Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs5883264

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:30915363-30915365 (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
delC
Variation Type
Indel Insertion and Deletion
Frequency
delC=0.205727 (54454/264690, TOPMED)
delC=0.204602 (28652/140038, GnomAD)
delC=0.00336 (95/28258, 14KJPN) (+ 12 more)
delC=0.17678 (3274/18520, ALFA)
delC=0.00346 (58/16758, 8.3KJPN)
delC=0.1774 (1136/6404, 1000G_30x)
delC=0.1683 (843/5008, 1000G)
delC=0.1161 (520/4480, Estonian)
delC=0.1666 (642/3854, ALSPAC)
delC=0.1769 (656/3708, TWINSUK)
delC=0.0093 (17/1832, Korea1K)
delC=0.204 (204/998, GoNL)
delC=0.118 (71/600, NorthernSweden)
delC=0.009 (2/214, Vietnamese)
delC=0.12 (5/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AQP1 : Intron Variant
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 18520 CCC=0.82322 CC=0.17678
European Sub 14152 CCC=0.85126 CC=0.14874
African Sub 2898 CCC=0.6798 CC=0.3202
African Others Sub 114 CCC=0.640 CC=0.360
African American Sub 2784 CCC=0.6814 CC=0.3186
Asian Sub 112 CCC=0.964 CC=0.036
East Asian Sub 86 CCC=0.98 CC=0.02
Other Asian Sub 26 CCC=0.92 CC=0.08
Latin American 1 Sub 146 CCC=0.719 CC=0.281
Latin American 2 Sub 610 CCC=0.875 CC=0.125
South Asian Sub 98 CCC=0.84 CC=0.16
Other Sub 504 CCC=0.794 CC=0.206


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 CCC=0.794273 delC=0.205727
gnomAD - Genomes Global Study-wide 140038 CCC=0.795398 delC=0.204602
gnomAD - Genomes European Sub 75896 CCC=0.83878 delC=0.16122
gnomAD - Genomes African Sub 41896 CCC=0.68489 delC=0.31511
gnomAD - Genomes American Sub 13642 CCC=0.82810 delC=0.17190
gnomAD - Genomes Ashkenazi Jewish Sub 3320 CCC=0.8738 delC=0.1262
gnomAD - Genomes East Asian Sub 3130 CCC=0.9911 delC=0.0089
gnomAD - Genomes Other Sub 2154 CCC=0.8041 delC=0.1959
14KJPN JAPANESE Study-wide 28258 CCC=0.99664 delC=0.00336
Allele Frequency Aggregator Total Global 18520 CCC=0.82322 delC=0.17678
Allele Frequency Aggregator European Sub 14152 CCC=0.85126 delC=0.14874
Allele Frequency Aggregator African Sub 2898 CCC=0.6798 delC=0.3202
Allele Frequency Aggregator Latin American 2 Sub 610 CCC=0.875 delC=0.125
Allele Frequency Aggregator Other Sub 504 CCC=0.794 delC=0.206
Allele Frequency Aggregator Latin American 1 Sub 146 CCC=0.719 delC=0.281
Allele Frequency Aggregator Asian Sub 112 CCC=0.964 delC=0.036
Allele Frequency Aggregator South Asian Sub 98 CCC=0.84 delC=0.16
8.3KJPN JAPANESE Study-wide 16758 CCC=0.99654 delC=0.00346
1000Genomes_30x Global Study-wide 6404 CCC=0.8226 delC=0.1774
1000Genomes_30x African Sub 1786 CCC=0.6775 delC=0.3225
1000Genomes_30x Europe Sub 1266 CCC=0.8341 delC=0.1659
1000Genomes_30x South Asian Sub 1202 CCC=0.8661 delC=0.1339
1000Genomes_30x East Asian Sub 1170 CCC=0.9880 delC=0.0120
1000Genomes_30x American Sub 980 CCC=0.821 delC=0.179
1000Genomes Global Study-wide 5008 CCC=0.8317 delC=0.1683
1000Genomes African Sub 1322 CCC=0.6853 delC=0.3147
1000Genomes East Asian Sub 1008 CCC=0.9891 delC=0.0109
1000Genomes Europe Sub 1006 CCC=0.8390 delC=0.1610
1000Genomes South Asian Sub 978 CCC=0.866 delC=0.134
1000Genomes American Sub 694 CCC=0.823 delC=0.177
Genetic variation in the Estonian population Estonian Study-wide 4480 CCC=0.8839 delC=0.1161
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 CCC=0.8334 delC=0.1666
UK 10K study - Twins TWIN COHORT Study-wide 3708 CCC=0.8231 delC=0.1769
Korean Genome Project KOREAN Study-wide 1832 CCC=0.9907 delC=0.0093
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 CCC=0.796 delC=0.204
Northern Sweden ACPOP Study-wide 600 CCC=0.882 delC=0.118
A Vietnamese Genetic Variation Database Global Study-wide 214 CCC=0.991 delC=0.009
The Danish reference pan genome Danish Study-wide 40 CCC=0.88 delC=0.12
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.p14 chr 7 NC_000007.14:g.30915365del
GRCh37.p13 chr 7 NC_000007.13:g.30954980del
Colton blood group RefSeqGene (LRG_808) NG_007475.2:g.66972del
Gene: AQP1, aquaporin 1 (Colton blood group) (plus strand)
Molecule type Change Amino acid[Codon] SO Term
AQP1 transcript variant 5 NM_001329872.2:c.384+3072…

