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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.

rs9633304

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:183667743 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.088655 (23466/264690, TOPMED)
T=0.084907 (11869/139788, GnomAD)
T=0.06141 (1160/18890, ALFA) (+ 14 more)
T=0.01426 (239/16760, 8.3KJPN)
T=0.1110 (556/5008, 1000G)
T=0.0234 (105/4480, Estonian)
T=0.0278 (107/3854, ALSPAC)
T=0.0264 (98/3708, TWINSUK)
T=0.0266 (78/2930, KOREAN)
T=0.032 (32/998, GoNL)
T=0.032 (19/600, NorthernSweden)
T=0.103 (34/330, HapMap)
T=0.065 (14/216, Qatari)
T=0.140 (30/214, Vietnamese)
A=0.48 (29/60, SGDP_PRJ)
A=0.5 (3/6, Siberian)
T=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RGL1 : Intron Variant
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 1 NC_000001.11:g.183667743A>T
GRCh37.p13 chr 1 NC_000001.10:g.183636878A>T
Gene: RGL1, ral guanine nucleotide dissociation stimulator like 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RGL1 transcript variant 2 NM_001297669.3:c.-142-296…

NM_001297669.3:c.-142-29660A>T

N/A Intron Variant
RGL1 transcript variant 3 NM_001297670.3:c.-33+3124…

NM_001297670.3:c.-33+31242A>T

N/A Intron Variant
RGL1 transcript variant 1 NM_015149.6:c.-33+31242A>T N/A Intron Variant
RGL1 transcript variant 4 NM_001297671.3:c. N/A Genic Upstream Transcript Variant
RGL1 transcript variant 5 NM_001297672.3:c. N/A Genic Upstream Transcript Variant
RGL1 transcript variant X1 XM_011509339.3:c.-142-296…

XM_011509339.3:c.-142-29660A>T

N/A Intron Variant
RGL1 transcript variant X2 XM_011509341.1:c.-33+3124…

XM_011509341.1:c.-33+31242A>T

N/A Intron Variant
RGL1 transcript variant X4 XM_011509342.2:c.-33+3124…

XM_011509342.2:c.-33+31242A>T

N/A Intron Variant
RGL1 transcript variant X3 XM_017000756.2:c. N/A Genic Upstream Transcript Variant
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=0.93859 T=0.06141
European Sub 14286 A=0.97256 T=0.02744
African Sub 2946 A=0.7675 T=0.2325
African Others Sub 114 A=0.728 T=0.272
African American Sub 2832 A=0.7691 T=0.2309
Asian Sub 112 A=0.884 T=0.116
East Asian Sub 86 A=0.88 T=0.12
Other Asian Sub 26 A=0.88 T=0.12
Latin American 1 Sub 146 A=0.973 T=0.027
Latin American 2 Sub 610 A=0.982 T=0.018
South Asian Sub 98 A=0.97 T=0.03
Other Sub 692 A=0.925 T=0.075


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=0.911345 T=0.088655
gnomAD - Genomes Global Study-wide 139788 A=0.915093 T=0.084907
gnomAD - Genomes European Sub 75746 A=0.97155 T=0.02845
gnomAD - Genomes African Sub 41856 A=0.79140 T=0.20860
gnomAD - Genomes American Sub 13602 A=0.96118 T=0.03882
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.9873 T=0.0127
gnomAD - Genomes East Asian Sub 3122 A=0.9148 T=0.0852
gnomAD - Genomes Other Sub 2142 A=0.9314 T=0.0686
8.3KJPN JAPANESE Study-wide 16760 A=0.98574 T=0.01426
1000Genomes Global Study-wide 5008 A=0.8890 T=0.1110
1000Genomes African Sub 1322 A=0.7610 T=0.2390
1000Genomes East Asian Sub 1008 A=0.8909 T=0.1091
1000Genomes Europe Sub 1006 A=0.9682 T=0.0318
1000Genomes South Asian Sub 978 A=0.929 T=0.071
1000Genomes American Sub 694 A=0.958 T=0.042
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9766 T=0.0234
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9722 T=0.0278
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9736 T=0.0264
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.9734 T=0.0266
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.968 T=0.032
Northern Sweden ACPOP Study-wide 600 A=0.968 T=0.032
HapMap Global Study-wide 330 A=0.897 T=0.103
HapMap African Sub 120 A=0.742 T=0.258
HapMap American Sub 120 A=0.975 T=0.025
HapMap Asian Sub 90 A=1.00 T=0.00
Qatari Global Study-wide 216 A=0.935 T=0.065
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.860 T=0.140
SGDP_PRJ Global Study-wide 60 A=0.48 T=0.52
Siberian Global Study-wide 6 A=0.5 T=0.5
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= T
GRCh38.p13 chr 1 NC_000001.11:g.183667743= NC_000001.11:g.183667743A>T
GRCh37.p13 chr 1 NC_000001.10:g.183636878= NC_000001.10:g.183636878A>T
RGL1 transcript variant 2 NM_001297669.3:c.-142-29660= NM_001297669.3:c.-142-29660A>T
RGL1 transcript variant 3 NM_001297670.3:c.-33+31242= NM_001297670.3:c.-33+31242A>T
RGL1 transcript NM_015149.3:c.-33+31242= NM_015149.3:c.-33+31242A>T
RGL1 transcript variant 1 NM_015149.6:c.-33+31242= NM_015149.6:c.-33+31242A>T
RGL1 transcript variant X2 XM_005245011.1:c.-33+31242= XM_005245011.1:c.-33+31242A>T
RGL1 transcript variant X3 XM_005245012.1:c.-142-29660= XM_005245012.1:c.-142-29660A>T
RGL1 transcript variant X1 XM_011509339.3:c.-142-29660= XM_011509339.3:c.-142-29660A>T
RGL1 transcript variant X2 XM_011509341.1:c.-33+31242= XM_011509341.1:c.-33+31242A>T
RGL1 transcript variant X4 XM_011509342.2:c.-33+31242= XM_011509342.2:c.-33+31242A>T
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#.

