Name: rs7653901
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.

rs7653901

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:25700043 (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: C>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.277600 (73478/264690, TOPMED)
T=0.287294 (40216/139982, GnomAD)
T=0.34266 (9683/28258, 14KJPN) (+ 15 more)
T=0.34308 (5750/16760, 8.3KJPN)
T=0.20452 (2662/13016, ALFA)
T=0.2419 (1549/6404, 1000G_30x)
T=0.2530 (1267/5008, 1000G)
T=0.3839 (1720/4480, Estonian)
T=0.3708 (1429/3854, ALSPAC)
T=0.3781 (1402/3708, TWINSUK)
T=0.3686 (1080/2930, KOREAN)
T=0.383 (382/998, GoNL)
T=0.372 (223/600, NorthernSweden)
C=0.385 (101/262, SGDP_PRJ)
T=0.236 (51/216, Qatari)
T=0.311 (66/212, Vietnamese)
T=0.47 (19/40, GENOME_DK)
C=0.37 (14/38, 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	13016	C=0.79548	A=0.00000, T=0.20452
European	Sub	9636	C=0.7330	A=0.0000, T=0.2670
African	Sub	2516	C=0.9944	A=0.0000, T=0.0056
African Others	Sub	114	C=1.000	A=0.000, T=0.000
African American	Sub	2402	C=0.9942	A=0.0000, T=0.0058
Asian	Sub	28	C=1.00	A=0.00, T=0.00
East Asian	Sub	22	C=1.00	A=0.00, T=0.00
Other Asian	Sub	6	C=1.0	A=0.0, T=0.0
Latin American 1	Sub	78	C=1.00	A=0.00, T=0.00
Latin American 2	Sub	246	C=1.000	A=0.000, T=0.000
South Asian	Sub	52	C=0.94	A=0.00, T=0.06
Other	Sub	460	C=0.843	A=0.000, T=0.157

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	C=0.722400	T=0.277600
gnomAD - Genomes	Global	Study-wide	139982	C=0.712706	T=0.287294
gnomAD - Genomes	European	Sub	75786	C=0.61451	T=0.38549
gnomAD - Genomes	African	Sub	41972	C=0.91980	T=0.08020
gnomAD - Genomes	American	Sub	13628	C=0.65622	T=0.34378
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.6406	T=0.3594
gnomAD - Genomes	East Asian	Sub	3122	C=0.6384	T=0.3616
gnomAD - Genomes	Other	Sub	2152	C=0.7086	T=0.2914
14KJPN	JAPANESE	Study-wide	28258	C=0.65734	T=0.34266
8.3KJPN	JAPANESE	Study-wide	16760	C=0.65692	T=0.34308
Allele Frequency Aggregator	Total	Global	13016	C=0.79548	A=0.00000, T=0.20452
Allele Frequency Aggregator	European	Sub	9636	C=0.7330	A=0.0000, T=0.2670
Allele Frequency Aggregator	African	Sub	2516	C=0.9944	A=0.0000, T=0.0056
Allele Frequency Aggregator	Other	Sub	460	C=0.843	A=0.000, T=0.157
Allele Frequency Aggregator	Latin American 2	Sub	246	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	78	C=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	52	C=0.94	A=0.00, T=0.06
Allele Frequency Aggregator	Asian	Sub	28	C=1.00	A=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.7581	T=0.2419
1000Genomes_30x	African	Sub	1786	C=0.9731	T=0.0269
1000Genomes_30x	Europe	Sub	1266	C=0.6280	T=0.3720
1000Genomes_30x	South Asian	Sub	1202	C=0.7271	T=0.2729
1000Genomes_30x	East Asian	Sub	1170	C=0.6504	T=0.3496
1000Genomes_30x	American	Sub	980	C=0.701	T=0.299
1000Genomes	Global	Study-wide	5008	C=0.7470	T=0.2530
1000Genomes	African	Sub	1322	C=0.9697	T=0.0303
1000Genomes	East Asian	Sub	1008	C=0.6429	T=0.3571
1000Genomes	Europe	Sub	1006	C=0.6213	T=0.3787
1000Genomes	South Asian	Sub	978	C=0.719	T=0.281
1000Genomes	American	Sub	694	C=0.696	T=0.304
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6161	T=0.3839
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6292	T=0.3708
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6219	T=0.3781
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6314	T=0.3686
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.617	T=0.383
Northern Sweden	ACPOP	Study-wide	600	C=0.628	T=0.372
SGDP_PRJ	Global	Study-wide	262	C=0.385	T=0.615
Qatari	Global	Study-wide	216	C=0.764	T=0.236
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.689	T=0.311
The Danish reference pan genome	Danish	Study-wide	40	C=0.53	T=0.47
Siberian	Global	Study-wide	38	C=0.37	T=0.63

