Name: rs1235299
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.

rs1235299

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:16279756 (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: A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.142321 (37671/264690, TOPMED)
A=0.23453 (14202/60554, ALFA)
A=0.0968 (465/4805, 1000G_30x) (+ 13 more)
A=0.0887 (335/3775, 1000G)
A=0.2349 (871/3708, TWINSUK)
A=0.0044 (13/2928, KOREAN)
A=0.2330 (673/2889, ALSPAC)
A=0.1018 (212/2082, HGDP_Stanford)
A=0.0723 (136/1880, HapMap)
A=0.040 (21/522, SGDP_PRJ)
A=0.139 (15/108, Qatari)
A=0.06 (3/50, Siberian)
A=0.04 (2/48, Vietnamese)
A=0.25 (10/40, GENOME_DK)
A=0.5 (4/8, Ancient Sardinia)
G=0.5 (4/8, Ancient Sardinia)

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	60554	A=0.23453	G=0.76547, T=0.00000
European	Sub	49382	A=0.26127	G=0.73873, T=0.00000
African	Sub	4397	A=0.0564	G=0.9436, T=0.0000
African Others	Sub	150	A=0.020	G=0.980, T=0.000
African American	Sub	4247	A=0.0577	G=0.9423, T=0.0000
Asian	Sub	94	A=0.02	G=0.98, T=0.00
East Asian	Sub	76	A=0.01	G=0.99, T=0.00
Other Asian	Sub	18	A=0.06	G=0.94, T=0.00
Latin American 1	Sub	126	A=0.254	G=0.746, T=0.000
Latin American 2	Sub	690	A=0.183	G=0.817, T=0.000
South Asian	Sub	4866	A=0.1397	G=0.8603, T=0.0000
Other	Sub	999	A=0.212	G=0.788, T=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	A=0.142321	G=0.857679
Allele Frequency Aggregator	Total	Global	60554	A=0.23453	G=0.76547, T=0.00000
Allele Frequency Aggregator	European	Sub	49382	A=0.26127	G=0.73873, T=0.00000
Allele Frequency Aggregator	South Asian	Sub	4866	A=0.1397	G=0.8603, T=0.0000
Allele Frequency Aggregator	African	Sub	4397	A=0.0564	G=0.9436, T=0.0000
Allele Frequency Aggregator	Other	Sub	999	A=0.212	G=0.788, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	690	A=0.183	G=0.817, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	126	A=0.254	G=0.746, T=0.000
Allele Frequency Aggregator	Asian	Sub	94	A=0.02	G=0.98, T=0.00
1000Genomes_30x	Global	Study-wide	4805	A=0.0968	G=0.9032
1000Genomes_30x	African	Sub	1328	A=0.0211	G=0.9789
1000Genomes_30x	Europe	Sub	961	A=0.216	G=0.784
1000Genomes_30x	South Asian	Sub	883	A=0.113	G=0.887
1000Genomes_30x	East Asian	Sub	878	A=0.010	G=0.990
1000Genomes_30x	American	Sub	755	A=0.159	G=0.841
1000Genomes	Global	Study-wide	3775	A=0.0887	G=0.9113
1000Genomes	African	Sub	1003	A=0.0189	G=0.9811
1000Genomes	Europe	Sub	766	A=0.202	G=0.798
1000Genomes	East Asian	Sub	764	A=0.010	G=0.990
1000Genomes	South Asian	Sub	718	A=0.104	G=0.896
1000Genomes	American	Sub	524	A=0.149	G=0.851
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.2349	G=0.7651
KOREAN population from KRGDB	KOREAN	Study-wide	2928	A=0.0044	G=0.9956, T=0.0000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	2889	A=0.2330	G=0.7670
HGDP-CEPH-db Supplement 1	Global	Study-wide	2082	A=0.1018	G=0.8982
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	A=0.015	G=0.985
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	A=0.159	G=0.841
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	A=0.140	G=0.860
HGDP-CEPH-db Supplement 1	Europe	Sub	318	A=0.151	G=0.849
HGDP-CEPH-db Supplement 1	Africa	Sub	242	A=0.004	G=0.996
HGDP-CEPH-db Supplement 1	America	Sub	216	A=0.144	G=0.856
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	A=0.14	G=0.86
HapMap	Global	Study-wide	1880	A=0.0723	G=0.9277
HapMap	American	Sub	766	A=0.117	G=0.883
HapMap	African	Sub	686	A=0.012	G=0.988
HapMap	Asian	Sub	254	A=0.012	G=0.988
HapMap	Europe	Sub	174	A=0.201	G=0.799
SGDP_PRJ	Global	Study-wide	522	A=0.040	G=0.960
Qatari	Global	Study-wide	108	A=0.139	G=0.861
Siberian	Global	Study-wide	50	A=0.06	G=0.94
A Vietnamese Genetic Variation Database	Global	Study-wide	48	A=0.04	G=0.96
The Danish reference pan genome	Danish	Study-wide	40	A=0.25	G=0.75
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	8	A=0.5	G=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.16279756A>G
GRCh38.p14 chr X	NC_000023.11:g.16279756A>T
GRCh37.p13 chr X	NC_000023.10:g.16297879A>G
GRCh37.p13 chr X	NC_000023.10:g.16297879A>T

