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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs45552332

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:47918523 (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=0.017114 (4530/264690, TOPMED)
A=0.008406 (1178/140142, GnomAD)
A=0.00770 (111/14420, ALFA) (+ 10 more)
A=0.0289 (185/6404, 1000G_30x)
A=0.0274 (137/5008, 1000G)
A=0.0008 (3/3854, ALSPAC)
A=0.0000 (0/3708, TWINSUK)
A=0.0007 (2/2870, KOREAN)
A=0.005 (1/216, Qatari)
A=0.005 (1/214, Vietnamese)
G=0.42 (16/38, SGDP_PRJ)
G=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC124900354 : Intron Variant
Publications
1 citation
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 14420 G=0.99230 A=0.00770
European Sub 9824 G=0.9993 A=0.0007
African Sub 2946 G=0.9963 A=0.0037
African Others Sub 114 G=1.000 A=0.000
African American Sub 2832 G=0.9961 A=0.0039
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=0.966 A=0.034
Latin American 2 Sub 610 G=0.884 A=0.116
South Asian Sub 98 G=0.96 A=0.04
Other Sub 684 G=0.981 A=0.019


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=0.982886 A=0.017114
gnomAD - Genomes Global Study-wide 140142 G=0.991594 A=0.008406
gnomAD - Genomes European Sub 75916 G=0.99970 A=0.00030
gnomAD - Genomes African Sub 42032 G=0.99695 A=0.00305
gnomAD - Genomes American Sub 13640 G=0.92859 A=0.07141
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3086 G=0.9955 A=0.0045
gnomAD - Genomes Other Sub 2148 G=0.9818 A=0.0182
Allele Frequency Aggregator Total Global 14420 G=0.99230 A=0.00770
Allele Frequency Aggregator European Sub 9824 G=0.9993 A=0.0007
Allele Frequency Aggregator African Sub 2946 G=0.9963 A=0.0037
Allele Frequency Aggregator Other Sub 684 G=0.981 A=0.019
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.884 A=0.116
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.966 A=0.034
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=0.96 A=0.04
1000Genomes_30x Global Study-wide 6404 G=0.9711 A=0.0289
1000Genomes_30x African Sub 1786 G=0.9972 A=0.0028
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=0.9251 A=0.0749
1000Genomes_30x East Asian Sub 1170 G=0.9940 A=0.0060
1000Genomes_30x American Sub 980 G=0.915 A=0.085
1000Genomes Global Study-wide 5008 G=0.9726 A=0.0274
1000Genomes African Sub 1322 G=0.9970 A=0.0030
1000Genomes East Asian Sub 1008 G=0.9940 A=0.0060
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=0.926 A=0.074
1000Genomes American Sub 694 G=0.921 A=0.079
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9992 A=0.0008
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=1.0000 A=0.0000
KOREAN population from KRGDB KOREAN Study-wide 2870 G=0.9993 A=0.0007
Qatari Global Study-wide 216 G=0.995 A=0.005
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.995 A=0.005
SGDP_PRJ Global Study-wide 38 G=0.42 A=0.58
Siberian 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 15 NC_000015.10:g.47918523G>A
GRCh37.p13 chr 15 NC_000015.9:g.48210720G>A
Gene: LOC124900354, uncharacterized LOC124900354 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124900354 transcript variant X1 XR_001751516.3:n. N/A Intron Variant
LOC124900354 transcript variant X2 XR_001751517.2:n. N/A Intron Variant
LOC124900354 transcript variant X3 XR_001751518.3:n. N/A Intron Variant
LOC124900354 transcript variant X4 XR_007064618.1:n. 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 G= A
GRCh38.p14 chr 15 NC_000015.10:g.47918523= NC_000015.10:g.47918523G>A
GRCh37.p13 chr 15 NC_000015.9:g.48210720= NC_000015.9:g.48210720G>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#.

