Name: rs4964853
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.

rs4964853

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:129058125 (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: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.287132 (76001/264690, TOPMED)
T=0.285407 (39953/139986, GnomAD)
T=0.24128 (6818/28258, 14KJPN) (+ 12 more)
T=0.25934 (4803/18520, ALFA)
T=0.24093 (4038/16760, 8.3KJPN)
T=0.2925 (1873/6404, 1000G_30x)
T=0.2913 (1459/5008, 1000G)
T=0.2542 (1139/4480, Estonian)
T=0.2945 (863/2930, KOREAN)
T=0.3068 (562/1832, Korea1K)
T=0.186 (186/998, GoNL)
T=0.205 (123/600, NorthernSweden)
T=0.173 (89/514, SGDP_PRJ)
T=0.222 (48/216, Qatari)
T=0.35 (14/40, 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	18520	T=0.25934	C=0.74066
European	Sub	14152	T=0.21962	C=0.78038
African	Sub	2898	T=0.4438	C=0.5562
African Others	Sub	114	T=0.518	C=0.482
African American	Sub	2784	T=0.4407	C=0.5593
Asian	Sub	112	T=0.259	C=0.741
East Asian	Sub	86	T=0.29	C=0.71
Other Asian	Sub	26	T=0.15	C=0.85
Latin American 1	Sub	146	T=0.247	C=0.753
Latin American 2	Sub	610	T=0.293	C=0.707
South Asian	Sub	98	T=0.21	C=0.79
Other	Sub	504	T=0.286	C=0.714

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	T=0.287132	C=0.712868
gnomAD - Genomes	Global	Study-wide	139986	T=0.285407	C=0.714593
gnomAD - Genomes	European	Sub	75870	T=0.21447	C=0.78553
gnomAD - Genomes	African	Sub	41892	T=0.43617	C=0.56383
gnomAD - Genomes	American	Sub	13632	T=0.24765	C=0.75235
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.1905	C=0.8095
gnomAD - Genomes	East Asian	Sub	3122	T=0.2649	C=0.7351
gnomAD - Genomes	Other	Sub	2148	T=0.2668	C=0.7332
14KJPN	JAPANESE	Study-wide	28258	T=0.24128	C=0.75872
Allele Frequency Aggregator	Total	Global	18520	T=0.25934	C=0.74066
Allele Frequency Aggregator	European	Sub	14152	T=0.21962	C=0.78038
Allele Frequency Aggregator	African	Sub	2898	T=0.4438	C=0.5562
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.293	C=0.707
Allele Frequency Aggregator	Other	Sub	504	T=0.286	C=0.714
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.247	C=0.753
Allele Frequency Aggregator	Asian	Sub	112	T=0.259	C=0.741
Allele Frequency Aggregator	South Asian	Sub	98	T=0.21	C=0.79
8.3KJPN	JAPANESE	Study-wide	16760	T=0.24093	C=0.75907
1000Genomes_30x	Global	Study-wide	6404	T=0.2925	C=0.7075
1000Genomes_30x	African	Sub	1786	T=0.4530	C=0.5470
1000Genomes_30x	Europe	Sub	1266	T=0.2117	C=0.7883
1000Genomes_30x	South Asian	Sub	1202	T=0.1988	C=0.8012
1000Genomes_30x	East Asian	Sub	1170	T=0.2701	C=0.7299
1000Genomes_30x	American	Sub	980	T=0.246	C=0.754
1000Genomes	Global	Study-wide	5008	T=0.2913	C=0.7087
1000Genomes	African	Sub	1322	T=0.4667	C=0.5333
1000Genomes	East Asian	Sub	1008	T=0.2669	C=0.7331
1000Genomes	Europe	Sub	1006	T=0.2107	C=0.7893
1000Genomes	South Asian	Sub	978	T=0.196	C=0.804
1000Genomes	American	Sub	694	T=0.244	C=0.756
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.2542	C=0.7458
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.2945	A=0.0000, C=0.7055
Korean Genome Project	KOREAN	Study-wide	1832	T=0.3068	C=0.6932
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.186	C=0.814
Northern Sweden	ACPOP	Study-wide	600	T=0.205	C=0.795
SGDP_PRJ	Global	Study-wide	514	T=0.173	C=0.827
Qatari	Global	Study-wide	216	T=0.222	C=0.778
The Danish reference pan genome	Danish	Study-wide	40	T=0.35	C=0.65