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	A=	G	T
GRCh38.p14 chr X	NC_000023.11:g.16279756=	NC_000023.11:g.16279756A>G	NC_000023.11:g.16279756A>T
GRCh37.p13 chr X	NC_000023.10:g.16297879=	NC_000023.10:g.16297879A>G	NC_000023.10:g.16297879A>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#.

96 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1850119	Oct 18, 2000 (87)
2	SC_JCM	ss2453260	Nov 08, 2000 (89)
3	TSC-CSHL	ss5236532	Oct 08, 2002 (108)
4	SC_SNP	ss8269111	Apr 21, 2003 (114)
5	SC_SNP	ss8521537	Jul 11, 2003 (116)
6	CSHL-HAPMAP	ss20398177	Feb 27, 2004 (120)
7	SSAHASNP	ss21062723	Apr 05, 2004 (121)
8	ABI	ss43584696	Mar 14, 2006 (126)
9	ILLUMINA	ss66701536	Nov 29, 2006 (127)
10	ILLUMINA	ss67000286	Nov 29, 2006 (127)
11	ILLUMINA	ss67318448	Nov 29, 2006 (127)
12	ILLUMINA	ss70408275	May 17, 2007 (127)
13	ILLUMINA	ss70564828	May 23, 2008 (130)
14	ILLUMINA	ss71104582	May 17, 2007 (127)
15	ILLUMINA	ss75620851	Dec 07, 2007 (129)
16	KRIBB_YJKIM	ss83704628	Dec 14, 2007 (130)
17	BCMHGSC_JDW	ss94237303	Mar 25, 2008 (129)
18	BGI	ss105716720	Feb 04, 2009 (130)
19	1000GENOMES	ss112800031	Jan 25, 2009 (130)
20	1000GENOMES	ss114478786	Jan 25, 2009 (130)
21	ILLUMINA-UK	ss115595283	Feb 04, 2009 (130)
22	ILLUMINA	ss121555930	Dec 01, 2009 (131)
23	ENSEMBL	ss133698146	Dec 01, 2009 (131)
24	ENSEMBL	ss144502489	Dec 01, 2009 (131)
25	ILLUMINA	ss153179350	Dec 01, 2009 (131)
26	ILLUMINA	ss159213582	Dec 01, 2009 (131)
27	COMPLETE_GENOMICS	ss163044668	Jul 04, 2010 (132)
28	COMPLETE_GENOMICS	ss164510053	Jul 04, 2010 (132)
29	COMPLETE_GENOMICS	ss166114859	Jul 04, 2010 (132)
30	ILLUMINA	ss170101911	Jul 04, 2010 (132)
31	ILLUMINA	ss172026102	Jul 04, 2010 (132)
32	BUSHMAN	ss204168176	Jul 04, 2010 (132)
33	GMI	ss283702853	May 04, 2012 (137)
34	GMI	ss287596643	Apr 25, 2013 (138)
35	PJP	ss294529894	May 09, 2011 (134)
36	1000GENOMES	ss341332688	May 09, 2011 (134)
37	ILLUMINA	ss482848055	May 04, 2012 (137)
38	ILLUMINA	ss484351709	May 04, 2012 (137)
39	ILLUMINA	ss534793242	Sep 08, 2015 (146)
40	TISHKOFF	ss566780163	Apr 25, 2013 (138)
41	SSMP	ss662711666	Apr 25, 2013 (138)
42	ILLUMINA	ss780083221	Aug 21, 2014 (142)
43	ILLUMINA	ss781897737	Aug 21, 2014 (142)
44	ILLUMINA	ss825377549	Apr 01, 2015 (144)
45	ILLUMINA	ss832725986	Aug 21, 2014 (142)
46	ILLUMINA	ss833316816	Aug 21, 2014 (142)
47	ILLUMINA	ss835565287	Aug 21, 2014 (142)
48	JMKIDD_LAB	ss1082809409	Aug 21, 2014 (142)
49	DDI	ss1432009610	Apr 01, 2015 (144)
50	1000GENOMES	ss1553639421	Apr 01, 2015 (144)
51	EVA_GENOME_DK	ss1583337124	Apr 01, 2015 (144)
52	EVA_UK10K_ALSPAC	ss1640393264	Apr 01, 2015 (144)
53	EVA_UK10K_TWINSUK	ss1683387297	Apr 01, 2015 (144)
54	WEILL_CORNELL_DGM	ss1939172650	Feb 12, 2016 (147)
55	GENOMED	ss1971348703	Jul 19, 2016 (147)
56	USC_VALOUEV	ss2158964027	Dec 20, 2016 (150)
57	HUMAN_LONGEVITY	ss2315913671	Dec 20, 2016 (150)
