Name: rs1538925
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.

rs1538925

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:28561157 (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>C / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.318032 (84180/264690, TOPMED)
A=0.243553 (32792/134640, ALFA)
A=0.06356 (1796/28258, 14KJPN) (+ 17 more)
A=0.06331 (1061/16760, 8.3KJPN)
A=0.3070 (1966/6404, 1000G_30x)
A=0.2939 (1472/5008, 1000G)
A=0.2719 (1218/4480, Estonian)
A=0.2148 (828/3854, ALSPAC)
A=0.2238 (830/3708, TWINSUK)
A=0.1014 (297/2930, KOREAN)
A=0.1059 (194/1832, Korea1K)
A=0.2218 (252/1136, Daghestan)
A=0.224 (224/998, GoNL)
A=0.277 (166/600, NorthernSweden)
A=0.167 (83/498, SGDP_PRJ)
A=0.264 (57/216, Qatari)
A=0.103 (22/214, Vietnamese)
A=0.160 (33/206, HapMap)
A=0.17 (9/54, Siberian)
A=0.33 (13/40, GENOME_DK)

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	134640	A=0.243553	C=0.756447, T=0.000000
European	Sub	115672	A=0.223892	C=0.776108, T=0.000000
African	Sub	6452	A=0.5586	C=0.4414, T=0.0000
African Others	Sub	240	A=0.696	C=0.304, T=0.000
African American	Sub	6212	A=0.5533	C=0.4467, T=0.0000
Asian	Sub	514	A=0.111	C=0.889, T=0.000
East Asian	Sub	406	A=0.103	C=0.897, T=0.000
Other Asian	Sub	108	A=0.139	C=0.861, T=0.000
Latin American 1	Sub	602	A=0.336	C=0.664, T=0.000
Latin American 2	Sub	5600	A=0.2879	C=0.7121, T=0.0000
South Asian	Sub	102	A=0.265	C=0.735, T=0.000
Other	Sub	5698	A=0.2443	C=0.7557, T=0.0000

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=0.318032	C=0.681968
Allele Frequency Aggregator	Total	Global	134640	A=0.243553	C=0.756447, T=0.000000
Allele Frequency Aggregator	European	Sub	115672	A=0.223892	C=0.776108, T=0.000000
Allele Frequency Aggregator	African	Sub	6452	A=0.5586	C=0.4414, T=0.0000
Allele Frequency Aggregator	Other	Sub	5698	A=0.2443	C=0.7557, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	5600	A=0.2879	C=0.7121, T=0.0000
Allele Frequency Aggregator	Latin American 1	Sub	602	A=0.336	C=0.664, T=0.000
Allele Frequency Aggregator	Asian	Sub	514	A=0.111	C=0.889, T=0.000
Allele Frequency Aggregator	South Asian	Sub	102	A=0.265	C=0.735, T=0.000
14KJPN	JAPANESE	Study-wide	28258	A=0.06356	C=0.93644
8.3KJPN	JAPANESE	Study-wide	16760	A=0.06331	C=0.93669
1000Genomes_30x	Global	Study-wide	6404	A=0.3070	C=0.6930
1000Genomes_30x	African	Sub	1786	A=0.5845	C=0.4155
1000Genomes_30x	Europe	Sub	1266	A=0.2409	C=0.7591
1000Genomes_30x	South Asian	Sub	1202	A=0.2005	C=0.7995
1000Genomes_30x	East Asian	Sub	1170	A=0.0897	C=0.9103
1000Genomes_30x	American	Sub	980	A=0.277	C=0.723
1000Genomes	Global	Study-wide	5008	A=0.2939	C=0.7061
1000Genomes	African	Sub	1322	A=0.5832	C=0.4168
1000Genomes	East Asian	Sub	1008	A=0.0893	C=0.9107
1000Genomes	Europe	Sub	1006	A=0.2416	C=0.7584
1000Genomes	South Asian	Sub	978	A=0.190	C=0.810
1000Genomes	American	Sub	694	A=0.262	C=0.738
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.2719	C=0.7281
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.2148	C=0.7852
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.2238	C=0.7762
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.1014	C=0.8986, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	A=0.1059	C=0.8941
Genome-wide autozygosity in Daghestan	Global	Study-wide	1136	A=0.2218	C=0.7782
Genome-wide autozygosity in Daghestan	Daghestan	Sub	628	A=0.197	C=0.803
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	A=0.264	C=0.736
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	A=0.230	C=0.770
Genome-wide autozygosity in Daghestan	Europe	Sub	108	A=0.250	C=0.750
Genome-wide autozygosity in Daghestan	South Asian	Sub	98	A=0.30	C=0.70
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	A=0.17	C=0.83
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.224	C=0.776
Northern Sweden	ACPOP	Study-wide	600	A=0.277	C=0.723
SGDP_PRJ	Global	Study-wide	498	A=0.167	C=0.833
Qatari	Global	Study-wide	216	A=0.264	C=0.736
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.103	C=0.897
HapMap	Global	Study-wide	206	A=0.160	C=0.840
HapMap	American	Sub	116	A=0.250	C=0.750
HapMap	Asian	Sub	90	A=0.04	C=0.96
Siberian	Global	Study-wide	54	A=0.17	C=0.83
The Danish reference pan genome	Danish	Study-wide	40	A=0.33	C=0.68

