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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.

rs2928100

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:82889 (GRCh38.p13) 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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.499747 (132278/264690, TOPMED)
A=0.496477 (69469/139924, GnomAD)
G=0.47994 (9066/18890, ALFA) (+ 14 more)
G=0.25471 (4269/16760, 8.3KJPN)
G=0.4349 (2178/5008, 1000G)
G=0.4751 (1831/3854, ALSPAC)
G=0.4717 (1749/3708, TWINSUK)
G=0.2386 (699/2930, KOREAN)
G=0.2265 (415/1832, Korea1K)
A=0.499 (498/998, GoNL)
G=0.423 (254/600, NorthernSweden)
G=0.393 (210/534, MGP)
A=0.338 (123/364, SGDP_PRJ)
G=0.458 (99/216, Qatari)
G=0.302 (64/212, Vietnamese)
A=0.45 (18/40, GENOME_DK)
A=0.42 (15/36, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 10 NC_000010.11:g.82889A>G
GRCh37.p13 chr 10 NC_000010.10:g.128829A>G
IL9RP2 pseudogene NG_009864.2:g.3457T>C
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.72889A>G
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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 A=0.52006 G=0.47994
European Sub 14286 A=0.53836 G=0.46164
African Sub 2946 A=0.3873 G=0.6127
African Others Sub 114 A=0.430 G=0.570
African American Sub 2832 A=0.3856 G=0.6144
Asian Sub 112 A=0.786 G=0.214
East Asian Sub 86 A=0.80 G=0.20
Other Asian Sub 26 A=0.73 G=0.27
Latin American 1 Sub 146 A=0.493 G=0.507
Latin American 2 Sub 610 A=0.646 G=0.354
South Asian Sub 98 A=0.68 G=0.32
Other Sub 692 A=0.536 G=0.464


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
TopMed Global Study-wide 264690 A=0.499747 G=0.500253
gnomAD - Genomes Global Study-wide 139924 A=0.496477 G=0.503523
gnomAD - Genomes European Sub 75802 A=0.53323 G=0.46677
gnomAD - Genomes African Sub 41906 A=0.39331 G=0.60669
gnomAD - Genomes American Sub 13628 A=0.53860 G=0.46140
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.5346 G=0.4654
gnomAD - Genomes East Asian Sub 3122 A=0.7611 G=0.2389
gnomAD - Genomes Other Sub 2144 A=0.5014 G=0.4986
8.3KJPN JAPANESE Study-wide 16760 A=0.74529 G=0.25471
1000Genomes Global Study-wide 5008 A=0.5651 G=0.4349
1000Genomes African Sub 1322 A=0.3699 G=0.6301
1000Genomes East Asian Sub 1008 A=0.7679 G=0.2321
1000Genomes Europe Sub 1006 A=0.5338 G=0.4662
1000Genomes South Asian Sub 978 A=0.687 G=0.313
1000Genomes American Sub 694 A=0.516 G=0.484
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.5249 G=0.4751
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.5283 G=0.4717
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.7614 G=0.2386
Korean Genome Project KOREAN Study-wide 1832 A=0.7735 G=0.2265
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.499 G=0.501
Northern Sweden ACPOP Study-wide 600 A=0.577 G=0.423
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.607 G=0.393
SGDP_PRJ Global Study-wide 364 A=0.338 G=0.662
Qatari Global Study-wide 216 A=0.542 G=0.458
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.698 G=0.302
The Danish reference pan genome Danish Study-wide 40 A=0.45 G=0.55
Siberian Global Study-wide 36 A=0.42 G=0.58
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 A= G
GRCh38.p13 chr 10 NC_000010.11:g.82889= NC_000010.11:g.82889A>G
GRCh37.p13 chr 10 NC_000010.10:g.128829= NC_000010.10:g.128829A>G
IL9RP2 pseudogene NG_009864.2:g.3457= NG_009864.2:g.3457T>C
GRCh37.p13 chr 10 fix patch HG905_PATCH NW_003571043.1:g.72889= NW_003571043.1:g.72889A>G
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#.