58	SYSTEMSBIOZJU	ss2629670815	Nov 08, 2017 (151)
59	ILLUMINA	ss2634942142	Nov 08, 2017 (151)
60	GRF	ss2710092588	Nov 08, 2017 (151)
61	GNOMAD	ss2976810480	Nov 08, 2017 (151)
62	SWEGEN	ss3019678016	Nov 08, 2017 (151)
63	BIOINF_KMB_FNS_UNIBA	ss3029012992	Nov 08, 2017 (151)
64	ILLUMINA	ss3630401834	Oct 12, 2018 (152)
65	ILLUMINA	ss3632829238	Oct 12, 2018 (152)
66	ILLUMINA	ss3638847899	Oct 12, 2018 (152)
67	ILLUMINA	ss3639428619	Oct 12, 2018 (152)
68	ILLUMINA	ss3639748928	Oct 12, 2018 (152)
69	ILLUMINA	ss3642724746	Oct 12, 2018 (152)
70	ILLUMINA	ss3643772472	Oct 12, 2018 (152)
71	URBANLAB	ss3651252777	Oct 12, 2018 (152)
72	EVA	ss3769952129	Jul 13, 2019 (153)
73	PACBIO	ss3788877879	Jul 13, 2019 (153)
74	PACBIO	ss3793740589	Jul 13, 2019 (153)
75	PACBIO	ss3798625782	Jul 13, 2019 (153)
76	KHV_HUMAN_GENOMES	ss3822800397	Jul 13, 2019 (153)
77	EVA	ss3836104035	Apr 27, 2020 (154)
78	EVA	ss3841669480	Apr 27, 2020 (154)
79	EVA	ss3847186325	Apr 27, 2020 (154)
80	HGDP	ss3847968666	Apr 27, 2020 (154)
81	SGDP_PRJ	ss3891059504	Apr 27, 2020 (154)
82	KRGDB	ss3941401871	Apr 27, 2020 (154)
83	EVA	ss3985931184	Apr 26, 2021 (155)
84	TOPMED	ss5116482725	Apr 26, 2021 (155)
85	TOMMO_GENOMICS	ss5233667792	Apr 26, 2021 (155)
86	TOMMO_GENOMICS	ss5233667793	Apr 26, 2021 (155)
87	1000G_HIGH_COVERAGE	ss5311903423	Oct 16, 2022 (156)
88	EVA	ss5316074041	Oct 16, 2022 (156)
89	HUGCELL_USP	ss5503641516	Oct 16, 2022 (156)
90	1000G_HIGH_COVERAGE	ss5619786457	Oct 16, 2022 (156)
91	SANFORD_IMAGENETICS	ss5664923501	Oct 16, 2022 (156)
92	TOMMO_GENOMICS	ss5795135487	Oct 16, 2022 (156)
93	TOMMO_GENOMICS	ss5795135488	Oct 16, 2022 (156)
94	YY_MCH	ss5818909340	Oct 16, 2022 (156)
95	EVA	ss5857023318	Oct 16, 2022 (156)
96	EVA	ss5977886145	Oct 16, 2022 (156)
97	1000Genomes	NC_000023.10 - 16297879	Oct 12, 2018 (152)
98	1000Genomes_30x	NC_000023.11 - 16279756	Oct 16, 2022 (156)
99	The Avon Longitudinal Study of Parents and Children	NC_000023.10 - 16297879	Oct 12, 2018 (152)
100	The Danish reference pan genome	NC_000023.10 - 16297879	Apr 27, 2020 (154)
101	HGDP-CEPH-db Supplement 1	NC_000023.9 - 16207800	Apr 27, 2020 (154)
102	HapMap	NC_000023.11 - 16279756	Apr 27, 2020 (154)
103	KOREAN population from KRGDB	NC_000023.10 - 16297879	Apr 27, 2020 (154)
104	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000023.10 - 16297879	Apr 26, 2021 (155)
105	Qatari	NC_000023.10 - 16297879	Apr 27, 2020 (154)
106	SGDP_PRJ	NC_000023.10 - 16297879	Apr 27, 2020 (154)
107	Siberian	NC_000023.10 - 16297879	Apr 27, 2020 (154)
108	8.3KJPN Submission ignored due to conflicting rows: Row 91637099 (NC_000023.10:16297878:A:G 12570/12843) Row 91637100 (NC_000023.10:16297878:A:T 1/12843)	-	Apr 26, 2021 (155)
109	8.3KJPN Submission ignored due to conflicting rows: Row 91637099 (NC_000023.10:16297878:A:G 12570/12843) Row 91637100 (NC_000023.10:16297878:A:T 1/12843)	-	Apr 26, 2021 (155)