NM_001329872.2:c.384+3072del

N/A Intron Variant
AQP1 transcript variant 1 NM_198098.4:c.384+3072del N/A Intron 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
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 CCC= delC
GRCh38.p14 chr 7 NC_000007.14:g.30915363_30915365= NC_000007.14:g.30915365del
GRCh37.p13 chr 7 NC_000007.13:g.30954978_30954980= NC_000007.13:g.30954980del
Colton blood group RefSeqGene (LRG_808) NG_007475.2:g.66970_66972= NG_007475.2:g.66972del
AQP1 transcript variant 5 NM_001329872.2:c.384+3070= NM_001329872.2:c.384+3072del
AQP1 transcript variant 1 NM_198098.2:c.384+3070= NM_198098.2:c.384+3072del
AQP1 transcript variant 1 NM_198098.4:c.384+3070= NM_198098.4:c.384+3072del
AQP1 transcript variant X1 XM_005249747.1:c.384+3070= XM_005249747.1:c.384+3072del
AQP1 transcript variant X2 XM_005249748.1:c.291+3070= XM_005249748.1:c.291+3072del
AQP1 transcript variant X3 XM_005249749.1:c.198+3070= XM_005249749.1:c.198+3072del
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#.

42 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 PGA-UW-FHCRC ss35077936 May 24, 2005 (125)
2 ABI ss42900005 Mar 13, 2006 (137)
3 BGI ss104775676 Dec 06, 2013 (138)
4 1000GENOMES ss326971485 May 09, 2011 (137)
5 1000GENOMES ss327253058 May 09, 2011 (137)
6 1000GENOMES ss499820044 May 04, 2012 (137)
7 LUNTER ss551718250 Apr 25, 2013 (138)
8 LUNTER ss551922955 Apr 25, 2013 (138)
9 TISHKOFF ss554329568 Apr 25, 2013 (138)
10 SSMP ss663772316 Apr 01, 2015 (144)
11 EVA-GONL ss984110668 Aug 21, 2014 (142)
12 1000GENOMES ss1376919463 Aug 21, 2014 (142)
13 EVA_GENOME_DK ss1576966666 Apr 01, 2015 (144)
14 EVA_DECODE ss1593681662 Apr 01, 2015 (144)
15 EVA_UK10K_ALSPAC ss1705574040 Apr 01, 2015 (144)
16 EVA_UK10K_TWINSUK ss1705574052 Apr 01, 2015 (144)
17 HAMMER_LAB ss1804936481 Sep 08, 2015 (146)
18 GENOMED ss1970661775 Jul 19, 2016 (147)
19 JJLAB ss2030830777 Sep 14, 2016 (149)
20 GNOMAD ss2851407239 Nov 08, 2017 (151)
21 SWEGEN ss3000863684 Nov 08, 2017 (151)
22 BIOINF_KMB_FNS_UNIBA ss3646018969 Oct 12, 2018 (152)
23 EGCUT_WGS ss3668792870 Jul 13, 2019 (153)
24 EVA_DECODE ss3719388856 Jul 13, 2019 (153)
25 ACPOP ss3734489871 Jul 13, 2019 (153)
26 KHV_HUMAN_GENOMES ss3809535239 Jul 13, 2019 (153)
27 EVA ss3830492292 Apr 26, 2020 (154)
28 EVA ss3838733397 Apr 26, 2020 (154)
29 EVA ss3844184863 Apr 26, 2020 (154)
30 KOGIC ss3961162454 Apr 26, 2020 (154)
31 TOPMED ss4740657232 Apr 26, 2021 (155)
32 TOMMO_GENOMICS ss5182459620 Apr 26, 2021 (155)
33 1000G_HIGH_COVERAGE ss5272339862 Oct 14, 2022 (156)
34 HUGCELL_USP ss5469574861 Oct 14, 2022 (156)
35 1000G_HIGH_COVERAGE ss5560237584 Oct 14, 2022 (156)
36 SANFORD_IMAGENETICS ss5642639378 Oct 14, 2022 (156)
37 TOMMO_GENOMICS ss5722096827 Oct 14, 2022 (156)
38 YY_MCH ss5808464126 Oct 14, 2022 (156)
