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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.

rs17884503

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:152983099 (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=0.001198 (317/264690, TOPMED)
A=0.001034 (145/140238, GnomAD)
A=0.00004 (1/28256, 14KJPN) (+ 11 more)
A=0.00111 (21/18890, ALFA)
A=0.0050 (32/6404, 1000G_30x)
A=0.0052 (26/5008, 1000G)
A=0.0007 (3/4480, Estonian)
A=0.0005 (2/3854, ALSPAC)
A=0.0016 (6/3708, TWINSUK)
A=0.0003 (1/2922, KOREAN)
A=0.002 (2/998, GoNL)
A=0.032 (7/216, Qatari)
G=0.5 (2/4, SGDP_PRJ)
A=0.5 (2/4, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SPRR1A : 2KB Upstream 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 18890 G=0.99889 A=0.00111
European Sub 14286 G=0.99923 A=0.00077
African Sub 2946 G=0.9997 A=0.0003
African Others Sub 114 G=1.000 A=0.000
African American Sub 2832 G=0.9996 A=0.0004
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=0.993 A=0.007
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=0.95 A=0.05
Other Sub 692 G=0.996 A=0.004


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 G=0.998802 A=0.001198
gnomAD - Genomes Global Study-wide 140238 G=0.998966 A=0.001034
gnomAD - Genomes European Sub 75940 G=0.99887 A=0.00113
gnomAD - Genomes African Sub 42044 G=0.99941 A=0.00059
gnomAD - Genomes American Sub 13654 G=0.99780 A=0.00220
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3130 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9981 A=0.0019
14KJPN JAPANESE Study-wide 28256 G=0.99996 A=0.00004
Allele Frequency Aggregator Total Global 18890 G=0.99889 A=0.00111
Allele Frequency Aggregator European Sub 14286 G=0.99923 A=0.00077
Allele Frequency Aggregator African Sub 2946 G=0.9997 A=0.0003
Allele Frequency Aggregator Other Sub 692 G=0.996 A=0.004
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.993 A=0.007
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=0.95 A=0.05
1000Genomes_30x Global Study-wide 6404 G=0.9950 A=0.0050
1000Genomes_30x African Sub 1786 G=0.9989 A=0.0011
1000Genomes_30x Europe Sub 1266 G=0.9992 A=0.0008
1000Genomes_30x South Asian Sub 1202 G=0.9767 A=0.0233
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.999 A=0.001
1000Genomes Global Study-wide 5008 G=0.9948 A=0.0052
1000Genomes African Sub 1322 G=0.9992 A=0.0008
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9990 A=0.0010
1000Genomes South Asian Sub 978 G=0.976 A=0.024
1000Genomes American Sub 694 G=0.999 A=0.001
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9993 A=0.0007
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9995 A=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9984 A=0.0016
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9997 A=0.0003
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.998 A=0.002
Qatari Global Study-wide 216 G=0.968 A=0.032
SGDP_PRJ Global Study-wide 4 G=0.5 A=0.5
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 1 NC_000001.11:g.152983099G>A
GRCh37.p13 chr 1 NC_000001.10:g.152955575G>A
Gene: SPRR1A, small proline rich protein 1A (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SPRR1A transcript variant 1 NM_001199828.2:c. N/A Upstream Transcript Variant
SPRR1A transcript variant 2 NM_005987.4:c. N/A 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
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 G= A
GRCh38.p14 chr 1 NC_000001.11:g.152983099= NC_000001.11:g.152983099G>A
GRCh37.p13 chr 1 NC_000001.10:g.152955575= NC_000001.10:g.152955575G>A
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#.