110	14KJPN Submission ignored due to conflicting rows: Row 128972591 (NC_000023.11:16279755:A:G 21753/22223) Row 128972592 (NC_000023.11:16279755:A:T 2/22223)	-	Oct 16, 2022 (156)
111	14KJPN Submission ignored due to conflicting rows: Row 128972591 (NC_000023.11:16279755:A:G 21753/22223) Row 128972592 (NC_000023.11:16279755:A:T 2/22223)	-	Oct 16, 2022 (156)
112	TopMed	NC_000023.11 - 16279756	Apr 26, 2021 (155)
113	UK 10K study - Twins	NC_000023.10 - 16297879	Oct 12, 2018 (152)
114	A Vietnamese Genetic Variation Database	NC_000023.10 - 16297879	Jul 13, 2019 (153)
115	ALFA	NC_000023.11 - 16279756	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)
rs57409433	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss3639428619, ss3639748928	NC_000023.8:16057535:A:G	NC_000023.11:16279755:A:G	(self)
646558, ss94237303, ss112800031, ss114478786, ss115595283, ss163044668, ss164510053, ss166114859, ss204168176, ss283702853, ss287596643, ss294529894, ss484351709, ss825377549, ss3643772472, ss3847968666	NC_000023.9:16207799:A:G	NC_000023.11:16279755:A:G	(self)
81622241, 45088906, 9502061, 48579265, 1157111, 21214572, 43076484, 11480381, 45088906, 9948168, ss341332688, ss482848055, ss534793242, ss566780163, ss662711666, ss780083221, ss781897737, ss832725986, ss833316816, ss835565287, ss1082809409, ss1432009610, ss1553639421, ss1583337124, ss1640393264, ss1683387297, ss1939172650, ss1971348703, ss2158964027, ss2629670815, ss2634942142, ss2710092588, ss2976810480, ss3019678016, ss3630401834, ss3632829238, ss3638847899, ss3642724746, ss3769952129, ss3788877879, ss3793740589, ss3798625782, ss3836104035, ss3841669480, ss3891059504, ss3941401871, ss3985931184, ss5233667792, ss5316074041, ss5664923501, ss5977886145	NC_000023.10:16297878:A:G	NC_000023.11:16279755:A:G	(self)
107312392, 3952710, 680089082, 15079195046, ss2315913671, ss3029012992, ss3651252777, ss3822800397, ss3847186325, ss5116482725, ss5311903423, ss5503641516, ss5619786457, ss5795135487, ss5818909340, ss5857023318	NC_000023.11:16279755:A:G	NC_000023.11:16279755:A:G	(self)
ss8521537	NT_011757.12:3212345:A:G	NC_000023.11:16279755:A:G	(self)
ss20398177, ss21062723	NT_011757.13:12264443:A:G	NC_000023.11:16279755:A:G	(self)
ss1850119, ss2453260, ss5236532, ss8269111, ss43584696, ss66701536, ss67000286, ss67318448, ss70408275, ss70564828, ss71104582, ss75620851, ss83704628, ss105716720, ss121555930, ss133698146, ss144502489, ss153179350, ss159213582, ss170101911, ss172026102	NT_167197.1:14179640:A:G	NC_000023.11:16279755:A:G	(self)
48579265, ss3941401871, ss5233667793	NC_000023.10:16297878:A:T	NC_000023.11:16279755:A:T	(self)
15079195046, ss5795135488	NC_000023.11:16279755:A:T	NC_000023.11:16279755:A: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 rs1235299

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

rs1235299