62 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4129580 Nov 05, 2001 (101)
2 SC_SNP ss12973426 Dec 05, 2003 (119)
3 SC_SNP ss16089682 Feb 27, 2004 (120)
4 SSAHASNP ss20626500 Apr 05, 2004 (121)
5 ABI ss39869386 Mar 14, 2006 (126)
6 HGSV ss82220985 Dec 16, 2007 (130)
7 HGSV ss84495620 Dec 16, 2007 (130)
8 BCMHGSC_JDW ss88057416 Mar 23, 2008 (129)
9 HUMANGENOME_JCVI ss97613050 Feb 05, 2009 (131)
10 ENSEMBL ss107935990 Feb 13, 2009 (131)
11 ILLUMINA-UK ss118963235 Feb 15, 2009 (130)
12 ENSEMBL ss138799306 Dec 01, 2009 (131)
13 GMI ss158077366 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss168823575 Jul 04, 2010 (132)
15 BUSHMAN ss201023308 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss207426130 Jul 04, 2010 (132)
17 1000GENOMES ss235012260 Jul 15, 2010 (132)
18 1000GENOMES ss241753214 Jul 15, 2010 (132)
19 BL ss253971524 May 09, 2011 (134)
20 GMI ss280440380 May 04, 2012 (137)
21 PJP ss290815790 May 09, 2011 (134)
22 TISHKOFF ss561707916 Apr 25, 2013 (138)
23 SSMP ss656208254 Apr 25, 2013 (138)
24 EVA-GONL ss987096735 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1076687389 Aug 21, 2014 (142)
26 1000GENOMES ss1335912728 Aug 21, 2014 (142)
27 DDI ss1426189098 Apr 09, 2015 (144)
28 EVA_GENOME_DK ss1574842090 Apr 09, 2015 (144)
29 EVA_DECODE ss1596744229 Apr 01, 2015 (144)
30 EVA_UK10K_ALSPAC ss1623797534 Apr 09, 2015 (144)
31 EVA_UK10K_TWINSUK ss1666791567 Apr 09, 2015 (144)
32 EVA_MGP ss1711245171 Apr 09, 2015 (144)
33 HAMMER_LAB ss1806212547 Sep 11, 2015 (146)
34 WEILL_CORNELL_DGM ss1930414720 Feb 17, 2016 (147)
35 JJLAB ss2025929551 Sep 28, 2016 (149)
36 USC_VALOUEV ss2154169612 Oct 12, 2018 (152)
37 TOPMED ss2334635005 Oct 12, 2018 (152)
38 SYSTEMSBIOZJU ss2627432619 Oct 12, 2018 (152)
39 GRF ss2698389002 Oct 12, 2018 (152)
40 GNOMAD ss2884518758 Oct 12, 2018 (152)
41 SWEGEN ss3005784356 Oct 12, 2018 (152)
42 BIOINF_KMB_FNS_UNIBA ss3026746703 Nov 08, 2017 (151)
43 TOPMED ss3109331432 Nov 08, 2017 (151)
44 CSHL ss3348911601 Oct 12, 2018 (152)
45 OMUKHERJEE_ADBS ss3646401708 Oct 12, 2018 (152)
46 URBANLAB ss3649265490 Oct 12, 2018 (152)
47 EVA_DECODE ss3689095279 Jul 13, 2019 (153)
48 ACPOP ss3736974281 Jul 13, 2019 (153)
49 EVA ss3747627295 Jul 13, 2019 (153)
50 PACBIO ss3786553487 Jul 13, 2019 (153)
51 PACBIO ss3791748143 Jul 13, 2019 (153)
52 PACBIO ss3796629765 Jul 13, 2019 (153)
53 KHV_HUMAN_GENOMES ss3812993284 Jul 13, 2019 (153)
54 EVA ss3831916724 Apr 26, 2020 (154)
55 EVA ss3839487145 Apr 26, 2020 (154)
56 EVA ss3844952613 Apr 26, 2020 (154)
57 SGDP_PRJ ss3873326375 Apr 26, 2020 (154)
58 KRGDB ss3921253386 Apr 26, 2020 (154)
59 KOGIC ss3967022781 Apr 26, 2020 (154)
60 GNOMAD ss4211409683 Apr 26, 2021 (155)
61 TOPMED ss4839522640 Apr 26, 2021 (155)
62 TOMMO_GENOMICS ss5195847929 Apr 26, 2021 (155)
63 1000Genomes NC_000010.10 - 128829 Oct 12, 2018 (152)
