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dbSNP Short Genetic Variations

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.

rs28399747

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr21:10648224 (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>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.071992 (10071/139890, GnomAD)
G=0.22712 (6418/28258, 14KJPN)
G=0.22858 (3831/16760, 8.3KJPN) (+ 7 more)
G=0.1032 (517/5008, 1000G)
G=0.2147 (629/2930, KOREAN)
G=0.2249 (412/1832, Korea1K)
G=0.0685 (81/1182, ALFA)
G=0.115 (64/556, SGDP_PRJ)
G=0.028 (6/216, Qatari)
G=0.05 (3/56, 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 1182 G=0.0685 A=0.9315, T=0.0000
European Sub 656 G=0.023 A=0.977, T=0.000
African Sub 522 G=0.125 A=0.875, T=0.000
African Others Sub 24 G=0.25 A=0.75, T=0.00
African American Sub 498 G=0.118 A=0.882, T=0.000
Asian Sub 0 G=0 A=0, T=0
East Asian Sub 0 G=0 A=0, T=0
Other Asian Sub 0 G=0 A=0, T=0
Latin American 1 Sub 0 G=0 A=0, T=0
Latin American 2 Sub 0 G=0 A=0, T=0
South Asian Sub 0 G=0 A=0, T=0
Other Sub 4 G=0.2 A=0.8, T=0.0


Help

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
gnomAD - Genomes Global Study-wide 139890 G=0.071992 A=0.928008
gnomAD - Genomes European Sub 75912 G=0.02437 A=0.97563
gnomAD - Genomes African Sub 41812 G=0.14137 A=0.85863
gnomAD - Genomes American Sub 13586 G=0.10518 A=0.89482
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.0328 A=0.9672
gnomAD - Genomes East Asian Sub 3108 G=0.1889 A=0.8111
gnomAD - Genomes Other Sub 2152 G=0.0860 A=0.9140
14KJPN JAPANESE Study-wide 28258 G=0.22712 A=0.77288
8.3KJPN JAPANESE Study-wide 16760 G=0.22858 A=0.77142
1000Genomes Global Study-wide 5008 G=0.1032 A=0.8968
1000Genomes African Sub 1322 G=0.1271 A=0.8729
1000Genomes East Asian Sub 1008 G=0.1468 A=0.8532
1000Genomes Europe Sub 1006 G=0.0159 A=0.9841
1000Genomes South Asian Sub 978 G=0.122 A=0.878
1000Genomes American Sub 694 G=0.095 A=0.905
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.2147 A=0.7853
Korean Genome Project KOREAN Study-wide 1832 G=0.2249 A=0.7751
Allele Frequency Aggregator Total Global 1182 G=0.0685 A=0.9315, T=0.0000
Allele Frequency Aggregator European Sub 656 G=0.023 A=0.977, T=0.000
Allele Frequency Aggregator African Sub 522 G=0.125 A=0.875, T=0.000
Allele Frequency Aggregator Other Sub 4 G=0.2 A=0.8, T=0.0
Allele Frequency Aggregator Latin American 1 Sub 0 G=0 A=0, T=0
Allele Frequency Aggregator Latin American 2 Sub 0 G=0 A=0, T=0
Allele Frequency Aggregator South Asian Sub 0 G=0 A=0, T=0
Allele Frequency Aggregator Asian Sub 0 G=0 A=0, T=0
SGDP_PRJ Global Study-wide 556 G=0.115 A=0.885
Qatari Global Study-wide 216 G=0.028 A=0.972
Siberian Global Study-wide 56 G=0.05 A=0.95
Help

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.10648224G>A
GRCh38.p14 chr 21 NC_000021.9:g.10648224G>T
GRCh37.p13 chr 21 NC_000021.8:g.10864233C>T
GRCh37.p13 chr 21 NC_000021.8:g.10864233C>A
Help

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
Help

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= A T
GRCh38.p14 chr 21 NC_000021.9:g.10648224= NC_000021.9:g.10648224G>A NC_000021.9:g.10648224G>T
GRCh37.p13 chr 21 NC_000021.8:g.10864233= NC_000021.8:g.10864233C>T NC_000021.8:g.10864233C>A
Help

