Name: rs9983399
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.

rs9983399

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr21:38040294 (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: T>A / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.310102 (82081/264690, TOPMED)
T=0.321266 (44994/140052, GnomAD)
T=0.13433 (3796/28258, 14KJPN) (+ 21 more)
T=0.34530 (7879/22818, ALFA)
T=0.13395 (2245/16760, 8.3KJPN)
T=0.2645 (1694/6404, 1000G_30x)
T=0.2578 (1291/5008, 1000G)
T=0.4498 (2015/4480, Estonian)
T=0.3972 (1531/3854, ALSPAC)
T=0.3962 (1469/3708, TWINSUK)
T=0.2726 (568/2084, HGDP_Stanford)
T=0.2484 (470/1892, HapMap)
T=0.1943 (356/1832, Korea1K)
T=0.415 (414/998, GoNL)
T=0.300 (180/600, NorthernSweden)
T=0.211 (108/512, SGDP_PRJ)
T=0.241 (52/216, Qatari)
T=0.226 (48/212, Vietnamese)
T=0.26 (16/62, Ancient Sardinia)
T=0.26 (11/42, Siberian)
T=0.35 (14/40, GENOME_DK)
T=0.0 (0/8, KOREAN)
A=0.0 (0/8, KOREAN)
G=0.0 (0/8, KOREAN)

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	22818	T=0.34530	C=0.65470
European	Sub	16610	T=0.38302	C=0.61698
African	Sub	4114	T=0.1935	C=0.8065
African Others	Sub	148	T=0.169	C=0.831
African American	Sub	3966	T=0.1944	C=0.8056
Asian	Sub	124	T=0.258	C=0.742
East Asian	Sub	96	T=0.22	C=0.78
Other Asian	Sub	28	T=0.39	C=0.61
Latin American 1	Sub	168	T=0.321	C=0.679
Latin American 2	Sub	670	T=0.399	C=0.601
South Asian	Sub	98	T=0.29	C=0.71
Other	Sub	1034	T=0.3288	C=0.6712

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	T=0.310102	C=0.689898
gnomAD - Genomes	Global	Study-wide	140052	T=0.321266	C=0.678734
gnomAD - Genomes	European	Sub	75820	T=0.39618	C=0.60382
gnomAD - Genomes	African	Sub	41976	T=0.18496	C=0.81504
gnomAD - Genomes	American	Sub	13650	T=0.35421	C=0.64579
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.2681	C=0.7319
gnomAD - Genomes	East Asian	Sub	3130	T=0.2553	C=0.7447
gnomAD - Genomes	Other	Sub	2152	T=0.3099	C=0.6901
14KJPN	JAPANESE	Study-wide	28258	T=0.13433	C=0.86567
Allele Frequency Aggregator	Total	Global	22818	T=0.34530	C=0.65470
Allele Frequency Aggregator	European	Sub	16610	T=0.38302	C=0.61698
Allele Frequency Aggregator	African	Sub	4114	T=0.1935	C=0.8065
Allele Frequency Aggregator	Other	Sub	1034	T=0.3288	C=0.6712
Allele Frequency Aggregator	Latin American 2	Sub	670	T=0.399	C=0.601
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.321	C=0.679
Allele Frequency Aggregator	Asian	Sub	124	T=0.258	C=0.742
Allele Frequency Aggregator	South Asian	Sub	98	T=0.29	C=0.71
8.3KJPN	JAPANESE	Study-wide	16760	T=0.13395	C=0.86605
1000Genomes_30x	Global	Study-wide	6404	T=0.2645	C=0.7355
1000Genomes_30x	African	Sub	1786	T=0.1540	C=0.8460
1000Genomes_30x	Europe	Sub	1266	T=0.3341	C=0.6659
1000Genomes_30x	South Asian	Sub	1202	T=0.3070	C=0.6930
1000Genomes_30x	East Asian	Sub	1170	T=0.2094	C=0.7906
1000Genomes_30x	American	Sub	980	T=0.390	C=0.610
1000Genomes	Global	Study-wide	5008	T=0.2578	C=0.7422
1000Genomes	African	Sub	1322	T=0.1543	C=0.8457
1000Genomes	East Asian	Sub	1008	T=0.1964	C=0.8036
1000Genomes	Europe	Sub	1006	T=0.3260	C=0.6740
1000Genomes	South Asian	Sub	978	T=0.304	C=0.696
1000Genomes	American	Sub	694	T=0.380	C=0.620
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.4498	C=0.5502
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.3972	C=0.6028
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.3962	C=0.6038
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	T=0.2726	C=0.7274
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	T=0.200	C=0.800
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	T=0.312	C=0.688
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	T=0.234	C=0.766
HGDP-CEPH-db Supplement 1	Europe	Sub	320	T=0.356	C=0.644
HGDP-CEPH-db Supplement 1	Africa	Sub	242	T=0.132	C=0.868
HGDP-CEPH-db Supplement 1	America	Sub	216	T=0.481	C=0.519
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	T=0.18	C=0.82
HapMap	Global	Study-wide	1892	T=0.2484	C=0.7516
HapMap	American	Sub	770	T=0.321	C=0.679
HapMap	African	Sub	692	T=0.207	C=0.793
HapMap	Asian	Sub	254	T=0.154	C=0.846
HapMap	Europe	Sub	176	T=0.233	C=0.767
Korean Genome Project	KOREAN	Study-wide	1832	T=0.1943	C=0.8057
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.415	C=0.585
Northern Sweden	ACPOP	Study-wide	600	T=0.300	C=0.700
SGDP_PRJ	Global	Study-wide	512	T=0.211	C=0.789
Qatari	Global	Study-wide	216	T=0.241	C=0.759
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.226	C=0.774
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	62	T=0.26	C=0.74
Siberian	Global	Study-wide	42	T=0.26	C=0.74
The Danish reference pan genome	Danish	Study-wide	40	T=0.35	C=0.65
KOREAN population from KRGDB	KOREAN	Study-wide	8	T=0.0	A=0.0, C=1.0, G=0.0

