Name: rs3883945
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.

rs3883945

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr21:10649858 (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>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.46808 (13227/28258, 14KJPN)
G=0.46820 (7847/16760, 8.3KJPN)
G=0.39870 (5412/13574, ALFA) (+ 7 more)
G=0.4505 (2256/5008, 1000G)
G=0.4782 (1401/2930, KOREAN)
G=0.4765 (873/1832, Korea1K)
G=0.442 (245/554, SGDP_PRJ)
G=0.440 (235/534, MGP)
G=0.440 (95/216, Qatari)
G=0.36 (20/56, 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	13574	G=0.39870	A=0.60130, C=0.00000
European	Sub	10576	G=0.38587	A=0.61413, C=0.00000
African	Sub	642	G=0.489	A=0.511, C=0.000
African Others	Sub	10	G=0.6	A=0.4, C=0.0
African American	Sub	632	G=0.487	A=0.513, C=0.000
Asian	Sub	58	G=0.50	A=0.50, C=0.00
East Asian	Sub	28	G=0.54	A=0.46, C=0.00
Other Asian	Sub	30	G=0.47	A=0.53, C=0.00
Latin American 1	Sub	0	G=0	A=0, C=0
Latin American 2	Sub	0	G=0	A=0, C=0
South Asian	Sub	0	G=0	A=0, C=0
Other	Sub	2298	G=0.4299	A=0.5701, C=0.0000

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
14KJPN	JAPANESE	Study-wide	28258	G=0.46808	A=0.53192
8.3KJPN	JAPANESE	Study-wide	16760	G=0.46820	A=0.53180
Allele Frequency Aggregator	Total	Global	13574	G=0.39870	A=0.60130, C=0.00000
Allele Frequency Aggregator	European	Sub	10576	G=0.38587	A=0.61413, C=0.00000
Allele Frequency Aggregator	Other	Sub	2298	G=0.4299	A=0.5701, C=0.0000
Allele Frequency Aggregator	African	Sub	642	G=0.489	A=0.511, C=0.000
Allele Frequency Aggregator	Asian	Sub	58	G=0.50	A=0.50, C=0.00
Allele Frequency Aggregator	Latin American 1	Sub	0	G=0	A=0, C=0
Allele Frequency Aggregator	Latin American 2	Sub	0	G=0	A=0, C=0
Allele Frequency Aggregator	South Asian	Sub	0	G=0	A=0, C=0
1000Genomes	Global	Study-wide	5008	G=0.4505	A=0.5495
1000Genomes	African	Sub	1322	G=0.5182	A=0.4818
1000Genomes	East Asian	Sub	1008	G=0.4454	A=0.5546
1000Genomes	Europe	Sub	1006	G=0.3748	A=0.6252
1000Genomes	South Asian	Sub	978	G=0.440	A=0.560
1000Genomes	American	Sub	694	G=0.454	A=0.546
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.4782	C=0.0000, A=0.5218
Korean Genome Project	KOREAN	Study-wide	1832	G=0.4765	A=0.5235
SGDP_PRJ	Global	Study-wide	554	G=0.442	A=0.558
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	G=0.440	A=0.560
Qatari	Global	Study-wide	216	G=0.440	A=0.560
Siberian	Global	Study-wide	56	G=0.36	A=0.64

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.10649858G>A
GRCh38.p14 chr 21	NC_000021.9:g.10649858G>C
GRCh38.p14 chr 21	NC_000021.9:g.10649858G>T
GRCh37.p13 chr 21	NC_000021.8:g.10862599C>T
GRCh37.p13 chr 21	NC_000021.8:g.10862599C>G
GRCh37.p13 chr 21	NC_000021.8:g.10862599C>A
IGHV1OR21-1 pseudogene	NG_011680.1:g.78C>T
IGHV1OR21-1 pseudogene	NG_011680.1:g.78C>G
IGHV1OR21-1 pseudogene	NG_011680.1:g.78C>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	C	T
GRCh38.p14 chr 21	NC_000021.9:g.10649858=	NC_000021.9:g.10649858G>A	NC_000021.9:g.10649858G>C	NC_000021.9:g.10649858G>T
GRCh37.p13 chr 21	NC_000021.8:g.10862599=	NC_000021.8:g.10862599C>T	NC_000021.8:g.10862599C>G	NC_000021.8:g.10862599C>A
IGHV1OR21-1 pseudogene	NG_011680.1:g.78=	NG_011680.1:g.78C>T	NG_011680.1:g.78C>G	NG_011680.1:g.78C>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#.