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 12	NC_000012.12:g.129058125T>A
GRCh38.p14 chr 12	NC_000012.12:g.129058125T>C
GRCh37.p13 chr 12	NC_000012.11:g.129542670T>A
GRCh37.p13 chr 12	NC_000012.11:g.129542670T>C

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	T=	A	C
GRCh38.p14 chr 12	NC_000012.12:g.129058125=	NC_000012.12:g.129058125T>A	NC_000012.12:g.129058125T>C
GRCh37.p13 chr 12	NC_000012.11:g.129542670=	NC_000012.11:g.129542670T>A	NC_000012.11:g.129542670T>C

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#.

49 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss13623558	Dec 05, 2003 (126)
2	SC_SNP	ss15823289	Feb 28, 2004 (126)
3	SC_SNP	ss18749055	Feb 27, 2004 (126)
4	SC_SNP	ss18967272	Feb 27, 2004 (126)
5	CSHL-HAPMAP	ss19936419	Feb 27, 2004 (126)
6	SSAHASNP	ss20973665	Apr 05, 2004 (126)
7	BCMHGSC_JDW	ss89465938	Mar 24, 2008 (129)
8	ENSEMBL	ss137540378	Dec 01, 2009 (144)
9	BL	ss255389868	May 09, 2011 (144)
10	GMI	ss281598880	May 04, 2012 (144)
11	GMI	ss286649753	Apr 25, 2013 (144)
12	PJP	ss291368450	May 09, 2011 (144)
13	1000GENOMES	ss337704248	May 09, 2011 (144)
14	SSMP	ss659078014	Apr 25, 2013 (144)
15	EVA-GONL	ss990099405	Aug 21, 2014 (144)
16	1000GENOMES	ss1347169208	Aug 21, 2014 (144)
17	DDI	ss1427096074	Apr 01, 2015 (144)
18	EVA_GENOME_DK	ss1576608089	Apr 01, 2015 (144)
19	WEILL_CORNELL_DGM	ss1933458261	Feb 12, 2016 (147)
20	JJLAB	ss2027484996	Sep 14, 2016 (149)
21	SYSTEMSBIOZJU	ss2628226731	Nov 08, 2017 (151)
22	GRF	ss2700205487	Nov 08, 2017 (151)
23	GNOMAD	ss2916670426	Nov 08, 2017 (151)
24	SWEGEN	ss3010568905	Nov 08, 2017 (151)
25	CSHL	ss3350313762	Nov 08, 2017 (151)
26	URBANLAB	ss3649951412	Oct 12, 2018 (152)
27	EGCUT_WGS	ss3677869212	Jul 13, 2019 (153)
28	ACPOP	ss3739500842	Jul 13, 2019 (153)
29	EVA	ss3751130608	Jul 13, 2019 (153)
30	PACBIO	ss3787375487	Jul 13, 2019 (153)
31	PACBIO	ss3792451762	Jul 13, 2019 (153)
32	PACBIO	ss3797335021	Jul 13, 2019 (153)
33	KHV_HUMAN_GENOMES	ss3816458440	Jul 13, 2019 (153)
34	EVA	ss3833398503	Apr 27, 2020 (154)
35	EVA	ss3840270317	Apr 27, 2020 (154)
36	EVA	ss3845759405	Apr 27, 2020 (154)
37	SGDP_PRJ	ss3879394939	Apr 27, 2020 (154)
38	KRGDB	ss3928183081	Apr 27, 2020 (154)
39	KOGIC	ss3973017583	Apr 27, 2020 (154)
40	TOPMED	ss4937227912	Apr 26, 2021 (155)
41	TOMMO_GENOMICS	ss5208785847	Apr 26, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5292709912	Oct 16, 2022 (156)
43	1000G_HIGH_COVERAGE	ss5591153110	Oct 16, 2022 (156)
44	SANFORD_IMAGENETICS	ss5654223746	Oct 16, 2022 (156)
45	TOMMO_GENOMICS	ss5759303375	Oct 16, 2022 (156)
46	YY_MCH	ss5813763558	Oct 16, 2022 (156)