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.38040294T>A
GRCh38.p14 chr 21	NC_000021.9:g.38040294T>C
GRCh38.p14 chr 21	NC_000021.9:g.38040294T>G
GRCh37.p13 chr 21	NC_000021.8:g.39412596T>A
GRCh37.p13 chr 21	NC_000021.8:g.39412596T>C
GRCh37.p13 chr 21	NC_000021.8:g.39412596T>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	T=	A	C	G
GRCh38.p14 chr 21	NC_000021.9:g.38040294=	NC_000021.9:g.38040294T>A	NC_000021.9:g.38040294T>C	NC_000021.9:g.38040294T>G
GRCh37.p13 chr 21	NC_000021.8:g.39412596=	NC_000021.8:g.39412596T>A	NC_000021.8:g.39412596T>C	NC_000021.8:g.39412596T>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#.

88 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WUGSC_SSAHASNP	ss13826336	Dec 05, 2003 (119)
2	ILLUMINA	ss68073118	Nov 29, 2006 (127)
3	ILLUMINA	ss71637991	May 16, 2007 (127)
4	ILLUMINA	ss75380533	Dec 07, 2007 (129)
5	BCMHGSC_JDW	ss91837804	Mar 24, 2008 (129)
6	BGI	ss106213545	Feb 06, 2009 (130)
7	1000GENOMES	ss112470999	Jan 25, 2009 (130)
8	1000GENOMES	ss113890633	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss117524761	Feb 14, 2009 (130)
10	KRIBB_YJKIM	ss119609351	Dec 01, 2009 (131)
11	ENSEMBL	ss138316548	Dec 01, 2009 (131)
12	GMI	ss156903682	Dec 01, 2009 (131)
13	ENSEMBL	ss161361816	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss168021436	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss169485501	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss172027150	Jul 04, 2010 (132)
17	ILLUMINA	ss174941808	Jul 04, 2010 (132)
18	BUSHMAN	ss204016915	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss208803422	Jul 04, 2010 (132)
20	1000GENOMES	ss228563982	Jul 14, 2010 (132)
21	1000GENOMES	ss237982015	Jul 15, 2010 (132)
22	1000GENOMES	ss244120657	Jul 15, 2010 (132)
23	BL	ss255954378	May 09, 2011 (134)
24	GMI	ss283541649	May 04, 2012 (137)
25	GMI	ss287531029	Apr 25, 2013 (138)
26	PJP	ss292710581	May 09, 2011 (134)
27	ILLUMINA	ss537650913	Sep 08, 2015 (146)
28	TISHKOFF	ss566495717	Apr 25, 2013 (138)
29	SSMP	ss662406196	Apr 25, 2013 (138)
30	EVA-GONL	ss995120049	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1082500358	Aug 21, 2014 (142)
32	1000GENOMES	ss1366297057	Aug 21, 2014 (142)
33	DDI	ss1429184573	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1579663335	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1639565667	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1682559700	Apr 01, 2015 (144)
37	EVA_DECODE	ss1699190445	Apr 01, 2015 (144)
38	EVA_SVP	ss1713723350	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1809687008	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1938670116	Feb 12, 2016 (147)
41	GENOMED	ss1969225382	Jul 19, 2016 (147)