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 4	NC_000004.12:g.25700043C>A
GRCh38.p14 chr 4	NC_000004.12:g.25700043C>T
GRCh37.p13 chr 4	NC_000004.11:g.25701665C>A
GRCh37.p13 chr 4	NC_000004.11:g.25701665C>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	C=	A	T
GRCh38.p14 chr 4	NC_000004.12:g.25700043=	NC_000004.12:g.25700043C>A	NC_000004.12:g.25700043C>T
GRCh37.p13 chr 4	NC_000004.11:g.25701665=	NC_000004.11:g.25701665C>A	NC_000004.11:g.25701665C>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, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss11611500	Jul 11, 2003 (116)
2	SSAHASNP	ss22036440	Apr 05, 2004 (121)
3	ABI	ss42342328	Mar 13, 2006 (126)
4	BGI	ss104050831	Dec 01, 2009 (131)
5	GMI	ss156994821	Dec 01, 2009 (131)
6	BCM-HGSC-SUB	ss206518363	Jul 04, 2010 (132)
7	1000GENOMES	ss239618211	Jul 15, 2010 (132)
8	BL	ss253000763	May 09, 2011 (134)
9	GMI	ss277620731	May 04, 2012 (137)
10	SSMP	ss651155851	Apr 25, 2013 (138)
11	EVA-GONL	ss979888666	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1071367269	Aug 21, 2014 (142)
13	1000GENOMES	ss1308888022	Aug 21, 2014 (142)
14	DDI	ss1429811110	Apr 01, 2015 (144)
15	EVA_GENOME_DK	ss1580463628	Apr 01, 2015 (144)
16	EVA_DECODE	ss1589380019	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1609654261	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1652648294	Apr 01, 2015 (144)
19	WEILL_CORNELL_DGM	ss1923123576	Feb 12, 2016 (147)
20	JJLAB	ss2022139507	Sep 14, 2016 (149)
21	USC_VALOUEV	ss2150249137	Dec 20, 2016 (150)
22	HUMAN_LONGEVITY	ss2261336361	Dec 20, 2016 (150)
23	SYSTEMSBIOZJU	ss2625571110	Nov 08, 2017 (151)
24	GRF	ss2705699030	Nov 08, 2017 (151)
25	GNOMAD	ss2806899546	Nov 08, 2017 (151)
26	SWEGEN	ss2994323843	Nov 08, 2017 (151)
27	BIOINF_KMB_FNS_UNIBA	ss3024838825	Nov 08, 2017 (151)
28	CSHL	ss3345600062	Nov 08, 2017 (151)
29	URBANLAB	ss3647678091	Oct 12, 2018 (152)
30	EGCUT_WGS	ss3662237596	Jul 13, 2019 (153)
31	EVA_DECODE	ss3711635054	Jul 13, 2019 (153)
32	ACPOP	ss3730958762	Jul 13, 2019 (153)
33	EVA	ss3761543301	Jul 13, 2019 (153)
34	PACBIO	ss3784651237	Jul 13, 2019 (153)
35	PACBIO	ss3790117700	Jul 13, 2019 (153)
36	PACBIO	ss3794992794	Jul 13, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3804673720	Jul 13, 2019 (153)
38	EVA	ss3828429296	Apr 26, 2020 (154)
39	SGDP_PRJ	ss3858464076	Apr 26, 2020 (154)
40	KRGDB	ss3904626411	Apr 26, 2020 (154)
41	TOPMED	ss4606693085	Apr 26, 2021 (155)
42	TOMMO_GENOMICS	ss5164708257	Apr 26, 2021 (155)
43	1000G_HIGH_COVERAGE	ss5258445272	Oct 13, 2022 (156)
44	EVA	ss5347632435	Oct 13, 2022 (156)
45	HUGCELL_USP	ss5457303536	Oct 13, 2022 (156)
46	1000G_HIGH_COVERAGE	ss5539087209	Oct 13, 2022 (156)
47	SANFORD_IMAGENETICS	ss5634581566	Oct 13, 2022 (156)
48	TOMMO_GENOMICS	ss5698495945	Oct 13, 2022 (156)
49	YY_MCH	ss5804861600	Oct 13, 2022 (156)
