Name: rs4625581
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.

rs4625581

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:28627079 (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=0.217420 (57549/264690, TOPMED)
A=0.210936 (29556/140118, GnomAD)
A=0.15257 (5429/35584, ALFA) (+ 16 more)
A=0.11034 (3118/28258, 14KJPN)
A=0.11259 (1887/16760, 8.3KJPN)
A=0.2057 (1317/6404, 1000G_30x)
A=0.2027 (1015/5008, 1000G)
A=0.1016 (455/4480, Estonian)
A=0.1399 (539/3854, ALSPAC)
A=0.1421 (527/3708, TWINSUK)
A=0.0952 (279/2930, KOREAN)
A=0.123 (123/998, GoNL)
A=0.125 (75/600, NorthernSweden)
A=0.125 (68/546, SGDP_PRJ)
A=0.134 (29/216, Qatari)
A=0.137 (29/212, Vietnamese)
A=0.11 (6/56, Siberian)
A=0.07 (3/40, GENOME_DK)
A=0.09 (2/22, 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	35584	A=0.15257	G=0.84743, T=0.00000
European	Sub	27182	A=0.12387	G=0.87613, T=0.00000
African	Sub	3408	A=0.4093	G=0.5907, T=0.0000
African Others	Sub	116	A=0.466	G=0.534, T=0.000
African American	Sub	3292	A=0.4074	G=0.5926, T=0.0000
Asian	Sub	176	A=0.136	G=0.864, T=0.000
East Asian	Sub	116	A=0.129	G=0.871, T=0.000
Other Asian	Sub	60	A=0.15	G=0.85, T=0.00
Latin American 1	Sub	272	A=0.176	G=0.824, T=0.000
Latin American 2	Sub	1990	A=0.0955	G=0.9045, T=0.0000
South Asian	Sub	126	A=0.151	G=0.849, T=0.000
Other	Sub	2430	A=0.1588	G=0.8412, 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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	A=0.217420	G=0.782580
gnomAD - Genomes	Global	Study-wide	140118	A=0.210936	G=0.789064
gnomAD - Genomes	European	Sub	75914	A=0.12865	G=0.87135
gnomAD - Genomes	African	Sub	41942	A=0.39876	G=0.60124
gnomAD - Genomes	American	Sub	13656	A=0.13320	G=0.86680
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.1197	G=0.8803
gnomAD - Genomes	East Asian	Sub	3128	A=0.1384	G=0.8616
gnomAD - Genomes	Other	Sub	2154	A=0.1927	G=0.8073
Allele Frequency Aggregator	Total	Global	35584	A=0.15257	G=0.84743, T=0.00000
Allele Frequency Aggregator	European	Sub	27182	A=0.12387	G=0.87613, T=0.00000
Allele Frequency Aggregator	African	Sub	3408	A=0.4093	G=0.5907, T=0.0000
Allele Frequency Aggregator	Other	Sub	2430	A=0.1588	G=0.8412, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	1990	A=0.0955	G=0.9045, T=0.0000
Allele Frequency Aggregator	Latin American 1	Sub	272	A=0.176	G=0.824, T=0.000
Allele Frequency Aggregator	Asian	Sub	176	A=0.136	G=0.864, T=0.000
Allele Frequency Aggregator	South Asian	Sub	126	A=0.151	G=0.849, T=0.000
14KJPN	JAPANESE	Study-wide	28258	A=0.11034	G=0.88966
8.3KJPN	JAPANESE	Study-wide	16760	A=0.11259	G=0.88741
1000Genomes_30x	Global	Study-wide	6404	A=0.2057	G=0.7943
1000Genomes_30x	African	Sub	1786	A=0.3998	G=0.6002
1000Genomes_30x	Europe	Sub	1266	A=0.1453	G=0.8547
1000Genomes_30x	South Asian	Sub	1202	A=0.1173	G=0.8827
1000Genomes_30x	East Asian	Sub	1170	A=0.1325	G=0.8675
1000Genomes_30x	American	Sub	980	A=0.126	G=0.874
1000Genomes	Global	Study-wide	5008	A=0.2027	G=0.7973
1000Genomes	African	Sub	1322	A=0.4032	G=0.5968