66 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2864735	Oct 08, 2002 (108)
2	TSC-CSHL	ss5532368	Oct 08, 2002 (108)
3	HGSV	ss77567883	Dec 07, 2007 (129)
4	HGSV	ss78420106	Dec 07, 2007 (129)
5	HGSV	ss79037435	Dec 07, 2007 (129)
6	BCMHGSC_JDW	ss91761672	Mar 24, 2008 (129)
7	HUMANGENOME_JCVI	ss96153123	Feb 06, 2009 (130)
8	ILLUMINA-UK	ss117448226	Feb 14, 2009 (130)
9	ENSEMBL	ss135583613	Dec 01, 2009 (131)
10	ENSEMBL	ss138277986	Dec 01, 2009 (131)
11	GMI	ss156644565	Dec 01, 2009 (131)
12	BUSHMAN	ss203950752	Jul 04, 2010 (132)
13	BCM-HGSC-SUB	ss208767134	Jul 04, 2010 (132)
14	BL	ss255831047	May 09, 2011 (134)
15	GMI	ss283453224	May 04, 2012 (137)
16	GMI	ss287490076	Apr 25, 2013 (138)
17	PJP	ss292668637	May 09, 2011 (134)
18	TISHKOFF	ss566371981	Apr 25, 2013 (138)
19	1000GENOMES	ss1365539103	Aug 21, 2014 (142)
20	DDI	ss1429116625	Apr 01, 2015 (144)
21	EVA_EXAC	ss1694104730	Apr 01, 2015 (144)
22	EVA_EXAC	ss1694104731	Apr 01, 2015 (144)
23	EVA_MGP	ss1711548604	Apr 01, 2015 (144)
24	HAMMER_LAB	ss1809591596	Sep 08, 2015 (146)
25	WEILL_CORNELL_DGM	ss1938460041	Feb 12, 2016 (147)
26	ILLUMINA	ss1959936985	Feb 12, 2016 (147)
27	ILLUMINA	ss1959936986	Feb 12, 2016 (147)
28	USC_VALOUEV	ss2158593381	Dec 20, 2016 (150)
29	SYSTEMSBIOZJU	ss2629496008	Nov 08, 2017 (151)
30	GRF	ss2704306312	Nov 08, 2017 (151)
31	GNOMAD	ss2744772573	Nov 08, 2017 (151)
32	GNOMAD	ss2750435716	Nov 08, 2017 (151)
33	SWEGEN	ss3018557767	Nov 08, 2017 (151)
34	ILLUMINA	ss3022141438	Nov 08, 2017 (151)
35	ILLUMINA	ss3022141439	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3028835806	Nov 08, 2017 (151)
37	CSHL	ss3352618229	Nov 08, 2017 (151)
38	OMUKHERJEE_ADBS	ss3646553942	Oct 12, 2018 (152)
39	URBANLAB	ss3651070076	Oct 12, 2018 (152)
40	ILLUMINA	ss3652599739	Oct 12, 2018 (152)
41	ILLUMINA	ss3652599740	Oct 12, 2018 (152)
42	EVA_DECODE	ss3707355562	Jul 13, 2019 (153)
43	PACBIO	ss3788704297	Jul 13, 2019 (153)
44	PACBIO	ss3793586911	Jul 13, 2019 (153)
45	PACBIO	ss3798473699	Jul 13, 2019 (153)
46	KHV_HUMAN_GENOMES	ss3822036026	Jul 13, 2019 (153)
47	EVA	ss3825958594	Apr 27, 2020 (154)
48	EVA	ss3835770872	Apr 27, 2020 (154)
49	SGDP_PRJ	ss3889573436	Apr 27, 2020 (154)
50	KRGDB	ss3939960557	Apr 27, 2020 (154)
51	KOGIC	ss3982743756	Apr 27, 2020 (154)
52	FSA-LAB	ss3984222267	Apr 26, 2021 (155)
53	EVA	ss3986841110	Apr 26, 2021 (155)
54	TOMMO_GENOMICS	ss5230644081	Apr 26, 2021 (155)
55	EVA	ss5237253283	Apr 26, 2021 (155)
56	EVA	ss5438696577	Oct 16, 2022 (156)
57	EVA	ss5624116210	Oct 16, 2022 (156)
58	SANFORD_IMAGENETICS	ss5663616913	Oct 16, 2022 (156)
59	TOMMO_GENOMICS	ss5790929360	Oct 16, 2022 (156)
60	EVA	ss5800231607	Oct 16, 2022 (156)
61	YY_MCH	ss5818265872	Oct 16, 2022 (156)
62	EVA	ss5838775579	Oct 16, 2022 (156)
63	EVA	ss5848554847	Oct 16, 2022 (156)
64	EVA	ss5936578149	Oct 16, 2022 (156)