27 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss28531915 Dec 02, 2004 (124)
2 1000GENOMES ss328943682 May 09, 2011 (134)
3 SSMP ss648406994 Apr 25, 2013 (138)
4 EVA-GONL ss975672196 Aug 21, 2014 (142)
5 1000GENOMES ss1292881474 Aug 21, 2014 (142)
6 EVA_DECODE ss1585053060 Apr 01, 2015 (144)
7 EVA_UK10K_ALSPAC ss1601191101 Apr 01, 2015 (144)
8 EVA_UK10K_TWINSUK ss1644185134 Apr 01, 2015 (144)
9 WEILL_CORNELL_DGM ss1918905242 Feb 12, 2016 (147)
10 HUMAN_LONGEVITY ss2166451775 Dec 20, 2016 (150)
11 GNOMAD ss2761186051 Nov 08, 2017 (151)
12 SWEGEN ss2987734607 Nov 08, 2017 (151)
13 EGCUT_WGS ss3655674751 Jul 12, 2019 (153)
14 EVA_DECODE ss3687760258 Jul 12, 2019 (153)
15 KHV_HUMAN_GENOMES ss3799797229 Jul 12, 2019 (153)
16 SGDP_PRJ ss3849983811 Apr 25, 2020 (154)
17 KRGDB ss3895185083 Apr 25, 2020 (154)
18 TOPMED ss4467907156 Apr 25, 2021 (155)
19 1000G_HIGH_COVERAGE ss5244253890 Oct 12, 2022 (156)
20 EVA ss5321980413 Oct 12, 2022 (156)
21 HUGCELL_USP ss5444851507 Oct 12, 2022 (156)
22 1000G_HIGH_COVERAGE ss5517563442 Oct 12, 2022 (156)
23 SANFORD_IMAGENETICS ss5626569793 Oct 12, 2022 (156)
24 TOMMO_GENOMICS ss5673606362 Oct 12, 2022 (156)
25 EVA ss5832650746 Oct 12, 2022 (156)
26 EVA ss5910202416 Oct 12, 2022 (156)
27 EVA ss5938363289 Oct 12, 2022 (156)
28 1000Genomes NC_000001.10 - 152955575 Oct 11, 2018 (152)
29 1000Genomes_30x NC_000001.11 - 152983099 Oct 12, 2022 (156)
30 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 152955575 Oct 11, 2018 (152)
31 Genetic variation in the Estonian population NC_000001.10 - 152955575 Oct 11, 2018 (152)
32 gnomAD - Genomes NC_000001.11 - 152983099 Apr 25, 2021 (155)
33 Genome of the Netherlands Release 5 NC_000001.10 - 152955575 Apr 25, 2020 (154)
34 KOREAN population from KRGDB NC_000001.10 - 152955575 Apr 25, 2020 (154)
35 Qatari NC_000001.10 - 152955575 Apr 25, 2020 (154)
36 SGDP_PRJ NC_000001.10 - 152955575 Apr 25, 2020 (154)
37 14KJPN NC_000001.11 - 152983099 Oct 12, 2022 (156)
38 TopMed NC_000001.11 - 152983099 Apr 25, 2021 (155)
39 UK 10K study - Twins NC_000001.10 - 152955575 Oct 11, 2018 (152)
40 ALFA NC_000001.11 - 152983099 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1585053060 NC_000001.9:151222198:G:A NC_000001.11:152983098:G:A (self)
3671921, 1995847, 1412999, 868330, 2362477, 947172, 2000791, 1995847, ss328943682, ss648406994, ss975672196, ss1292881474, ss1601191101, ss1644185134, ss1918905242, ss2761186051, ss2987734607, ss3655674751, ss3849983811, ss3895185083, ss5321980413, ss5626569793, ss5832650746, ss5938363289 NC_000001.10:152955574:G:A NC_000001.11:152983098:G:A (self)
5089377, 26718765, 7443466, 31513491, 6688552624, ss2166451775, ss3687760258, ss3799797229, ss4467907156, ss5244253890, ss5444851507, ss5517563442, ss5673606362, ss5910202416 NC_000001.11:152983098:G:A NC_000001.11:152983098:G:A (self)
ss28531915 NT_004487.19:4444216:G:A NC_000001.11:152983098:G:A (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 rs17884503

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