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 13	NC_000013.11:g.28561157A>C
GRCh38.p14 chr 13	NC_000013.11:g.28561157A>T
GRCh37.p13 chr 13	NC_000013.10:g.29135294A>C
GRCh37.p13 chr 13	NC_000013.10:g.29135294A>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=	C	T
GRCh38.p14 chr 13	NC_000013.11:g.28561157=	NC_000013.11:g.28561157A>C	NC_000013.11:g.28561157A>T
GRCh37.p13 chr 13	NC_000013.10:g.29135294=	NC_000013.10:g.29135294A>C	NC_000013.10:g.29135294A>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#.

104 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2380521	Oct 23, 2000 (88)
2	BCM_SSAHASNP	ss11066577	Jul 11, 2003 (116)
3	SC_SNP	ss13254266	Dec 05, 2003 (119)
4	BCM_SSAHASNP	ss14156936	Dec 05, 2003 (119)
5	SSAHASNP	ss21104337	Apr 05, 2004 (121)
6	ABI	ss43462710	Mar 15, 2006 (126)
7	HGSV	ss78440054	Dec 07, 2007 (129)
8	HGSV	ss83692181	Dec 15, 2007 (130)
9	HGSV	ss84169955	Dec 15, 2007 (130)
10	BCMHGSC_JDW	ss89558292	Mar 24, 2008 (129)
11	HUMANGENOME_JCVI	ss96954651	Feb 05, 2009 (130)
12	BGI	ss106322346	Feb 05, 2009 (130)
13	1000GENOMES	ss112646732	Jan 25, 2009 (130)
14	1000GENOMES	ss114465914	Jan 25, 2009 (130)
15	ENSEMBL	ss133503973	Dec 01, 2009 (131)
16	ENSEMBL	ss137274237	Dec 01, 2009 (131)
17	GMI	ss154582926	Dec 01, 2009 (131)
18	ILLUMINA	ss160369073	Dec 01, 2009 (131)
19	COMPLETE_GENOMICS	ss167789779	Jul 04, 2010 (132)
20	COMPLETE_GENOMICS	ss169069735	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss208609355	Jul 04, 2010 (132)
22	1000GENOMES	ss226098905	Jul 14, 2010 (132)
23	1000GENOMES	ss236190300	Jul 15, 2010 (132)
24	1000GENOMES	ss242697830	Jul 15, 2010 (132)
25	BL	ss254884622	May 09, 2011 (134)
26	GMI	ss281652796	May 04, 2012 (137)
27	GMI	ss286675157	Apr 25, 2013 (138)
28	PJP	ss291564681	May 09, 2011 (134)
29	ILLUMINA	ss480022599	May 04, 2012 (137)
30	ILLUMINA	ss480031390	May 04, 2012 (137)
31	ILLUMINA	ss480693709	Sep 08, 2015 (146)
32	ILLUMINA	ss484809474	May 04, 2012 (137)
33	ILLUMINA	ss536889996	Sep 08, 2015 (146)
34	TISHKOFF	ss563571217	Apr 25, 2013 (138)
35	SSMP	ss659167024	Apr 25, 2013 (138)
36	ILLUMINA	ss778437502	Sep 08, 2015 (146)
37	ILLUMINA	ss782851303	Sep 08, 2015 (146)
38	ILLUMINA	ss783815836	Sep 08, 2015 (146)
39	ILLUMINA	ss832105188	Sep 08, 2015 (146)
40	ILLUMINA	ss833893015	Sep 08, 2015 (146)
41	EVA-GONL	ss990227882	Aug 21, 2014 (142)
42	JMKIDD_LAB	ss1078963276	Aug 21, 2014 (142)
43	1000GENOMES	ss1347617820	Aug 21, 2014 (142)
44	HAMMER_LAB	ss1397653060	Sep 08, 2015 (146)
45	DDI	ss1427140274	Apr 01, 2015 (144)
46	EVA_GENOME_DK	ss1576694586	Apr 01, 2015 (144)
47	EVA_UK10K_ALSPAC	ss1629956114	Apr 01, 2015 (144)
48	EVA_DECODE	ss1642332485	Apr 01, 2015 (144)
49	EVA_UK10K_TWINSUK	ss1672950147	Apr 01, 2015 (144)
50	ILLUMINA	ss1752099375	Sep 08, 2015 (146)
51	HAMMER_LAB	ss1807541464	Sep 08, 2015 (146)
52	WEILL_CORNELL_DGM	ss1933596812	Feb 12, 2016 (147)
53	GENOMED	ss1967743204	Jul 19, 2016 (147)
54	JJLAB	ss2027554019	Sep 14, 2016 (149)
55	USC_VALOUEV	ss2155918732	Dec 20, 2016 (150)
56	HUMAN_LONGEVITY	ss2195098920	Dec 20, 2016 (150)
57	SYSTEMSBIOZJU	ss2628265111	Nov 08, 2017 (151)