1000Genomes	East Asian	Sub	1008	A=0.1300	G=0.8700
1000Genomes	Europe	Sub	1006	A=0.1481	G=0.8519
1000Genomes	South Asian	Sub	978	A=0.118	G=0.882
1000Genomes	American	Sub	694	A=0.125	G=0.875
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.1016	G=0.8984
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.1399	G=0.8601
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.1421	G=0.8579
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.0952	G=0.9048
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.123	G=0.877
Northern Sweden	ACPOP	Study-wide	600	A=0.125	G=0.875
SGDP_PRJ	Global	Study-wide	546	A=0.125	G=0.875
Qatari	Global	Study-wide	216	A=0.134	G=0.866
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.137	G=0.863
Siberian	Global	Study-wide	56	A=0.11	G=0.89
The Danish reference pan genome	Danish	Study-wide	40	A=0.07	G=0.93
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	22	A=0.09	G=0.91

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.28627079A>G
GRCh38.p14 chr 13	NC_000013.11:g.28627079A>T
GRCh37.p13 chr 13	NC_000013.10:g.29201216A>G
GRCh37.p13 chr 13	NC_000013.10:g.29201216A>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 13	NC_000013.11:g.28627079=	NC_000013.11:g.28627079A>G	NC_000013.11:g.28627079A>T
GRCh37.p13 chr 13	NC_000013.10:g.29201216=	NC_000013.10:g.29201216A>G	NC_000013.10:g.29201216A>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#.

94 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss6276405	Feb 20, 2003 (111)
2	BCM_SSAHASNP	ss11074577	Jul 11, 2003 (116)
3	SC_SNP	ss13254274	Dec 05, 2003 (119)
4	SSAHASNP	ss21122143	Apr 05, 2004 (121)
5	PERLEGEN	ss23468798	Sep 20, 2004 (123)
6	ABI	ss43518351	Mar 13, 2006 (126)
7	AFFY	ss66485701	Nov 29, 2006 (127)
8	PERLEGEN	ss69129441	May 17, 2007 (127)
9	AFFY	ss76306038	Dec 06, 2007 (129)
10	KRIBB_YJKIM	ss82072462	Dec 14, 2007 (130)
11	HGSV	ss83903881	Dec 14, 2007 (130)
12	BCMHGSC_JDW	ss89558856	Mar 24, 2008 (129)
13	HUMANGENOME_JCVI	ss96954742	Feb 04, 2009 (130)
14	BGI	ss106322399	Feb 04, 2009 (130)
15	1000GENOMES	ss112647388	Jan 25, 2009 (130)
16	1000GENOMES	ss114467067	Jan 25, 2009 (130)
17	ILLUMINA-UK	ss118401667	Feb 14, 2009 (130)
18	ENSEMBL	ss133504426	Dec 01, 2009 (131)
19	ENSEMBL	ss137273967	Dec 01, 2009 (131)
20	GMI	ss154584176	Dec 01, 2009 (131)
21	COMPLETE_GENOMICS	ss167791451	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss169071854	Jul 04, 2010 (132)
23	COMPLETE_GENOMICS	ss170931937	Jul 04, 2010 (132)
24	AFFY	ss173199147	Jul 04, 2010 (132)
25	BUSHMAN	ss199013248	Jul 04, 2010 (132)
26	BCM-HGSC-SUB	ss208635676	Jul 04, 2010 (132)
27	1000GENOMES	ss226099281	Jul 14, 2010 (132)
28	1000GENOMES	ss236190564	Jul 15, 2010 (132)
29	1000GENOMES	ss242698067	Jul 15, 2010 (132)
30	GMI	ss281653068	May 04, 2012 (137)
31	GMI	ss286675308	Apr 25, 2013 (138)
32	PJP	ss291564852	May 09, 2011 (134)
33	ILLUMINA	ss483174025	May 04, 2012 (137)
34	ILLUMINA	ss483342792	May 04, 2012 (137)
35	ILLUMINA	ss535556719	Sep 08, 2015 (146)
36	TISHKOFF	ss563571622	Apr 25, 2013 (138)
