Name: rs4769633
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.

rs4769633

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:28685711 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.140870 (37287/264690, TOPMED)
T=0.133559 (18699/140006, GnomAD)
T=0.30600 (8647/28258, 14KJPN) (+ 17 more)
T=0.15442 (2917/18890, ALFA)
T=0.30943 (5186/16760, 8.3KJPN)
T=0.1655 (1060/6404, 1000G_30x)
T=0.1701 (852/5008, 1000G)
T=0.2085 (934/4480, Estonian)
T=0.1463 (564/3854, ALSPAC)
T=0.1459 (541/3708, TWINSUK)
T=0.3317 (972/2930, KOREAN)
T=0.3308 (606/1832, Korea1K)
T=0.143 (143/998, GoNL)
T=0.215 (129/600, NorthernSweden)
T=0.181 (39/216, Qatari)
T=0.333 (72/216, Vietnamese)
C=0.417 (80/192, SGDP_PRJ)
T=0.23 (9/40, GENOME_DK)
C=0.50 (7/14, Siberian)
T=0.50 (7/14, 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	18890	C=0.84558	T=0.15442
European	Sub	14286	C=0.82843	T=0.17157
African	Sub	2946	C=0.9545	T=0.0455
African Others	Sub	114	C=0.965	T=0.035
African American	Sub	2832	C=0.9541	T=0.0459
Asian	Sub	112	C=0.661	T=0.339
East Asian	Sub	86	C=0.63	T=0.37
Other Asian	Sub	26	C=0.77	T=0.23
Latin American 1	Sub	146	C=0.788	T=0.212
Latin American 2	Sub	610	C=0.764	T=0.236
South Asian	Sub	98	C=0.84	T=0.16
Other	Sub	692	C=0.851	T=0.149

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=0.859130	T=0.140870
gnomAD - Genomes	Global	Study-wide	140006	C=0.866441	T=0.133559
gnomAD - Genomes	European	Sub	75836	C=0.84335	T=0.15665
gnomAD - Genomes	African	Sub	41948	C=0.94979	T=0.05021
gnomAD - Genomes	American	Sub	13628	C=0.79880	T=0.20120
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.7941	T=0.2059
gnomAD - Genomes	East Asian	Sub	3128	C=0.6889	T=0.3111
gnomAD - Genomes	Other	Sub	2144	C=0.8535	T=0.1465
14KJPN	JAPANESE	Study-wide	28258	C=0.69400	T=0.30600
Allele Frequency Aggregator	Total	Global	18890	C=0.84558	T=0.15442
Allele Frequency Aggregator	European	Sub	14286	C=0.82843	T=0.17157
Allele Frequency Aggregator	African	Sub	2946	C=0.9545	T=0.0455
Allele Frequency Aggregator	Other	Sub	692	C=0.851	T=0.149
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.764	T=0.236
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.788	T=0.212
Allele Frequency Aggregator	Asian	Sub	112	C=0.661	T=0.339
Allele Frequency Aggregator	South Asian	Sub	98	C=0.84	T=0.16
8.3KJPN	JAPANESE	Study-wide	16760	C=0.69057	T=0.30943
1000Genomes_30x	Global	Study-wide	6404	C=0.8345	T=0.1655
1000Genomes_30x	African	Sub	1786	C=0.9703	T=0.0297
1000Genomes_30x	Europe	Sub	1266	C=0.8325	T=0.1675
1000Genomes_30x	South Asian	Sub	1202	C=0.8095	T=0.1905
1000Genomes_30x	East Asian	Sub	1170	C=0.6983	T=0.3017
1000Genomes_30x	American	Sub	980	C=0.783	T=0.217
1000Genomes	Global	Study-wide	5008	C=0.8299	T=0.1701
1000Genomes	African	Sub	1322	C=0.9667	T=0.0333
1000Genomes	East Asian	Sub	1008	C=0.6905	T=0.3095
1000Genomes	Europe	Sub	1006	C=0.8390	T=0.1610
1000Genomes	South Asian	Sub	978	C=0.809	T=0.191
1000Genomes	American	Sub	694	C=0.788	T=0.212
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7915	T=0.2085
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8537	T=0.1463
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8541	T=0.1459
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6683	T=0.3317
Korean Genome Project	KOREAN	Study-wide	1832	C=0.6692	T=0.3308
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.857	T=0.143
Northern Sweden	ACPOP	Study-wide	600	C=0.785	T=0.215
Qatari	Global	Study-wide	216	C=0.819	T=0.181
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.667	T=0.333
SGDP_PRJ	Global	Study-wide	192	C=0.417	T=0.583
The Danish reference pan genome	Danish	Study-wide	40	C=0.78	T=0.23
Siberian	Global	Study-wide	14	C=0.50	T=0.50