58	ILLUMINA	ss2633043764	Nov 08, 2017 (151)
59	GRF	ss2700290855	Nov 08, 2017 (151)
60	GNOMAD	ss2917939075	Nov 08, 2017 (151)
61	SWEGEN	ss3010773547	Nov 08, 2017 (151)
62	BIOINF_KMB_FNS_UNIBA	ss3027592510	Nov 08, 2017 (151)
63	CSHL	ss3350381680	Nov 08, 2017 (151)
64	ILLUMINA	ss3627029531	Oct 12, 2018 (152)
65	ILLUMINA	ss3631048009	Oct 12, 2018 (152)
66	ILLUMINA	ss3633044109	Oct 12, 2018 (152)
67	ILLUMINA	ss3633746225	Oct 12, 2018 (152)
68	ILLUMINA	ss3634537335	Oct 12, 2018 (152)
69	ILLUMINA	ss3635436447	Oct 12, 2018 (152)
70	ILLUMINA	ss3636223905	Oct 12, 2018 (152)
71	ILLUMINA	ss3637187502	Oct 12, 2018 (152)
72	ILLUMINA	ss3640244666	Oct 12, 2018 (152)
73	URBANLAB	ss3649996292	Oct 12, 2018 (152)
74	EGCUT_WGS	ss3678034315	Jul 13, 2019 (153)
75	EVA_DECODE	ss3694990676	Jul 13, 2019 (153)
76	ACPOP	ss3739611959	Jul 13, 2019 (153)
77	ILLUMINA	ss3744838069	Jul 13, 2019 (153)
78	EVA	ss3751275215	Jul 13, 2019 (153)
79	ILLUMINA	ss3772337184	Jul 13, 2019 (153)
80	PACBIO	ss3787414110	Jul 13, 2019 (153)
81	PACBIO	ss3792486792	Jul 13, 2019 (153)
82	PACBIO	ss3797370509	Jul 13, 2019 (153)
83	KHV_HUMAN_GENOMES	ss3816606229	Jul 13, 2019 (153)
84	EVA	ss3833466611	Apr 27, 2020 (154)
85	EVA	ss3840310446	Apr 27, 2020 (154)
86	EVA	ss3845795183	Apr 27, 2020 (154)
87	SGDP_PRJ	ss3879659824	Apr 27, 2020 (154)
88	KRGDB	ss3928481116	Apr 27, 2020 (154)
89	KOGIC	ss3973267206	Apr 27, 2020 (154)
90	TOPMED	ss4940982373	Apr 26, 2021 (155)
91	TOMMO_GENOMICS	ss5209314502	Apr 26, 2021 (155)
92	1000G_HIGH_COVERAGE	ss5293206843	Oct 16, 2022 (156)
93	EVA	ss5315671482	Oct 16, 2022 (156)
94	EVA	ss5409802510	Oct 16, 2022 (156)
95	HUGCELL_USP	ss5487623001	Oct 16, 2022 (156)
96	1000G_HIGH_COVERAGE	ss5591890742	Oct 16, 2022 (156)
97	SANFORD_IMAGENETICS	ss5654465630	Oct 16, 2022 (156)
98	TOMMO_GENOMICS	ss5760995495	Oct 16, 2022 (156)
99	EVA	ss5799892445	Oct 16, 2022 (156)
100	YY_MCH	ss5813978418	Oct 16, 2022 (156)
101	EVA	ss5839266089	Oct 16, 2022 (156)
102	EVA	ss5850661675	Oct 16, 2022 (156)
103	EVA	ss5924495365	Oct 16, 2022 (156)
104	EVA	ss5945871931	Oct 16, 2022 (156)
105	1000Genomes	NC_000013.10 - 29135294	Oct 12, 2018 (152)
106	1000Genomes_30x	NC_000013.11 - 28561157	Oct 16, 2022 (156)
107	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 29135294	Oct 12, 2018 (152)
108	Genome-wide autozygosity in Daghestan	NC_000013.9 - 28033294	Apr 27, 2020 (154)
109	Genetic variation in the Estonian population	NC_000013.10 - 29135294	Oct 12, 2018 (152)
110	The Danish reference pan genome	NC_000013.10 - 29135294	Apr 27, 2020 (154)
111	gnomAD - Genomes Submission ignored due to conflicting rows: Row 426371393 (NC_000013.11:28561156:A:C 95176/139906) Row 426371394 (NC_000013.11:28561156:A:T 8/139962)	-	Apr 26, 2021 (155)
112	gnomAD - Genomes Submission ignored due to conflicting rows: Row 426371393 (NC_000013.11:28561156:A:C 95176/139906) Row 426371394 (NC_000013.11:28561156:A:T 8/139962)	-	Apr 26, 2021 (155)
113	Genome of the Netherlands Release 5	NC_000013.10 - 29135294	Apr 27, 2020 (154)
114	HapMap	NC_000013.11 - 28561157	Apr 27, 2020 (154)
