Name: rs3020682
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.

rs3020682

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:86053 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.251728 (66630/264690, TOPMED)
A=0.248287 (34705/139778, GnomAD)
A=0.09007 (2545/28256, 14KJPN) (+ 11 more)
A=0.20254 (3826/18890, ALFA)
A=0.08688 (1456/16758, 8.3KJPN)
A=0.2423 (1552/6404, 1000G_30x)
A=0.2340 (1172/5008, 1000G)
A=0.1133 (332/2930, KOREAN)
A=0.144 (144/998, GoNL)
A=0.150 (90/600, NorthernSweden)
A=0.204 (44/216, Qatari)
G=0.356 (67/188, SGDP_PRJ)
G=0.5 (3/6, Siberian)
A=0.5 (3/6, 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	G=0.79746	A=0.20254
European	Sub	14286	G=0.85237	A=0.14763
African	Sub	2946	G=0.5139	A=0.4861
African Others	Sub	114	G=0.535	A=0.465
African American	Sub	2832	G=0.5131	A=0.4869
Asian	Sub	112	G=0.920	A=0.080
East Asian	Sub	86	G=0.93	A=0.07
Other Asian	Sub	26	G=0.88	A=0.12
Latin American 1	Sub	146	G=0.801	A=0.199
Latin American 2	Sub	610	G=0.856	A=0.144
South Asian	Sub	98	G=0.89	A=0.11
Other	Sub	692	G=0.786	A=0.214

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	G=0.748272	A=0.251728
gnomAD - Genomes	Global	Study-wide	139778	G=0.751713	A=0.248287
gnomAD - Genomes	European	Sub	75780	G=0.85496	A=0.14504
gnomAD - Genomes	African	Sub	41796	G=0.51912	A=0.48088
gnomAD - Genomes	American	Sub	13610	G=0.83115	A=0.16885
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.8710	A=0.1290
gnomAD - Genomes	East Asian	Sub	3126	G=0.8704	A=0.1296
gnomAD - Genomes	Other	Sub	2148	G=0.7747	A=0.2253
14KJPN	JAPANESE	Study-wide	28256	G=0.90993	A=0.09007
Allele Frequency Aggregator	Total	Global	18890	G=0.79746	A=0.20254
Allele Frequency Aggregator	European	Sub	14286	G=0.85237	A=0.14763
Allele Frequency Aggregator	African	Sub	2946	G=0.5139	A=0.4861
Allele Frequency Aggregator	Other	Sub	692	G=0.786	A=0.214
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.856	A=0.144
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.801	A=0.199
Allele Frequency Aggregator	Asian	Sub	112	G=0.920	A=0.080
Allele Frequency Aggregator	South Asian	Sub	98	G=0.89	A=0.11
8.3KJPN	JAPANESE	Study-wide	16758	G=0.91312	A=0.08688
1000Genomes_30x	Global	Study-wide	6404	G=0.7577	A=0.2423
1000Genomes_30x	African	Sub	1786	G=0.4670	A=0.5330
1000Genomes_30x	Europe	Sub	1266	G=0.8728	A=0.1272
1000Genomes_30x	South Asian	Sub	1202	G=0.9151	A=0.0849
1000Genomes_30x	East Asian	Sub	1170	G=0.8778	A=0.1222
1000Genomes_30x	American	Sub	980	G=0.802	A=0.198
1000Genomes	Global	Study-wide	5008	G=0.7660	A=0.2340
1000Genomes	African	Sub	1322	G=0.4652	A=0.5348
1000Genomes	East Asian	Sub	1008	G=0.8780	A=0.1220
1000Genomes	Europe	Sub	1006	G=0.8738	A=0.1262
1000Genomes	South Asian	Sub	978	G=0.918	A=0.082
1000Genomes	American	Sub	694	G=0.805	A=0.195
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.8867	A=0.1133
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.856	A=0.144
Northern Sweden	ACPOP	Study-wide	600	G=0.850	A=0.150
Qatari	Global	Study-wide	216	G=0.796	A=0.204
SGDP_PRJ	Global	Study-wide	188	G=0.356	A=0.644
Siberian	Global	Study-wide	6	G=0.5	A=0.5

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.86053G>A
GRCh37.p13 chr 10	NC_000010.10:g.131993G>A
IL9RP2 pseudogene	NG_009864.2:g.293C>T
GRCh37.p13 chr 10 fix patch HG905_PATCH	NW_003571043.1:g.76053G>A

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=	A
GRCh38.p14 chr 10	NC_000010.11:g.86053=	NC_000010.11:g.86053G>A
GRCh37.p13 chr 10	NC_000010.10:g.131993=	NC_000010.10:g.131993G>A
IL9RP2 pseudogene	NG_009864.2:g.293=	NG_009864.2:g.293C>T
GRCh37.p13 chr 10 fix patch HG905_PATCH	NW_003571043.1:g.76053=	NW_003571043.1:g.76053G>A