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, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35140415 May 24, 2005 (125)
2 HGSV ss77146976 Dec 07, 2007 (129)
3 HGSV ss81770378 Dec 14, 2007 (130)
4 HGSV ss84244231 Dec 14, 2007 (130)
5 BCMHGSC_JDW ss91761699 Mar 24, 2008 (129)
6 HUMANGENOME_JCVI ss96133541 Feb 04, 2009 (130)
7 BGI ss106199783 Feb 04, 2009 (130)
8 1000GENOMES ss112255906 Jan 25, 2009 (130)
9 ILLUMINA-UK ss117448236 Feb 14, 2009 (130)
10 ENSEMBL ss135583578 Dec 01, 2009 (131)
11 ENSEMBL ss138277998 Dec 01, 2009 (131)
12 GMI ss156644651 Dec 01, 2009 (131)
13 BUSHMAN ss203950767 Jul 04, 2010 (132)
14 BCM-HGSC-SUB ss208781033 Jul 04, 2010 (132)
15 GMI ss283453245 May 04, 2012 (137)
16 GMI ss287490089 Apr 25, 2013 (138)
17 PJP ss292668648 May 09, 2011 (134)
18 TISHKOFF ss566371993 Apr 25, 2013 (138)
19 SSMP ss662268870 Apr 25, 2013 (138)
20 1000GENOMES ss1365539174 Aug 21, 2014 (142)
21 DDI ss1429116641 Apr 01, 2015 (144)
22 HAMMER_LAB ss1809591611 Sep 08, 2015 (146)
23 WEILL_CORNELL_DGM ss1938460076 Feb 12, 2016 (147)
24 ILLUMINA ss1959937003 Feb 12, 2016 (147)
25 USC_VALOUEV ss2158593397 Dec 20, 2016 (150)
26 SYSTEMSBIOZJU ss2629496023 Nov 08, 2017 (151)
27 GRF ss2704306338 Nov 08, 2017 (151)
28 SWEGEN ss3018557824 Nov 08, 2017 (151)
29 ILLUMINA ss3022141454 Nov 08, 2017 (151)
30 CSHL ss3352618253 Nov 08, 2017 (151)
31 URBANLAB ss3651070067 Oct 12, 2018 (152)
32 ILLUMINA ss3652599755 Oct 12, 2018 (152)
33 EVA_DECODE ss3707355511 Jul 13, 2019 (153)
34 PACBIO ss3788704311 Jul 13, 2019 (153)
35 PACBIO ss3793586924 Jul 13, 2019 (153)
36 PACBIO ss3798473712 Jul 13, 2019 (153)
37 KHV_HUMAN_GENOMES ss3822036014 Jul 13, 2019 (153)
38 EVA ss3835770883 Apr 27, 2020 (154)
39 EVA ss3841510341 Apr 27, 2020 (154)
40 EVA ss3847023903 Apr 27, 2020 (154)
41 SGDP_PRJ ss3889573523 Apr 27, 2020 (154)
42 KRGDB ss3939960644 Apr 27, 2020 (154)
43 KOGIC ss3982743683 Apr 27, 2020 (154)
44 GNOMAD ss4357095378 Apr 26, 2021 (155)
45 TOMMO_GENOMICS ss5230644256 Apr 26, 2021 (155)
46 EVA ss5438696685 Oct 16, 2022 (156)
47 SANFORD_IMAGENETICS ss5663616942 Oct 16, 2022 (156)
48 TOMMO_GENOMICS ss5790929142 Oct 16, 2022 (156)
49 YY_MCH ss5818265828 Oct 16, 2022 (156)
50 EVA ss5838775626 Oct 16, 2022 (156)
51 EVA ss5891611723 Oct 16, 2022 (156)
52 EVA ss5981102358 Oct 16, 2022 (156)
53 1000Genomes NC_000021.8 - 10864233 Oct 12, 2018 (152)
54 gnomAD - Genomes NC_000021.9 - 10648224 Apr 26, 2021 (155)
55 KOREAN population from KRGDB NC_000021.8 - 10864233 Apr 27, 2020 (154)
56 Korean Genome Project NC_000021.9 - 10648224 Apr 27, 2020 (154)
57 Qatari NC_000021.8 - 10864233 Apr 27, 2020 (154)
58 SGDP_PRJ NC_000021.8 - 10864233 Apr 27, 2020 (154)
59 Siberian NC_000021.8 - 10864233 Apr 27, 2020 (154)
60 8.3KJPN NC_000021.8 - 10864233 Apr 26, 2021 (155)
61 14KJPN NC_000021.9 - 10648224 Oct 16, 2022 (156)
62 ALFA NC_000021.9 - 10648224 Apr 26, 2021 (155)
Help

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)
rs58081366 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35140415, ss77146976, ss81770378, ss84244231, ss91761699, ss112255906, ss117448236, ss203950767, ss208781033, ss283453245, ss287490089, ss292668648 NC_000021.7:9886103:C:T NC_000021.9:10648223:G:A (self)
79028812, 47138038, 20501998, 41590503, 11109751, 88613563, ss566371993, ss662268870, ss1365539174, ss1429116641, ss1809591611, ss1938460076, ss1959937003, ss2158593397, ss2629496023, ss2704306338, ss3018557824, ss3022141454, ss3352618253, ss3652599755, ss3788704311, ss3793586924, ss3798473712, ss3835770883, ss3841510341, ss3889573523, ss3939960644, ss5230644256, ss5438696685, ss5663616942, ss5838775626, ss5981102358 NC_000021.8:10864232:C:T NC_000021.9:10648223:G:A (self)
557820956, 39121684, 124766246, 13904173273, ss3651070067, ss3707355511, ss3822036014, ss3847023903, ss3982743683, ss4357095378, ss5790929142, ss5818265828, ss5891611723 NC_000021.9:10648223:G:A NC_000021.9:10648223:G:A (self)
ss96133541, ss106199783, ss135583578, ss138277998, ss156644651 NT_029490.4:166336:C:T NC_000021.9:10648223:G:A (self)
13904173273 NC_000021.9:10648223:G:T NC_000021.9:10648223:G:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs28399747

Help

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.

Software version is: 2.0.1.post761+d5e8e07