 27, 2020 (154)
43	KRGDB	ss3941471463	Apr 27, 2020 (154)
44	TOPMED	ss5117465365	Apr 26, 2021 (155)
45	TOMMO_GENOMICS	ss5233787549	Apr 26, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5312000171	Oct 16, 2022 (156)
47	1000G_HIGH_COVERAGE	ss5619934957	Oct 16, 2022 (156)
48	SANFORD_IMAGENETICS	ss5664966607	Oct 16, 2022 (156)
49	TOMMO_GENOMICS	ss5795292197	Oct 16, 2022 (156)
50	YY_MCH	ss5818927275	Oct 16, 2022 (156)
51	EVA	ss5857030447	Oct 16, 2022 (156)
52	EVA	ss5977937462	Oct 16, 2022 (156)
53	EVA	ss5981150949	Oct 16, 2022 (156)
54	1000Genomes	NC_000023.10 - 21971477	Oct 12, 2018 (152)
55	1000Genomes_30x	NC_000023.11 - 21953359	Oct 16, 2022 (156)
56	The Avon Longitudinal Study of Parents and Children	NC_000023.10 - 21971477	Oct 12, 2018 (152)
57	The Danish reference pan genome	NC_000023.10 - 21971477	Apr 27, 2020 (154)
58	KOREAN population from KRGDB	NC_000023.10 - 21971477	Apr 27, 2020 (154)
59	Qatari	NC_000023.10 - 21971477	Apr 27, 2020 (154)
60	SGDP_PRJ	NC_000023.10 - 21971477	Apr 27, 2020 (154)
61	Siberian	NC_000023.10 - 21971477	Apr 27, 2020 (154)
62	8.3KJPN	NC_000023.10 - 21971477	Apr 26, 2021 (155)
63	14KJPN	NC_000023.11 - 21953359	Oct 16, 2022 (156)
64	TopMed	NC_000023.11 - 21953359	Apr 26, 2021 (155)
65	UK 10K study - Twins	NC_000023.10 - 21971477	Oct 12, 2018 (152)
66	A Vietnamese Genetic Variation Database	NC_000023.10 - 21971477	Jul 13, 2019 (153)
67	ALFA	NC_000023.11 - 21953359	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)
rs4824212	Aug 27, 2003 (117)
rs60309841	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss82736260	NC_000023.8:21731133:G:A	NC_000023.11:21953358:G:A	(self)
ss94240136, ss163052782, ss164556588, ss166123768, ss204178219, ss208904730, ss255936241, ss283707812, ss287597930, ss294531986	NC_000023.9:21881397:G:A	NC_000023.11:21953358:G:A	(self)
81739903, 45150336, 9508253, 48648857, 21238785, 43129953, 11491669, 91756856, 45150336, 9957970, ss341353680, ss566792233, ss662724348, ss1082823867, ss1432012597, ss1553758251, ss1583343316, ss1640449584, ss1683443617, ss1939196863, ss2158975315, ss2629674020, ss2710102598, ss2977118021, ss3019719224, ss3352915393, ss3769982723, ss3788880301, ss3793743268, ss3798628417, ss3836111419, ss3891112973, ss3941471463, ss5233787549, ss5664966607, ss5977937462, ss5981150949	NC_000023.10:21971476:G:A	NC_000023.11:21953358:G:A	(self)
107460892, 129129301, 681071722, 1641365519, ss2316141234, ss3822825883, ss3847189131, ss5117465365, ss5312000171, ss5619934957, ss5795292197, ss5818927275, ss5857030447	NC_000023.11:21953358:G:A	NC_000023.11:21953358:G:A	(self)
ss12030894	NT_011757.12:8885943:G:A	NC_000023.11:21953358:G:A	(self)
ss18046803	NT_011757.13:17938041:G:A	NC_000023.11:21953358:G:A	(self)
ss2923528, ss6662813, ss8175408, ss43602572	NT_167197.1:19853238:G:A	NC_000023.11:21953358:G:A	(self)
48648857, ss3941471463	NC_000023.10:21971476:G:T	NC_000023.11:21953358:G: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 rs2013191

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

rs2013191