42	JJLAB	ss2030107045	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2158711959	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2245793569	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2629552542	Nov 08, 2017 (151)
46	ILLUMINA	ss2633848738	Nov 08, 2017 (151)
47	ILLUMINA	ss2635109701	Nov 08, 2017 (151)
48	GRF	ss2704442561	Nov 08, 2017 (151)
49	GNOMAD	ss2971825126	Nov 08, 2017 (151)
50	SWEGEN	ss3018895664	Nov 08, 2017 (151)
51	BIOINF_KMB_FNS_UNIBA	ss3028892389	Nov 08, 2017 (151)
52	CSHL	ss3352719369	Nov 08, 2017 (151)
53	ILLUMINA	ss3628480982	Oct 12, 2018 (152)
54	ILLUMINA	ss3638368061	Oct 12, 2018 (152)
55	ILLUMINA	ss3641134231	Oct 12, 2018 (152)
56	ILLUMINA	ss3641430558	Oct 12, 2018 (152)
57	ILLUMINA	ss3643328993	Oct 12, 2018 (152)
58	EGCUT_WGS	ss3685472640	Jul 13, 2019 (153)
59	EVA_DECODE	ss3707735726	Jul 13, 2019 (153)
60	ACPOP	ss3743733802	Jul 13, 2019 (153)
61	EVA	ss3759109867	Jul 13, 2019 (153)
62	PACBIO	ss3788762918	Jul 13, 2019 (153)
63	PACBIO	ss3793636982	Jul 13, 2019 (153)
64	PACBIO	ss3798523229	Jul 13, 2019 (153)
65	KHV_HUMAN_GENOMES	ss3822276151	Jul 13, 2019 (153)
66	EVA	ss3835874930	Apr 27, 2020 (154)
67	EVA	ss3841564636	Apr 27, 2020 (154)
68	EVA	ss3847078089	Apr 27, 2020 (154)
69	HGDP	ss3847680981	Apr 27, 2020 (154)
70	SGDP_PRJ	ss3890006292	Apr 27, 2020 (154)
71	KRGDB	ss3940358777	Apr 27, 2020 (154)
72	KOGIC	ss3983100276	Apr 27, 2020 (154)
73	EVA	ss3985903609	Apr 26, 2021 (155)
74	EVA	ss4017868164	Apr 26, 2021 (155)
75	TOPMED	ss5101713497	Apr 26, 2021 (155)
76	TOMMO_GENOMICS	ss5231543811	Apr 26, 2021 (155)
77	1000G_HIGH_COVERAGE	ss5310226940	Oct 13, 2022 (156)
78	EVA	ss5439904523	Oct 13, 2022 (156)
79	HUGCELL_USP	ss5502273479	Oct 13, 2022 (156)
80	1000G_HIGH_COVERAGE	ss5617373993	Oct 13, 2022 (156)
81	SANFORD_IMAGENETICS	ss5664018835	Oct 13, 2022 (156)
82	TOMMO_GENOMICS	ss5792059982	Oct 13, 2022 (156)
83	YY_MCH	ss5818445882	Oct 13, 2022 (156)
84	EVA	ss5839044087	Oct 13, 2022 (156)
85	EVA	ss5853305847	Oct 13, 2022 (156)
86	EVA	ss5892366242	Oct 13, 2022 (156)
87	EVA	ss5958914558	Oct 13, 2022 (156)
88	EVA	ss5981114699	Oct 13, 2022 (156)
89	1000Genomes	NC_000021.8 - 39412596	Oct 12, 2018 (152)
90	1000Genomes_30x	NC_000021.9 - 38040294	Oct 13, 2022 (156)
91	The Avon Longitudinal Study of Parents and Children	NC_000021.8 - 39412596	Oct 12, 2018 (152)
92	Genetic variation in the Estonian population	NC_000021.8 - 39412596	Oct 12, 2018 (152)
93	The Danish reference pan genome	NC_000021.8 - 39412596	Apr 27, 2020 (154)
94	gnomAD - Genomes	NC_000021.9 - 38040294	Apr 26, 2021 (155)
95	Genome of the Netherlands Release 5	NC_000021.8 - 39412596	Apr 27, 2020 (154)
96	HGDP-CEPH-db Supplement 1	NC_000021.7 - 38334466	Apr 27, 2020 (154)
97	HapMap	NC_000021.9 - 38040294	Apr 27, 2020 (154)
98	KOREAN population from KRGDB	NC_000021.8 - 39412596	Apr 27, 2020 (154)
99	Korean Genome Project	NC_000021.9 - 38040294	Apr 27, 2020 (154)