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.28685711C>T
GRCh37.p13 chr 13	NC_000013.10:g.29259848C>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=	T
GRCh38.p14 chr 13	NC_000013.11:g.28685711=	NC_000013.11:g.28685711C>T
GRCh37.p13 chr 13	NC_000013.10:g.29259848=	NC_000013.10:g.29259848C>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#.

52 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6579612	Feb 20, 2003 (111)
2	SC_SNP	ss13302760	Dec 05, 2003 (119)
3	CSHL-HAPMAP	ss19261447	Feb 27, 2004 (120)
4	ABI	ss40354961	Mar 13, 2006 (126)
5	BCMHGSC_JDW	ss89559181	Mar 24, 2008 (129)
6	GMI	ss281653252	May 04, 2012 (137)
7	1000GENOMES	ss337783557	May 09, 2011 (134)
8	TISHKOFF	ss563571977	Apr 25, 2013 (138)
9	SSMP	ss659167691	Apr 25, 2013 (138)
10	EVA-GONL	ss990228967	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1078964161	Aug 21, 2014 (142)
12	1000GENOMES	ss1347621599	Aug 21, 2014 (142)
13	DDI	ss1427140692	Apr 01, 2015 (144)
14	EVA_GENOME_DK	ss1576695370	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1629958251	Apr 01, 2015 (144)
16	EVA_DECODE	ss1642333435	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1672952284	Apr 01, 2015 (144)
18	WEILL_CORNELL_DGM	ss1933597954	Feb 12, 2016 (147)
19	JJLAB	ss2027554723	Sep 14, 2016 (149)
20	USC_VALOUEV	ss2155919335	Dec 20, 2016 (150)
21	HUMAN_LONGEVITY	ss2195106328	Dec 20, 2016 (150)
22	SYSTEMSBIOZJU	ss2628265456	Nov 08, 2017 (151)
23	GRF	ss2700291506	Nov 08, 2017 (151)
24	GNOMAD	ss2917949177	Nov 08, 2017 (151)
25	SWEGEN	ss3010775009	Nov 08, 2017 (151)
26	BIOINF_KMB_FNS_UNIBA	ss3027592857	Nov 08, 2017 (151)
27	CSHL	ss3350382171	Nov 08, 2017 (151)
28	EGCUT_WGS	ss3678035780	Jul 13, 2019 (153)
29	EVA_DECODE	ss3694992514	Jul 13, 2019 (153)
30	ACPOP	ss3739612905	Jul 13, 2019 (153)
31	EVA	ss3751276399	Jul 13, 2019 (153)
32	PACBIO	ss3787414411	Jul 13, 2019 (153)
33	PACBIO	ss3792487064	Jul 13, 2019 (153)
34	PACBIO	ss3797370781	Jul 13, 2019 (153)
35	KHV_HUMAN_GENOMES	ss3816607572	Jul 13, 2019 (153)
36	EVA	ss3833467283	Apr 27, 2020 (154)
37	SGDP_PRJ	ss3879661819	Apr 27, 2020 (154)
38	KRGDB	ss3928483256	Apr 27, 2020 (154)
39	KOGIC	ss3973269153	Apr 27, 2020 (154)
40	TOPMED	ss4941013068	Apr 27, 2021 (155)
41	TOMMO_GENOMICS	ss5209318695	Apr 27, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5293210192	Oct 16, 2022 (156)
43	EVA	ss5409808509	Oct 16, 2022 (156)
44	HUGCELL_USP	ss5487626227	Oct 16, 2022 (156)
45	1000G_HIGH_COVERAGE	ss5591895469	Oct 16, 2022 (156)
46	SANFORD_IMAGENETICS	ss5654467579	Oct 16, 2022 (156)
47	TOMMO_GENOMICS	ss5761000800	Oct 16, 2022 (156)
48	YY_MCH	ss5813979304	Oct 16, 2022 (156)
49	EVA	ss5839267482	Oct 16, 2022 (156)
50	EVA	ss5850662129	Oct 16, 2022 (156)
51	EVA	ss5924499244	Oct 16, 2022 (156)