37 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss13405690 Dec 05, 2003 (119)
2 SC_SNP ss19058876 Feb 28, 2004 (123)
3 1000GENOMES ss210687600 Jul 14, 2010 (132)
4 1000GENOMES ss218759100 Jul 14, 2010 (132)
5 1000GENOMES ss230811566 Jul 14, 2010 (132)
6 GMI ss284187458 Apr 25, 2013 (138)
7 TISHKOFF ss554931881 Apr 25, 2013 (138)
8 SSMP ss648547179 Apr 25, 2013 (138)
9 EVA-GONL ss975893625 Aug 21, 2014 (142)
10 JMKIDD_LAB ss1068423122 Aug 21, 2014 (142)
11 1000GENOMES ss1293729767 Aug 21, 2014 (142)
12 EVA_DECODE ss1585285412 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1601645349 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1644639382 Apr 01, 2015 (144)
15 HAMMER_LAB ss1795385081 Sep 08, 2015 (146)
16 WEILL_CORNELL_DGM ss1919129227 Feb 12, 2016 (147)
17 JJLAB ss2020081350 Sep 14, 2016 (149)
18 USC_VALOUEV ss2148109526 Dec 20, 2016 (150)
19 HUMAN_LONGEVITY ss2168185196 Dec 20, 2016 (150)
20 TOPMED ss2330740857 Dec 20, 2016 (150)
21 GRF ss2698091884 Nov 08, 2017 (151)
22 GNOMAD ss2763592391 Nov 08, 2017 (151)
23 SWEGEN ss2988074688 Nov 08, 2017 (151)
24 TOPMED ss3097358866 Nov 08, 2017 (151)
25 CSHL ss3343804945 Nov 08, 2017 (151)
26 EGCUT_WGS ss3656025008 Jul 12, 2019 (153)
27 EVA_DECODE ss3688174211 Jul 12, 2019 (153)
28 ACPOP ss3727660066 Jul 12, 2019 (153)
29 EVA ss3747053830 Jul 12, 2019 (153)
30 KHV_HUMAN_GENOMES ss3800054568 Jul 12, 2019 (153)
31 EVA ss3826528605 Apr 25, 2020 (154)
32 EVA ss3836660728 Apr 25, 2020 (154)
33 EVA ss3842071110 Apr 25, 2020 (154)
34 SGDP_PRJ ss3850418816 Apr 25, 2020 (154)
35 KRGDB ss3895680877 Apr 25, 2020 (154)
36 TOPMED ss4475389928 Apr 25, 2021 (155)
37 TOMMO_GENOMICS ss5147388338 Apr 25, 2021 (155)
38 1000Genomes NC_000001.10 - 183636878 Oct 11, 2018 (152)
39 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 183636878 Oct 11, 2018 (152)
40 Genetic variation in the Estonian population NC_000001.10 - 183636878 Oct 11, 2018 (152)
41 gnomAD - Genomes NC_000001.11 - 183667743 Apr 25, 2021 (155)
42 Genome of the Netherlands Release 5 NC_000001.10 - 183636878 Apr 25, 2020 (154)
43 HapMap NC_000001.11 - 183667743 Apr 25, 2020 (154)
44 KOREAN population from KRGDB NC_000001.10 - 183636878 Apr 25, 2020 (154)
45 Northern Sweden NC_000001.10 - 183636878 Jul 12, 2019 (153)
46 Qatari NC_000001.10 - 183636878 Apr 25, 2020 (154)
47 SGDP_PRJ NC_000001.10 - 183636878 Apr 25, 2020 (154)
48 Siberian NC_000001.10 - 183636878 Apr 25, 2020 (154)
49 8.3KJPN NC_000001.10 - 183636878 Apr 25, 2021 (155)
50 TopMed NC_000001.11 - 183667743 Apr 25, 2021 (155)
51 UK 10K study - Twins NC_000001.10 - 183636878 Oct 11, 2018 (152)
52 A Vietnamese Genetic Variation Database NC_000001.10 - 183636878 Jul 12, 2019 (153)
53 ALFA NC_000001.11 - 183667743 Apr 25, 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)
rs12380993 Sep 24, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss210687600, ss284187458, ss1585285412 NC_000001.9:181903500:A:T NC_000001.11:183667742:A:T (self)
4550080, 2494698, 1763256, 1083617, 2858271, 944931, 1171157, 2435796, 625880, 5357645, 2494698, 534567, ss218759100, ss230811566, ss554931881, ss648547179, ss975893625, ss1068423122, ss1293729767, ss1601645349, ss1644639382, ss1795385081, ss1919129227, ss2020081350, ss2148109526, ss2330740857, ss2698091884, ss2763592391, ss2988074688, ss3343804945, ss3656025008, ss3727660066, ss3747053830, ss3826528605, ss3836660728, ss3850418816, ss3895680877, ss5147388338 NC_000001.10:183636877:A:T NC_000001.11:183667742:A:T (self)
32843520, 219269, 24481901, 38996263, 11946030879, ss2168185196, ss3097358866, ss3688174211, ss3800054568, ss3842071110, ss4475389928 NC_000001.11:183667742:A:T NC_000001.11:183667742:A:T (self)
ss13405690 NT_004487.15:12429914:A:T NC_000001.11:183667742:A:T (self)
ss19058876 NT_004487.19:35125519:A:T NC_000001.11:183667742:A:T (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 rs9633304

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