Name: rs28478340
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.

rs28478340

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr21:10719267 (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: G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.45453 (12795/28150, 14KJPN)
G=0.06163 (1033/16760, 8.3KJPN)
G=0.00067 (8/11862, ALFA) (+ 6 more)
G=0.0162 (81/5008, 1000G)
G=0.0648 (190/2930, KOREAN)
G=0.4858 (890/1832, Korea1K)
G=0.027 (15/556, SGDP_PRJ)
G=0.005 (1/216, Qatari)
G=0.00 (0/56, 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	11862	G=0.00067	C=0.99933
European	Sub	7618	G=0.0000	C=1.0000
African	Sub	2816	G=0.0014	C=0.9986
African Others	Sub	108	G=0.000	C=1.000
African American	Sub	2708	G=0.0015	C=0.9985
Asian	Sub	108	G=0.019	C=0.981
East Asian	Sub	84	G=0.01	C=0.99
Other Asian	Sub	24	G=0.04	C=0.96
Latin American 1	Sub	146	G=0.000	C=1.000
Latin American 2	Sub	610	G=0.000	C=1.000
South Asian	Sub	94	G=0.02	C=0.98
Other	Sub	470	G=0.000	C=1.000

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
14KJPN	JAPANESE	Study-wide	28150	G=0.45453	C=0.54547
8.3KJPN	JAPANESE	Study-wide	16760	G=0.06163	C=0.93837
Allele Frequency Aggregator	Total	Global	11862	G=0.00067	C=0.99933
Allele Frequency Aggregator	European	Sub	7618	G=0.0000	C=1.0000
Allele Frequency Aggregator	African	Sub	2816	G=0.0014	C=0.9986
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.000	C=1.000
Allele Frequency Aggregator	Other	Sub	470	G=0.000	C=1.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.000	C=1.000
Allele Frequency Aggregator	Asian	Sub	108	G=0.019	C=0.981
Allele Frequency Aggregator	South Asian	Sub	94	G=0.02	C=0.98
1000Genomes	Global	Study-wide	5008	G=0.0162	C=0.9838
1000Genomes	African	Sub	1322	G=0.0008	C=0.9992
1000Genomes	East Asian	Sub	1008	G=0.0724	C=0.9276
1000Genomes	Europe	Sub	1006	G=0.0000	C=1.0000
1000Genomes	South Asian	Sub	978	G=0.007	C=0.993
1000Genomes	American	Sub	694	G=0.000	C=1.000
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.0648	C=0.9352
Korean Genome Project	KOREAN	Study-wide	1832	G=0.4858	C=0.5142
SGDP_PRJ	Global	Study-wide	556	G=0.027	C=0.973
Qatari	Global	Study-wide	216	G=0.005	C=0.995
Siberian	Global	Study-wide	56	G=0.00	C=1.00

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 21	NC_000021.9:g.10719267G>C
GRCh37.p13 chr 21	NC_000021.8:g.10793190C>G

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	G=	C
GRCh38.p14 chr 21	NC_000021.9:g.10719267=	NC_000021.9:g.10719267G>C
GRCh37.p13 chr 21	NC_000021.8:g.10793190=	NC_000021.8:g.10793190C>G

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#.