39 EVA ss5822609418 Oct 14, 2022 (156)
40 EVA ss5855827349 Oct 14, 2022 (156)
41 EVA ss5858294711 Oct 14, 2022 (156)
42 EVA ss5971845447 Oct 14, 2022 (156)
43 1000Genomes NC_000007.13 - 30954978 Oct 12, 2018 (152)
44 1000Genomes_30x NC_000007.14 - 30915363 Oct 14, 2022 (156)
45 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 30954978 Oct 12, 2018 (152)
46 Genetic variation in the Estonian population NC_000007.13 - 30954978 Oct 12, 2018 (152)
47 The Danish reference pan genome NC_000007.13 - 30954978 Apr 26, 2020 (154)
48 gnomAD - Genomes NC_000007.14 - 30915363 Apr 26, 2021 (155)
49 Genome of the Netherlands Release 5 NC_000007.13 - 30954978 Apr 26, 2020 (154)
50 Korean Genome Project NC_000007.14 - 30915363 Apr 26, 2020 (154)
51 Northern Sweden NC_000007.13 - 30954978 Jul 13, 2019 (153)
52 8.3KJPN NC_000007.13 - 30954978 Apr 26, 2021 (155)
53 14KJPN NC_000007.14 - 30915363 Oct 14, 2022 (156)
54 TopMed NC_000007.14 - 30915363 Apr 26, 2021 (155)
55 UK 10K study - Twins NC_000007.13 - 30954978 Oct 12, 2018 (152)
56 A Vietnamese Genetic Variation Database NC_000007.13 - 30954978 Jul 13, 2019 (153)
57 ALFA NC_000007.14 - 30915363 Apr 26, 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)
rs34159947 May 11, 2012 (137)
rs78236400 May 11, 2012 (137)
rs150101283 May 04, 2012 (137)
rs370469203 May 13, 2013 (138)
rs371062404 May 15, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss326971485, ss327253058, ss551718250, ss551922955, ss1593681662 NC_000007.12:30921502:C: NC_000007.14:30915362:CCC:CC (self)
36463091, 20331324, 14531118, 1141472, 9065219, 7774736, 40428927, 20331324, 4529620, ss499820044, ss663772316, ss984110668, ss1376919463, ss1576966666, ss1705574040, ss1705574052, ss1804936481, ss1970661775, ss2030830777, ss2851407239, ss3000863684, ss3668792870, ss3734489871, ss3830492292, ss3838733397, ss5182459620, ss5642639378, ss5822609418, ss5971845447 NC_000007.13:30954977:C: NC_000007.14:30915362:CCC:CC (self)
ss554329568 NC_000007.13:30954979:C: NC_000007.14:30915362:CCC:CC (self)
47763519, 257094200, 17540455, 55933931, 578034791, ss3646018969, ss3719388856, ss3809535239, ss3844184863, ss3961162454, ss4740657232, ss5272339862, ss5469574861, ss5560237584, ss5722096827, ss5808464126, ss5855827349, ss5858294711 NC_000007.14:30915362:C: NC_000007.14:30915362:CCC:CC (self)
12590480972 NC_000007.14:30915362:CCC:CC NC_000007.14:30915362:CCC:CC (self)
ss42900005 NT_007819.17:30944977:C: NC_000007.14:30915362:CCC:CC (self)
ss104775676 NT_007819.17:30944978:C: NC_000007.14:30915362:CCC:CC (self)
ss35077936 NT_007819.17:30944979:C: NC_000007.14:30915362:CCC:CC (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 rs5883264

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.post761+d5e8e07