37	SSMP	ss659167403	Apr 25, 2013 (138)
38	ILLUMINA	ss779411924	Sep 08, 2015 (146)
39	ILLUMINA	ss782114517	Sep 08, 2015 (146)
40	ILLUMINA	ss834880989	Sep 08, 2015 (146)
41	EVA-GONL	ss990228440	Aug 21, 2014 (142)
42	JMKIDD_LAB	ss1078963734	Aug 21, 2014 (142)
43	1000GENOMES	ss1347619873	Aug 21, 2014 (142)
44	DDI	ss1427140519	Apr 01, 2015 (144)
45	EVA_GENOME_DK	ss1576695076	Apr 01, 2015 (144)
46	EVA_UK10K_ALSPAC	ss1629957282	Apr 01, 2015 (144)
47	EVA_DECODE	ss1642333014	Apr 01, 2015 (144)
48	EVA_UK10K_TWINSUK	ss1672951315	Apr 01, 2015 (144)
49	EVA_SVP	ss1713378460	Apr 01, 2015 (144)
50	HAMMER_LAB	ss1807541794	Sep 08, 2015 (146)
51	WEILL_CORNELL_DGM	ss1933597402	Feb 12, 2016 (147)
52	GENOMED	ss1967743384	Jul 19, 2016 (147)
53	JJLAB	ss2027554366	Sep 14, 2016 (149)
54	USC_VALOUEV	ss2155919107	Dec 20, 2016 (150)
55	HUMAN_LONGEVITY	ss2195102885	Dec 20, 2016 (150)
56	SYSTEMSBIOZJU	ss2628265331	Nov 08, 2017 (151)
57	ILLUMINA	ss2633043873	Nov 08, 2017 (151)
58	GRF	ss2700291256	Nov 08, 2017 (151)
59	GNOMAD	ss2917944459	Nov 08, 2017 (151)
60	SWEGEN	ss3010774373	Nov 08, 2017 (151)
61	BIOINF_KMB_FNS_UNIBA	ss3027592728	Nov 08, 2017 (151)
62	CSHL	ss3350381978	Nov 08, 2017 (151)
63	ILLUMINA	ss3627029681	Oct 12, 2018 (152)
64	ILLUMINA	ss3631048117	Oct 12, 2018 (152)
65	URBANLAB	ss3649996483	Oct 12, 2018 (152)
66	EGCUT_WGS	ss3678035111	Jul 13, 2019 (153)
67	EVA_DECODE	ss3694991605	Jul 13, 2019 (153)
68	ACPOP	ss3739612525	Jul 13, 2019 (153)
69	EVA	ss3751275923	Jul 13, 2019 (153)
70	PACBIO	ss3787414316	Jul 13, 2019 (153)
71	PACBIO	ss3792486990	Jul 13, 2019 (153)
72	PACBIO	ss3797370706	Jul 13, 2019 (153)
73	KHV_HUMAN_GENOMES	ss3816606927	Jul 13, 2019 (153)
74	EVA	ss3833466945	Apr 27, 2020 (154)
75	EVA	ss3840310671	Apr 27, 2020 (154)
76	EVA	ss3845795413	Apr 27, 2020 (154)
77	SGDP_PRJ	ss3879660906	Apr 27, 2020 (154)
78	KRGDB	ss3928482360	Apr 27, 2020 (154)
79	EVA	ss3985630924	Apr 26, 2021 (155)
80	TOPMED	ss4940998753	Apr 26, 2021 (155)
81	TOMMO_GENOMICS	ss5209316912	Apr 26, 2021 (155)
82	1000G_HIGH_COVERAGE	ss5293208661	Oct 16, 2022 (156)
83	EVA	ss5315671569	Oct 16, 2022 (156)
84	EVA	ss5409805850	Oct 16, 2022 (156)
85	HUGCELL_USP	ss5487624772	Oct 16, 2022 (156)
86	EVA	ss5510918781	Oct 16, 2022 (156)
87	1000G_HIGH_COVERAGE	ss5591893297	Oct 16, 2022 (156)
88	SANFORD_IMAGENETICS	ss5654466635	Oct 16, 2022 (156)
89	TOMMO_GENOMICS	ss5760998551	Oct 16, 2022 (156)
90	YY_MCH	ss5813978947	Oct 16, 2022 (156)
91	EVA	ss5839266795	Oct 16, 2022 (156)
92	EVA	ss5850661940	Oct 16, 2022 (156)
93	EVA	ss5924497455	Oct 16, 2022 (156)
94	EVA	ss5945873035	Oct 16, 2022 (156)
95	1000Genomes	NC_000013.10 - 29201216	Oct 12, 2018 (152)
96	1000Genomes_30x	NC_000013.11 - 28627079	Oct 16, 2022 (156)
97	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 29201216	Oct 12, 2018 (152)
98	Genetic variation in the Estonian population	NC_000013.10 - 29201216	Oct 12, 2018 (152)
99	The Danish reference pan genome	NC_000013.10 - 29201216	Apr 27, 2020 (154)
100	gnomAD - Genomes	NC_000013.11 - 28627079	Apr 26, 2021 (155)