44 SubSNP, 9 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss35233415	May 24, 2005 (125)
2	HGSV	ss80747064	Dec 16, 2007 (130)
3	BCMHGSC_JDW	ss91760038	Mar 24, 2008 (129)
4	ILLUMINA-UK	ss117448205	Dec 01, 2009 (131)
5	ENSEMBL	ss135584425	Dec 01, 2009 (131)
6	ENSEMBL	ss138276501	Dec 01, 2009 (131)
7	GMI	ss156640149	Dec 01, 2009 (131)
8	BUSHMAN	ss203949904	Jul 04, 2010 (132)
9	BCM-HGSC-SUB	ss208768923	Jul 04, 2010 (132)
10	GMI	ss283451596	May 04, 2012 (137)
11	GMI	ss287489103	Apr 25, 2013 (138)
12	PJP	ss292668061	May 09, 2011 (134)
13	1000GENOMES	ss1365536224	Aug 21, 2014 (142)
14	DDI	ss1429115601	Apr 01, 2015 (144)
15	HAMMER_LAB	ss1809591106	Sep 08, 2015 (146)
16	WEILL_CORNELL_DGM	ss1938457742	Feb 12, 2016 (147)
17	USC_VALOUEV	ss2158589985	Dec 20, 2016 (150)
18	HUMAN_LONGEVITY	ss2244309388	Dec 20, 2016 (150)
19	SYSTEMSBIOZJU	ss2629495369	Nov 08, 2017 (151)
20	GRF	ss2704303502	Nov 08, 2017 (151)
21	SWEGEN	ss3018552117	Nov 08, 2017 (151)
22	BIOINF_KMB_FNS_UNIBA	ss3028836584	Nov 08, 2017 (151)
23	CSHL	ss3352616077	Nov 08, 2017 (151)
24	URBANLAB	ss3651070769	Oct 12, 2018 (152)
25	URBANLAB	ss3651070770	Oct 12, 2018 (152)
26	EVA_DECODE	ss3707358893	Jul 13, 2019 (153)
27	PACBIO	ss3788703389	Jul 13, 2019 (153)
28	PACBIO	ss3793586037	Jul 13, 2019 (153)
29	PACBIO	ss3798472903	Jul 13, 2019 (153)
30	KHV_HUMAN_GENOMES	ss3822036691	Jul 13, 2019 (153)
31	EVA	ss3835769836	Apr 27, 2020 (154)
32	EVA	ss3841510208	Apr 27, 2020 (154)
33	EVA	ss3847024043	Apr 27, 2020 (154)
34	SGDP_PRJ	ss3889566430	Apr 27, 2020 (154)
35	KRGDB	ss3939948058	Apr 27, 2020 (154)
36	KOGIC	ss3982749675	Apr 27, 2020 (154)
37	TOMMO_GENOMICS	ss5230628466	Apr 26, 2021 (155)
38	EVA	ss5438688845	Oct 13, 2022 (156)
39	SANFORD_IMAGENETICS	ss5663613554	Oct 13, 2022 (156)
40	TOMMO_GENOMICS	ss5790949320	Oct 13, 2022 (156)
41	YY_MCH	ss5818269219	Oct 13, 2022 (156)
42	EVA	ss5838773007	Oct 13, 2022 (156)
43	EVA	ss5891619687	Oct 13, 2022 (156)
44	EVA	ss5981102110	Oct 13, 2022 (156)
45	1000Genomes	NC_000021.8 - 10793190	Oct 12, 2018 (152)
46	KOREAN population from KRGDB	NC_000021.8 - 10793190	Apr 27, 2020 (154)
47	Korean Genome Project	NC_000021.9 - 10719267	Apr 27, 2020 (154)
48	Qatari	NC_000021.8 - 10793190	Apr 27, 2020 (154)
49	SGDP_PRJ	NC_000021.8 - 10793190	Apr 27, 2020 (154)
50	Siberian	NC_000021.8 - 10793190	Apr 27, 2020 (154)
51	8.3KJPN	NC_000021.8 - 10793190	Apr 26, 2021 (155)
52	14KJPN	NC_000021.9 - 10719267	Oct 13, 2022 (156)
53	ALFA	NC_000021.9 - 10719267	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)
rs61626253	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss35233415, ss80747064, ss91760038, ss117448205, ss203949904, ss208768923, ss283451596, ss287489103, ss292668061	NC_000021.7:9815060:C:G	NC_000021.9:10719266:G:C	(self)
79025811, 47125452, 20499664, 41583410, 11106339, 88597773, ss1365536224, ss1429115601, ss1809591106, ss1938457742, ss2158589985, ss2629495369, ss2704303502, ss3018552117, ss3352616077, ss3788703389, ss3793586037, ss3798472903, ss3835769836, ss3841510208, ss3889566430, ss3939948058, ss5230628466, ss5438688845, ss5663613554, ss5838773007, ss5981102110	NC_000021.8:10793189:C:G	NC_000021.9:10719266:G:C	(self)
39127676, 124786424, 4108872181, ss2244309388, ss3028836584, ss3651070769, ss3651070770, ss3707358893, ss3822036691, ss3847024043, ss3982749675, ss5790949320, ss5818269219, ss5891619687	NC_000021.9:10719266:G:C	NC_000021.9:10719266:G:C	(self)
ss135584425, ss138276501, ss156640149	NT_029490.4:95293:C:G	NC_000021.9:10719266:G: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 rs28478340

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

rs28478340