65	EVA	ss5981102348	Oct 16, 2022 (156)
66	EVA	ss5981318677	Oct 16, 2022 (156)
67	1000Genomes	NC_000021.8 - 10862599	Oct 12, 2018 (152)
68	ExAC Submission ignored due to conflicting rows: Row 5667117 (NC_000021.8:10862598:C:C 49998/120736, NC_000021.8:10862598:C:T 70738/120736) Row 5667118 (NC_000021.8:10862598:C:C 120735/120736, NC_000021.8:10862598:C:A 1/120736)	-	Oct 12, 2018 (152)
69	ExAC Submission ignored due to conflicting rows: Row 5667117 (NC_000021.8:10862598:C:C 49998/120736, NC_000021.8:10862598:C:T 70738/120736) Row 5667118 (NC_000021.8:10862598:C:C 120735/120736, NC_000021.8:10862598:C:A 1/120736)	-	Oct 12, 2018 (152)
70	KOREAN population from KRGDB	NC_000021.8 - 10862599	Apr 27, 2020 (154)
71	Korean Genome Project	NC_000021.9 - 10649858	Apr 27, 2020 (154)
72	Medical Genome Project healthy controls from Spanish population	NC_000021.8 - 10862599	Apr 27, 2020 (154)
73	Qatari	NC_000021.8 - 10862599	Apr 27, 2020 (154)
74	SGDP_PRJ	NC_000021.8 - 10862599	Apr 27, 2020 (154)
75	Siberian	NC_000021.8 - 10862599	Apr 27, 2020 (154)
76	8.3KJPN	NC_000021.8 - 10862599	Apr 26, 2021 (155)
77	14KJPN	NC_000021.9 - 10649858	Oct 16, 2022 (156)
78	ALFA	NC_000021.9 - 10649858	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77567883, ss78420106, ss79037435, ss91761672, ss117448226, ss203950752, ss208767134, ss255831047, ss283453224, ss287490076, ss292668637	NC_000021.7:9884469:C:T	NC_000021.9:10649857:G:A	(self)
79028740, 47137951, 664364, 20501963, 41590416, 11109735, 88613388, ss566371981, ss1365539103, ss1429116625, ss1694104730, ss1711548604, ss1809591596, ss1938460041, ss1959936985, ss1959936986, ss2158593381, ss2629496008, ss2704306312, ss2744772573, ss2750435716, ss3018557767, ss3022141438, ss3022141439, ss3352618229, ss3646553942, ss3652599739, ss3652599740, ss3788704297, ss3793586911, ss3798473699, ss3825958594, ss3835770872, ss3889573436, ss3939960557, ss3984222267, ss3986841110, ss5230644081, ss5438696577, ss5624116210, ss5663616913, ss5800231607, ss5838775579, ss5848554847, ss5936578149, ss5981102348, ss5981318677	NC_000021.8:10862598:C:T	NC_000021.9:10649857:G:A	(self)
39121757, 124766464, 7416697920, ss3028835806, ss3651070076, ss3707355562, ss3822036026, ss3982743756, ss5237253283, ss5790929360, ss5818265872	NC_000021.9:10649857:G:A	NC_000021.9:10649857:G:A	(self)
ss2864735, ss5532368, ss96153123, ss135583613, ss138277986, ss156644565	NT_029490.4:164702:C:T	NC_000021.9:10649857:G:A	(self)
47137951, ss3939960557	NC_000021.8:10862598:C:G	NC_000021.9:10649857:G:C	(self)
7416697920	NC_000021.9:10649857:G:C	NC_000021.9:10649857:G:C	(self)
ss1694104731, ss2744772573	NC_000021.8:10862598:C:A	NC_000021.9:10649857:G:T	(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 rs3883945

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

rs3883945