47	EVA	ss5838701032	Oct 16, 2022 (156)
48	EVA	ss5906561206	Oct 16, 2022 (156)
49	EVA	ss5945638936	Oct 16, 2022 (156)
50	1000Genomes	NC_000012.11 - 129542670	Oct 12, 2018 (152)
51	1000Genomes_30x	NC_000012.12 - 129058125	Oct 16, 2022 (156)
52	Genetic variation in the Estonian population	NC_000012.11 - 129542670	Oct 12, 2018 (152)
53	The Danish reference pan genome	NC_000012.11 - 129542670	Apr 27, 2020 (154)
54	gnomAD - Genomes	NC_000012.12 - 129058125	Apr 26, 2021 (155)
55	Genome of the Netherlands Release 5	NC_000012.11 - 129542670	Apr 27, 2020 (154)
56	KOREAN population from KRGDB	NC_000012.11 - 129542670	Apr 27, 2020 (154)
57	Korean Genome Project	NC_000012.12 - 129058125	Apr 27, 2020 (154)
58	Northern Sweden	NC_000012.11 - 129542670	Jul 13, 2019 (153)
59	Qatari	NC_000012.11 - 129542670	Apr 27, 2020 (154)
60	SGDP_PRJ	NC_000012.11 - 129542670	Apr 27, 2020 (154)
61	8.3KJPN	NC_000012.11 - 129542670	Apr 26, 2021 (155)
62	14KJPN	NC_000012.12 - 129058125	Oct 16, 2022 (156)
63	TopMed	NC_000012.12 - 129058125	Apr 26, 2021 (155)
64	ALFA	NC_000012.12 - 129058125	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)
rs9795617	Mar 11, 2006 (126)
rs10847750	Mar 11, 2006 (126)
rs11513681	Mar 11, 2006 (126)
rs79430489	Jul 01, 2015 (144)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
35360475, ss3928183081	NC_000012.11:129542669:T:A	NC_000012.12:129058124:T:A	(self)
ss89465938, ss255389868, ss281598880, ss286649753, ss291368450	NC_000012.10:128108622:T:C	NC_000012.12:129058124:T:C	(self)
59999986, 23607460, 3181260, 14862600, 35360475, 12785707, 15500191, 31411919, 66755154, ss337704248, ss659078014, ss990099405, ss1347169208, ss1427096074, ss1576608089, ss1933458261, ss2027484996, ss2628226731, ss2700205487, ss2916670426, ss3010568905, ss3350313762, ss3677869212, ss3739500842, ss3751130608, ss3787375487, ss3792451762, ss3797335021, ss3833398503, ss3840270317, ss3879394939, ss3928183081, ss5208785847, ss5654223746, ss5838701032, ss5945638936	NC_000012.11:129542669:T:C	NC_000012.12:129058124:T:C	(self)
78679045, 423140777, 29395584, 93140479, 152773569, 178928352, ss3649951412, ss3816458440, ss3845759405, ss3973017583, ss4937227912, ss5292709912, ss5591153110, ss5759303375, ss5813763558, ss5906561206	NC_000012.12:129058124:T:C	NC_000012.12:129058124:T:C	(self)
ss13623558, ss15823289, ss18749055, ss18967272, ss19936419, ss20973665	NT_009755.16:6851822:T:C	NC_000012.12:129058124:T:C	(self)
ss137540378	NT_009755.19:6962046:T:C	NC_000012.12:129058124:T:C	(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 rs4964853

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

rs4964853