101	Genome of the Netherlands Release 5	NC_000013.10 - 29201216	Apr 27, 2020 (154)
102	KOREAN population from KRGDB	NC_000013.10 - 29201216	Apr 27, 2020 (154)
103	Northern Sweden	NC_000013.10 - 29201216	Jul 13, 2019 (153)
104	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000013.10 - 29201216	Apr 26, 2021 (155)
105	Qatari	NC_000013.10 - 29201216	Apr 27, 2020 (154)
106	SGDP_PRJ	NC_000013.10 - 29201216	Apr 27, 2020 (154)
107	Siberian	NC_000013.10 - 29201216	Apr 27, 2020 (154)
108	8.3KJPN	NC_000013.10 - 29201216	Apr 26, 2021 (155)
109	14KJPN	NC_000013.11 - 28627079	Oct 16, 2022 (156)
110	TopMed	NC_000013.11 - 28627079	Apr 26, 2021 (155)
111	UK 10K study - Twins	NC_000013.10 - 29201216	Oct 12, 2018 (152)
112	A Vietnamese Genetic Variation Database	NC_000013.10 - 29201216	Jul 13, 2019 (153)
113	ALFA	NC_000013.11 - 28627079	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)
rs56713168	Feb 26, 2009 (130)
rs57338479	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss83903881, ss89558856, ss112647388, ss114467067, ss118401667, ss167791451, ss169071854, ss170931937, ss199013248, ss208635676, ss281653068, ss286675308, ss291564852, ss483174025, ss1642333014, ss1713378460	NC_000013.9:28099215:A:G	NC_000013.11:28627078:A:G	(self)
60468292, 33584131, 23773359, 3234474, 14984920, 35659754, 12897390, 856851, 15639332, 31677886, 8435461, 67286219, 33584131, 7449615, ss226099281, ss236190564, ss242698067, ss483342792, ss535556719, ss563571622, ss659167403, ss779411924, ss782114517, ss834880989, ss990228440, ss1078963734, ss1347619873, ss1427140519, ss1576695076, ss1629957282, ss1672951315, ss1807541794, ss1933597402, ss1967743384, ss2027554366, ss2155919107, ss2628265331, ss2633043873, ss2700291256, ss2917944459, ss3010774373, ss3350381978, ss3627029681, ss3631048117, ss3678035111, ss3739612525, ss3751275923, ss3787414316, ss3792486990, ss3797370706, ss3833466945, ss3840310671, ss3879660906, ss3928482360, ss3985630924, ss5209316912, ss5315671569, ss5409805850, ss5510918781, ss5654466635, ss5839266795, ss5945873035	NC_000013.10:29201215:A:G	NC_000013.11:28627078:A:G	(self)
79419232, 426387090, 94835655, 156544411, 1067106092, ss2195102885, ss3027592728, ss3649996483, ss3694991605, ss3816606927, ss3845795413, ss4940998753, ss5293208661, ss5487624772, ss5591893297, ss5760998551, ss5813978947, ss5850661940, ss5924497455	NC_000013.11:28627078:A:G	NC_000013.11:28627078:A:G	(self)
ss11074577, ss13254274	NT_009799.12:10181215:A:G	NC_000013.11:28627078:A:G	(self)
ss21122143	NT_024524.13:10181215:A:G	NC_000013.11:28627078:A:G	(self)
ss6276405, ss23468798, ss43518351, ss66485701, ss69129441, ss76306038, ss82072462, ss96954742, ss106322399, ss133504426, ss137273967, ss154584176, ss173199147	NT_024524.14:10181215:A:G	NC_000013.11:28627078:A:G	(self)
1067106092	NC_000013.11:28627078:A:T	NC_000013.11:28627078: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 rs4625581

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

rs4625581