Name: rs2928100
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.

rs2928100

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:82889 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.499747 (132278/264690, TOPMED)
A=0.496477 (69469/139924, GnomAD)
G=0.25816 (7295/28258, 14KJPN) (+ 16 more)
G=0.47994 (9066/18890, ALFA)
G=0.25471 (4269/16760, 8.3KJPN)
G=0.4428 (2836/6404, 1000G_30x)
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

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	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

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	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
14KJPN	JAPANESE	Study-wide	28258	A=0.74184	G=0.25816
Allele Frequency Aggregator	Total	Global	18890	A=0.52006	G=0.47994
Allele Frequency Aggregator	European	Sub	14286	A=0.53836	G=0.46164
Allele Frequency Aggregator	African	Sub	2946	A=0.3873	G=0.6127
Allele Frequency Aggregator	Other	Sub	692	A=0.536	G=0.464
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.646	G=0.354
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.493	G=0.507
Allele Frequency Aggregator	Asian	Sub	112	A=0.786	G=0.214
Allele Frequency Aggregator	South Asian	Sub	98	A=0.68	G=0.32
8.3KJPN	JAPANESE	Study-wide	16760	A=0.74529	G=0.25471
1000Genomes_30x	Global	Study-wide	6404	A=0.5572	G=0.4428
1000Genomes_30x	African	Sub	1786	A=0.3718	G=0.6282
1000Genomes_30x	Europe	Sub	1266	A=0.5348	G=0.4652
1000Genomes_30x	South Asian	Sub	1202	A=0.6947	G=0.3053
1000Genomes_30x	East Asian	Sub	1170	A=0.7675	G=0.2325
1000Genomes_30x	American	Sub	980	A=0.504	G=0.496
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

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 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

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	A=	G
GRCh38.p14 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

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#.

73 SubSNP, 19 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	SYSTEMSBIOZJU	ss2627432619	Oct 12, 2018 (152)
38	GRF	ss2698389002	Oct 12, 2018 (152)
39	GNOMAD	ss2884518758	Oct 12, 2018 (152)
40	SWEGEN	ss3005784356	Oct 12, 2018 (152)
41	BIOINF_KMB_FNS_UNIBA	ss3026746703	Nov 08, 2017 (151)
42	CSHL	ss3348911601	Oct 12, 2018 (152)
43	OMUKHERJEE_ADBS	ss3646401708	Oct 12, 2018 (152)
44	URBANLAB	ss3649265490	Oct 12, 2018 (152)
45	EVA_DECODE	ss3689095279	Jul 13, 2019 (153)
46	ACPOP	ss3736974281	Jul 13, 2019 (153)
47	EVA	ss3747627295	Jul 13, 2019 (153)
48	PACBIO	ss3786553487	Jul 13, 2019 (153)
49	PACBIO	ss3791748143	Jul 13, 2019 (153)
50	PACBIO	ss3796629765	Jul 13, 2019 (153)
51	KHV_HUMAN_GENOMES	ss3812993284	Jul 13, 2019 (153)
52	EVA	ss3831916724	Apr 26, 2020 (154)
53	EVA	ss3839487145	Apr 26, 2020 (154)
54	EVA	ss3844952613	Apr 26, 2020 (154)
55	SGDP_PRJ	ss3873326375	Apr 26, 2020 (154)
56	KRGDB	ss3921253386	Apr 26, 2020 (154)
57	KOGIC	ss3967022781	Apr 26, 2020 (154)
58	GNOMAD	ss4211409683	Apr 26, 2021 (155)
59	TOPMED	ss4839522640	Apr 26, 2021 (155)
60	TOMMO_GENOMICS	ss5195847929	Apr 26, 2021 (155)
61	1000G_HIGH_COVERAGE	ss5282596002	Oct 16, 2022 (156)
62	EVA	ss5391011017	Oct 16, 2022 (156)
63	HUGCELL_USP	ss5478409046	Oct 16, 2022 (156)
64	EVA	ss5509874331	Oct 16, 2022 (156)
65	1000G_HIGH_COVERAGE	ss5575841133	Oct 16, 2022 (156)
66	SANFORD_IMAGENETICS	ss5648489353	Oct 16, 2022 (156)
67	TOMMO_GENOMICS	ss5740572765	Oct 16, 2022 (156)
68	YY_MCH	ss5811109550	Oct 16, 2022 (156)
69	EVA	ss5823842339	Oct 16, 2022 (156)
70	EVA	ss5849394420	Oct 16, 2022 (156)
71	EVA	ss5939768769	Oct 16, 2022 (156)
72	EVA	ss5980588194	Oct 16, 2022 (156)
73	EVA	ss5981258256	Oct 16, 2022 (156)
74	1000Genomes	NC_000010.10 - 128829	Oct 12, 2018 (152)
75	1000Genomes_30x	NC_000010.11 - 82889	Oct 16, 2022 (156)
76	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 128829	Oct 12, 2018 (152)
77	The Danish reference pan genome	NC_000010.10 - 128829	Apr 26, 2020 (154)
78	gnomAD - Genomes	NC_000010.11 - 82889	Apr 26, 2021 (155)
79	Genome of the Netherlands Release 5	NC_000010.10 - 128829	Apr 26, 2020 (154)
80	KOREAN population from KRGDB	NC_000010.10 - 128829	Apr 26, 2020 (154)
81	Korean Genome Project	NC_000010.11 - 82889	Apr 26, 2020 (154)
82	Medical Genome Project healthy controls from Spanish population	NC_000010.10 - 128829	Apr 26, 2020 (154)
83	Northern Sweden	NC_000010.10 - 128829	Jul 13, 2019 (153)
84	Qatari	NC_000010.10 - 128829	Apr 26, 2020 (154)
85	SGDP_PRJ	NC_000010.10 - 128829	Apr 26, 2020 (154)
86	Siberian	NC_000010.10 - 128829	Apr 26, 2020 (154)
87	8.3KJPN	NC_000010.10 - 128829	Apr 26, 2021 (155)
88	14KJPN	NC_000010.11 - 82889	Oct 16, 2022 (156)
89	TopMed	NC_000010.11 - 82889	Apr 26, 2021 (155)
90	UK 10K study - Twins	NC_000010.10 - 128829	Oct 12, 2018 (152)
91	A Vietnamese Genetic Variation Database	NC_000010.10 - 128829	Jul 13, 2019 (153)
92	ALFA	NC_000010.11 - 82889	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)
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, ss2627432619, ss2698389002, ss2884518758, ss3005784356, ss3348911601, ss3646401708, ss3736974281, ss3747627295, ss3786553487, ss3791748143, ss3796629765, ss3831916724, ss3839487145, ss3873326375, ss3921253386, ss5195847929, ss5391011017, ss5509874331, ss5648489353, ss5823842339, ss5939768769, ss5980588194, ss5981258256	NC_000010.10:128828:A:G	NC_000010.11:82888:A:G	(self)
63367068, 340932862, 23400782, 74409869, 55068295, 12169364138, ss3026746703, ss3649265490, ss3689095279, ss3812993284, ss3844952613, ss3967022781, ss4211409683, ss4839522640, ss5282596002, ss5478409046, ss5575841133, ss5740572765, ss5811109550, ss5849394420	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)

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

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

rs2928100