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, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss4249089	Nov 05, 2001 (101)
2	BCM_SSAHASNP	ss10594327	Jul 11, 2003 (116)
3	SC_SNP	ss12973449	Dec 05, 2003 (119)
4	SC_SNP	ss15593683	Feb 27, 2004 (120)
5	HGSV	ss78940094	Dec 07, 2007 (129)
6	HGSV	ss85302020	Dec 15, 2007 (130)
7	HUMANGENOME_JCVI	ss97613053	Feb 05, 2009 (131)
8	ILLUMINA-UK	ss118963247	Feb 15, 2009 (130)
9	GMI	ss158077383	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss168823578	Jul 04, 2010 (132)
11	BUSHMAN	ss201023362	Jul 04, 2010 (132)
12	1000GENOMES	ss224512376	Jul 14, 2010 (132)
13	1000GENOMES	ss235012272	Jul 15, 2010 (132)
14	1000GENOMES	ss241753221	Jul 15, 2010 (132)
15	GMI	ss280440386	May 04, 2012 (137)
16	PJP	ss290815795	May 09, 2011 (134)
17	TISHKOFF	ss561707927	Apr 25, 2013 (138)
18	SSMP	ss656208266	Apr 25, 2013 (138)
19	EVA-GONL	ss987096762	Aug 21, 2014 (142)
20	1000GENOMES	ss1335912867	Aug 21, 2014 (142)
21	HAMMER_LAB	ss1806212554	Sep 11, 2015 (146)
22	WEILL_CORNELL_DGM	ss1930414746	Feb 17, 2016 (147)
23	USC_VALOUEV	ss2154169621	Oct 12, 2018 (152)
24	SYSTEMSBIOZJU	ss2627432623	Oct 12, 2018 (152)
25	GRF	ss2698389013	Oct 12, 2018 (152)
26	GNOMAD	ss2884519071	Oct 12, 2018 (152)
27	SWEGEN	ss3005784405	Oct 12, 2018 (152)
28	URBANLAB	ss3649265495	Oct 12, 2018 (152)
29	ACPOP	ss3736974305	Jul 13, 2019 (153)
30	EVA	ss3747627335	Jul 13, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3812993320	Jul 13, 2019 (153)
32	SGDP_PRJ	ss3873326431	Apr 26, 2020 (154)
33	KRGDB	ss3921253451	Apr 26, 2020 (154)
34	GNOMAD	ss4211410419	Apr 26, 2021 (155)
35	TOPMED	ss4839523545	Apr 26, 2021 (155)
36	TOMMO_GENOMICS	ss5195848045	Apr 26, 2021 (155)
37	1000G_HIGH_COVERAGE	ss5282596110	Oct 16, 2022 (156)
38	EVA	ss5391011223	Oct 16, 2022 (156)
39	1000G_HIGH_COVERAGE	ss5575841298	Oct 16, 2022 (156)
40	SANFORD_IMAGENETICS	ss5648489403	Oct 16, 2022 (156)
41	TOMMO_GENOMICS	ss5740572919	Oct 16, 2022 (156)
42	YY_MCH	ss5811109569	Oct 16, 2022 (156)
43	EVA	ss5823842369	Oct 16, 2022 (156)
44	EVA	ss5939768813	Oct 16, 2022 (156)
45	1000Genomes	NC_000010.10 - 131993	Oct 12, 2018 (152)
46	1000Genomes_30x	NC_000010.11 - 86053	Oct 16, 2022 (156)
47	gnomAD - Genomes	NC_000010.11 - 86053	Apr 26, 2021 (155)
48	Genome of the Netherlands Release 5	NC_000010.10 - 131993	Apr 26, 2020 (154)
49	KOREAN population from KRGDB	NC_000010.10 - 131993	Apr 26, 2020 (154)
50	Northern Sweden	NC_000010.10 - 131993	Jul 13, 2019 (153)
51	Qatari	NC_000010.10 - 131993	Apr 26, 2020 (154)
52	SGDP_PRJ	NC_000010.10 - 131993	Apr 26, 2020 (154)
53	Siberian	NC_000010.10 - 131993	Apr 26, 2020 (154)
54	8.3KJPN	NC_000010.10 - 131993	Apr 26, 2021 (155)
55	14KJPN	NC_000010.11 - 86053	Oct 16, 2022 (156)
56	TopMed	NC_000010.11 - 86053	Apr 26, 2021 (155)
57	ALFA	NC_000010.11 - 86053	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)
rs59518167	May 25, 2008 (130)
rs67172557	Dec 02, 2009 (131)
rs67172558	Feb 26, 2009 (130)
rs67172559	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78940094, ss85302020	NC_000010.8:121992:G:A	NC_000010.11:86052:G:A	(self)
ss118963247, ss168823578, ss201023362, ss280440386, ss290815795	NC_000010.9:121992:G:A	NC_000010.11:86052:G:A	(self)
48246572, 11953889, 28430845, 10259170, 12456676, 25343411, 6685975, 53817352, ss224512376, ss235012272, ss241753221, ss561707927, ss656208266, ss987096762, ss1335912867, ss1806212554, ss1930414746, ss2154169621, ss2627432623, ss2698389013, ss2884519071, ss3005784405, ss3736974305, ss3747627335, ss3873326431, ss3921253451, ss5195848045, ss5391011223, ss5648489403, ss5823842369, ss5939768813	NC_000010.10:131992:G:A	NC_000010.11:86052:G:A	(self)
63367233, 340933598, 74410023, 55069200, 10808099138, ss3649265495, ss3812993320, ss4211410419, ss4839523545, ss5282596110, ss5575841298, ss5740572919, ss5811109569	NC_000010.11:86052:G:A	NC_000010.11:86052:G:A	(self)
ss4249089, ss97613053, ss158077383	NT_008705.16:71992:G:A	NC_000010.11:86052:G:A	(self)
ss10594327, ss12973449	NT_024115.14:71992:G:A	NC_000010.11:86052:G:A	(self)
ss15593683	NT_077567.3:71992:G:A	NC_000010.11:86052:G:A	(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 rs3020682

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

rs3020682