115	KOREAN population from KRGDB	NC_000013.10 - 29135294	Apr 27, 2020 (154)
116	Korean Genome Project	NC_000013.11 - 28561157	Apr 27, 2020 (154)
117	Northern Sweden	NC_000013.10 - 29135294	Jul 13, 2019 (153)
118	Qatari	NC_000013.10 - 29135294	Apr 27, 2020 (154)
119	SGDP_PRJ	NC_000013.10 - 29135294	Apr 27, 2020 (154)
120	Siberian	NC_000013.10 - 29135294	Apr 27, 2020 (154)
121	8.3KJPN	NC_000013.10 - 29135294	Apr 26, 2021 (155)
122	14KJPN	NC_000013.11 - 28561157	Oct 16, 2022 (156)
123	TopMed	NC_000013.11 - 28561157	Apr 26, 2021 (155)
124	UK 10K study - Twins	NC_000013.10 - 29135294	Oct 12, 2018 (152)
125	A Vietnamese Genetic Variation Database	NC_000013.10 - 29135294	Jul 13, 2019 (153)
126	ALFA	NC_000013.11 - 28561157	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)
rs59187452	May 25, 2008 (130)
rs386536414	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
123740, ss78440054, ss83692181, ss84169955, ss89558292, ss112646732, ss114465914, ss167789779, ss169069735, ss208609355, ss254884622, ss281652796, ss286675157, ss291564681, ss480022599, ss1397653060, ss1642332485	NC_000013.9:28033293:A:C	NC_000013.11:28561156:A:C	(self)
60466170, 33582834, 23772563, 3234191, 14984368, 35658510, 12896824, 15638742, 31676804, 8435086, 67283809, 33582834, 7449304, ss226098905, ss236190300, ss242697830, ss480031390, ss480693709, ss484809474, ss536889996, ss563571217, ss659167024, ss778437502, ss782851303, ss783815836, ss832105188, ss833893015, ss990227882, ss1078963276, ss1347617820, ss1427140274, ss1576694586, ss1629956114, ss1672950147, ss1752099375, ss1807541464, ss1933596812, ss1967743204, ss2027554019, ss2155918732, ss2628265111, ss2633043764, ss2700290855, ss2917939075, ss3010773547, ss3350381680, ss3627029531, ss3631048009, ss3633044109, ss3633746225, ss3634537335, ss3635436447, ss3636223905, ss3637187502, ss3640244666, ss3678034315, ss3739611959, ss3744838069, ss3751275215, ss3772337184, ss3787414110, ss3792486792, ss3797370509, ss3833466611, ss3840310446, ss3879659824, ss3928481116, ss5209314502, ss5315671482, ss5409802510, ss5654465630, ss5799892445, ss5839266089, ss5945871931	NC_000013.10:29135293:A:C	NC_000013.11:28561156:A:C	(self)
79416677, 954993, 29645207, 94832599, 156528031, 5611480182, ss2195098920, ss3027592510, ss3649996292, ss3694990676, ss3816606229, ss3845795183, ss3973267206, ss4940982373, ss5293206843, ss5487623001, ss5591890742, ss5760995495, ss5813978418, ss5850661675, ss5924495365	NC_000013.11:28561156:A:C	NC_000013.11:28561156:A:C	(self)
ss11066577, ss13254266	NT_009799.12:10115293:A:C	NC_000013.11:28561156:A:C	(self)
ss14156936, ss21104337	NT_024524.13:10115293:A:C	NC_000013.11:28561156:A:C	(self)
ss2380521, ss43462710, ss96954651, ss106322346, ss133503973, ss137274237, ss154582926, ss160369073	NT_024524.14:10115293:A:C	NC_000013.11:28561156:A:C	(self)
35658510, ss2917939075, ss3928481116	NC_000013.10:29135293:A:T	NC_000013.11:28561156:A:T	(self)
5611480182	NC_000013.11:28561156:A:T	NC_000013.11:28561156: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 rs1538925

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

rs1538925