100	Northern Sweden	NC_000021.8 - 39412596	Jul 13, 2019 (153)
101	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000021.8 - 39412596	Apr 26, 2021 (155)
102	Qatari	NC_000021.8 - 39412596	Apr 27, 2020 (154)
103	SGDP_PRJ	NC_000021.8 - 39412596	Apr 27, 2020 (154)
104	Siberian	NC_000021.8 - 39412596	Apr 27, 2020 (154)
105	8.3KJPN	NC_000021.8 - 39412596	Apr 26, 2021 (155)
106	14KJPN	NC_000021.9 - 38040294	Oct 13, 2022 (156)
107	TopMed	NC_000021.9 - 38040294	Apr 26, 2021 (155)
108	UK 10K study - Twins	NC_000021.8 - 39412596	Oct 12, 2018 (152)
109	A Vietnamese Genetic Variation Database	NC_000021.8 - 39412596	Jul 13, 2019 (153)
110	ALFA	NC_000021.9 - 38040294	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
47536171, ss3940358777	NC_000021.8:39412595:T:A	NC_000021.9:38040293:T:A	(self)
ss2245793569	NC_000021.9:38040293:T:A	NC_000021.9:38040293:T:A	(self)
358873, ss91837804, ss112470999, ss113890633, ss117524761, ss168021436, ss169485501, ss172027150, ss204016915, ss208803422, ss255954378, ss283541649, ss287531029, ss292710581, ss1699190445, ss1713723350, ss2635109701, ss3643328993, ss3847680981	NC_000021.7:38334465:T:C	NC_000021.9:38040293:T:C	(self)
79817301, 44173793, 31210888, 5828274, 19677821, 47536171, 17018667, 1129536, 20712038, 42023272, 11228313, 89513118, 44173793, 9746398, ss228563982, ss237982015, ss244120657, ss537650913, ss566495717, ss662406196, ss995120049, ss1082500358, ss1366297057, ss1429184573, ss1579663335, ss1639565667, ss1682559700, ss1809687008, ss1938670116, ss1969225382, ss2030107045, ss2158711959, ss2629552542, ss2633848738, ss2704442561, ss2971825126, ss3018895664, ss3352719369, ss3628480982, ss3638368061, ss3641134231, ss3641430558, ss3685472640, ss3743733802, ss3759109867, ss3788762918, ss3793636982, ss3798523229, ss3835874930, ss3841564636, ss3890006292, ss3940358777, ss3985903609, ss4017868164, ss5231543811, ss5439904523, ss5664018835, ss5839044087, ss5958914558, ss5981114699	NC_000021.8:39412595:T:C	NC_000021.9:38040293:T:C	(self)
104899928, 563270121, 2209525, 39478277, 125897086, 376822443, 328793768, ss2245793569, ss3028892389, ss3707735726, ss3822276151, ss3847078089, ss3983100276, ss5101713497, ss5310226940, ss5502273479, ss5617373993, ss5792059982, ss5818445882, ss5853305847, ss5892366242	NC_000021.9:38040293:T:C	NC_000021.9:38040293:T:C	(self)
ss13826336	NT_011512.9:25072991:T:C	NC_000021.9:38040293:T:C	(self)
ss68073118, ss71637991, ss75380533, ss106213545, ss119609351, ss138316548, ss156903682, ss161361816, ss174941808	NT_011512.11:25074466:T:C	NC_000021.9:38040293:T:C	(self)
47536171, ss3940358777	NC_000021.8:39412595:T:G	NC_000021.9:38040293:T: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 rs9983399

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs9983399