50	EVA	ss5843707930	Oct 13, 2022 (156)
51	EVA	ss5854130351	Oct 13, 2022 (156)
52	EVA	ss5862604632	Oct 13, 2022 (156)
53	EVA	ss5962966742	Oct 13, 2022 (156)
54	1000Genomes	NC_000004.11 - 25701665	Oct 12, 2018 (152)
55	1000Genomes_30x	NC_000004.12 - 25700043	Oct 13, 2022 (156)
56	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 25701665	Oct 12, 2018 (152)
57	Genetic variation in the Estonian population	NC_000004.11 - 25701665	Oct 12, 2018 (152)
58	The Danish reference pan genome	NC_000004.11 - 25701665	Apr 26, 2020 (154)
59	gnomAD - Genomes	NC_000004.12 - 25700043	Apr 26, 2021 (155)
60	Genome of the Netherlands Release 5	NC_000004.11 - 25701665	Apr 26, 2020 (154)
61	KOREAN population from KRGDB	NC_000004.11 - 25701665	Apr 26, 2020 (154)
62	Northern Sweden	NC_000004.11 - 25701665	Jul 13, 2019 (153)
63	Qatari	NC_000004.11 - 25701665	Apr 26, 2020 (154)
64	SGDP_PRJ	NC_000004.11 - 25701665	Apr 26, 2020 (154)
65	Siberian	NC_000004.11 - 25701665	Apr 26, 2020 (154)
66	8.3KJPN	NC_000004.11 - 25701665	Apr 26, 2021 (155)
67	14KJPN	NC_000004.12 - 25700043	Oct 13, 2022 (156)
68	TopMed	NC_000004.12 - 25700043	Apr 26, 2021 (155)
69	UK 10K study - Twins	NC_000004.11 - 25701665	Oct 12, 2018 (152)
70	A Vietnamese Genetic Variation Database	NC_000004.11 - 25701665	Jul 13, 2019 (153)
71	ALFA	NC_000004.12 - 25700043	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
11930435733	NC_000004.12:25700042:C:A	NC_000004.12:25700042:C:A	(self)
ss206518363, ss253000763, ss277620731, ss1589380019	NC_000004.10:25310762:C:T	NC_000004.12:25700042:C:T	(self)
20252083, 11284841, 7975844, 6628567, 4966828, 11803805, 4243627, 5165506, 10481056, 2765491, 22677564, 11284841, 2470311, ss239618211, ss651155851, ss979888666, ss1071367269, ss1308888022, ss1429811110, ss1580463628, ss1609654261, ss1652648294, ss1923123576, ss2022139507, ss2150249137, ss2625571110, ss2705699030, ss2806899546, ss2994323843, ss3345600062, ss3662237596, ss3730958762, ss3761543301, ss3784651237, ss3790117700, ss3794992794, ss3828429296, ss3858464076, ss3904626411, ss5164708257, ss5347632435, ss5634581566, ss5843707930, ss5962966742	NC_000004.11:25701664:C:T	NC_000004.12:25700042:C:T	(self)
26613144, 143474790, 32333049, 444070641, 11930435733, ss2261336361, ss3024838825, ss3647678091, ss3711635054, ss3804673720, ss4606693085, ss5258445272, ss5457303536, ss5539087209, ss5698495945, ss5804861600, ss5854130351, ss5862604632	NC_000004.12:25700042:C:T	NC_000004.12:25700042:C:T	(self)
ss11611500, ss22036440	NT_006316.15:16377022:C:T	NC_000004.12:25700042:C:T	(self)
ss42342328, ss104050831, ss156994821	NT_006316.16:16883461:C:T	NC_000004.12:25700042:C: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 rs7653901

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

rs7653901