52	EVA	ss5945874054	Oct 16, 2022 (156)
53	1000Genomes	NC_000013.10 - 29259848	Oct 12, 2018 (152)
54	1000Genomes_30x	NC_000013.11 - 28685711	Oct 16, 2022 (156)
55	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 29259848	Oct 12, 2018 (152)
56	Genetic variation in the Estonian population	NC_000013.10 - 29259848	Oct 12, 2018 (152)
57	The Danish reference pan genome	NC_000013.10 - 29259848	Apr 27, 2020 (154)
58	gnomAD - Genomes	NC_000013.11 - 28685711	Apr 27, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000013.10 - 29259848	Apr 27, 2020 (154)
60	KOREAN population from KRGDB	NC_000013.10 - 29259848	Apr 27, 2020 (154)
61	Korean Genome Project	NC_000013.11 - 28685711	Apr 27, 2020 (154)
62	Northern Sweden	NC_000013.10 - 29259848	Jul 13, 2019 (153)
63	Qatari	NC_000013.10 - 29259848	Apr 27, 2020 (154)
64	SGDP_PRJ	NC_000013.10 - 29259848	Apr 27, 2020 (154)
65	Siberian	NC_000013.10 - 29259848	Apr 27, 2020 (154)
66	8.3KJPN	NC_000013.10 - 29259848	Apr 27, 2021 (155)
67	14KJPN	NC_000013.11 - 28685711	Oct 16, 2022 (156)
68	TopMed	NC_000013.11 - 28685711	Apr 27, 2021 (155)
69	UK 10K study - Twins	NC_000013.10 - 29259848	Oct 12, 2018 (152)
70	A Vietnamese Genetic Variation Database	NC_000013.10 - 29259848	Jul 13, 2019 (153)
71	ALFA	NC_000013.11 - 28685711	Apr 27, 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
ss89559181, ss281653252, ss1642333435	NC_000013.9:28157847:C:T	NC_000013.11:28685710:C:T	(self)
60470107, 33585217, 23774028, 3234664, 14985435, 35660650, 12897770, 15639884, 31678799, 8435689, 67288002, 33585217, 7449845, ss337783557, ss563571977, ss659167691, ss990228967, ss1078964161, ss1347621599, ss1427140692, ss1576695370, ss1629958251, ss1672952284, ss1933597954, ss2027554723, ss2155919335, ss2628265456, ss2700291506, ss2917949177, ss3010775009, ss3350382171, ss3678035780, ss3739612905, ss3751276399, ss3787414411, ss3792487064, ss3797370781, ss3833467283, ss3879661819, ss3928483256, ss5209318695, ss5409808509, ss5654467579, ss5839267482, ss5945874054	NC_000013.10:29259847:C:T	NC_000013.11:28685710:C:T	(self)
79421404, 426398726, 29647154, 94837904, 156558726, 420117142, ss2195106328, ss3027592857, ss3694992514, ss3816607572, ss3973269153, ss4941013068, ss5293210192, ss5487626227, ss5591895469, ss5761000800, ss5813979304, ss5850662129, ss5924499244	NC_000013.11:28685710:C:T	NC_000013.11:28685710:C:T	(self)
ss13302760	NT_009799.12:10239847:C:T	NC_000013.11:28685710:C:T	(self)
ss19261447	NT_024524.13:10239847:C:T	NC_000013.11:28685710:C:T	(self)
ss6579612, ss40354961	NT_024524.14:10239847:C:T	NC_000013.11:28685710: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 rs4769633

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

rs4769633