64 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 128829 Oct 12, 2018 (152)
65 The Danish reference pan genome NC_000010.10 - 128829 Apr 26, 2020 (154)
66 gnomAD - Genomes NC_000010.11 - 82889 Apr 26, 2021 (155)
67 Genome of the Netherlands Release 5 NC_000010.10 - 128829 Apr 26, 2020 (154)
68 KOREAN population from KRGDB NC_000010.10 - 128829 Apr 26, 2020 (154)
69 Korean Genome Project NC_000010.11 - 82889 Apr 26, 2020 (154)
70 Medical Genome Project healthy controls from Spanish population NC_000010.10 - 128829 Apr 26, 2020 (154)
71 Northern Sweden NC_000010.10 - 128829 Jul 13, 2019 (153)
72 Qatari NC_000010.10 - 128829 Apr 26, 2020 (154)
73 SGDP_PRJ NC_000010.10 - 128829 Apr 26, 2020 (154)
74 Siberian NC_000010.10 - 128829 Apr 26, 2020 (154)
75 8.3KJPN NC_000010.10 - 128829 Apr 26, 2021 (155)
76 TopMed NC_000010.11 - 82889 Apr 26, 2021 (155)
77 UK 10K study - Twins NC_000010.10 - 128829 Oct 12, 2018 (152)
78 A Vietnamese Genetic Variation Database NC_000010.10 - 128829 Jul 13, 2019 (153)
79 ALFA NC_000010.11 - 82889 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)
rs61060135 May 26, 2008 (130)
rs67098764 Dec 02, 2009 (131)
rs67098765 Feb 26, 2009 (130)
rs67098766 Feb 26, 2009 (130)
rs72651777 Dec 02, 2009 (131)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82220985, ss84495620 NC_000010.8:118828:A:G NC_000010.11:82888:A:G (self)
ss88057416, ss118963235, ss168823575, ss201023308, ss207426130, ss253971524, ss280440380, ss290815790, ss1596744229 NC_000010.9:118828:A:G NC_000010.11:82888:A:G (self)
48246428, 26806305, 1988103, 11953862, 28430780, 360931, 10259146, 12456650, 25343355, 6685966, 53817236, 26806305, 5948662, ss235012260, ss241753214, ss561707916, ss656208254, ss987096735, ss1076687389, ss1335912728, ss1426189098, ss1574842090, ss1623797534, ss1666791567, ss1711245171, ss1806212547, ss1930414720, ss2025929551, ss2154169612, ss2334635005, ss2627432619, ss2698389002, ss2884518758, ss3005784356, ss3348911601, ss3646401708, ss3736974281, ss3747627295, ss3786553487, ss3791748143, ss3796629765, ss3831916724, ss3839487145, ss3873326375, ss3921253386, ss5195847929 NC_000010.10:128828:A:G NC_000010.11:82888:A:G (self)
340932862, 23400782, 34601701, 55068295, 12169364138, ss3026746703, ss3109331432, ss3649265490, ss3689095279, ss3812993284, ss3844952613, ss3967022781, ss4211409683, ss4839522640 NC_000010.11:82888:A:G NC_000010.11:82888:A:G (self)
ss4129580, ss39869386, ss97613050, ss107935990, ss138799306, ss158077366 NT_008705.16:68828:A:G NC_000010.11:82888:A:G (self)
ss12973426 NT_024115.14:68828:A:G NC_000010.11:82888:A:G (self)
ss16089682, ss20626500 NT_077567.3:68828:A:G NC_000010.11:82888:A:G (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 rs2928100

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.post596+ae089ad