30 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss69356376 May 17, 2007 (127)
2 1000GENOMES ss338760637 May 09, 2011 (134)
3 SSMP ss660184600 Apr 25, 2013 (138)
4 JMKIDD_LAB ss1080103006 Aug 21, 2014 (142)
5 1000GENOMES ss1353352948 Aug 21, 2014 (142)
6 EVA_UK10K_ALSPAC ss1632937583 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1675931616 Apr 01, 2015 (144)
8 EVA_DECODE ss1695774119 Apr 01, 2015 (144)
9 WEILL_CORNELL_DGM ss1935162210 Feb 12, 2016 (147)
10 GENOMED ss1968099507 Jul 19, 2016 (147)
11 JJLAB ss2028360259 Sep 14, 2016 (149)
12 USC_VALOUEV ss2156761365 Dec 20, 2016 (150)
13 HUMAN_LONGEVITY ss2206543964 Dec 20, 2016 (150)
14 GNOMAD ss2934585373 Nov 08, 2017 (151)
15 EVA_DECODE ss3697838676 Jul 13, 2019 (153)
16 EVA ss3753050068 Jul 13, 2019 (153)
17 KHV_HUMAN_GENOMES ss3818368815 Jul 13, 2019 (153)
18 SGDP_PRJ ss3882859702 Apr 27, 2020 (154)
19 KRGDB ss3932017664 Apr 27, 2020 (154)
20 TOPMED ss4990391576 Apr 27, 2021 (155)
21 1000G_HIGH_COVERAGE ss5298345987 Oct 16, 2022 (156)
22 EVA ss5419060320 Oct 16, 2022 (156)
23 HUGCELL_USP ss5492084793 Oct 16, 2022 (156)
24 1000G_HIGH_COVERAGE ss5599700919 Oct 16, 2022 (156)
25 SANFORD_IMAGENETICS ss5657455640 Oct 16, 2022 (156)
26 YY_MCH ss5815308988 Oct 16, 2022 (156)
27 EVA ss5828165411 Oct 16, 2022 (156)
28 EVA ss5851281327 Oct 16, 2022 (156)
29 EVA ss5875764492 Oct 16, 2022 (156)
30 EVA ss5948853820 Oct 16, 2022 (156)
31 1000Genomes NC_000015.9 - 48210720 Oct 12, 2018 (152)
32 1000Genomes_30x NC_000015.10 - 47918523 Oct 16, 2022 (156)
33 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 48210720 Oct 12, 2018 (152)
34 gnomAD - Genomes NC_000015.10 - 47918523 Apr 27, 2021 (155)
35 KOREAN population from KRGDB NC_000015.9 - 48210720 Apr 27, 2020 (154)
36 Qatari NC_000015.9 - 48210720 Apr 27, 2020 (154)
37 SGDP_PRJ NC_000015.9 - 48210720 Apr 27, 2020 (154)
38 Siberian NC_000015.9 - 48210720 Apr 27, 2020 (154)
39 TopMed NC_000015.10 - 47918523 Apr 27, 2021 (155)
40 UK 10K study - Twins NC_000015.9 - 48210720 Oct 12, 2018 (152)
41 A Vietnamese Genetic Variation Database NC_000015.9 - 48210720 Jul 13, 2019 (153)
42 ALFA NC_000015.10 - 47918523 Apr 27, 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
ss1695774119 NC_000015.8:45998011:G:A NC_000015.10:47918522:G:A (self)
66420829, 36870200, 39195058, 17204140, 34876682, 9277719, 36870200, 8202016, ss338760637, ss660184600, ss1080103006, ss1353352948, ss1632937583, ss1675931616, ss1935162210, ss1968099507, ss2028360259, ss2156761365, ss2934585373, ss3753050068, ss3882859702, ss3932017664, ss5419060320, ss5657455640, ss5828165411, ss5948853820 NC_000015.9:48210719:G:A NC_000015.10:47918522:G:A (self)
87226854, 468250505, 205937236, 6738835107, ss2206543964, ss3697838676, ss3818368815, ss4990391576, ss5298345987, ss5492084793, ss5599700919, ss5815308988, ss5851281327, ss5875764492 NC_000015.10:47918522:G:A NC_000015.10:47918522:G:A (self)
ss69356376 NT_010194.17:19001276:G:A NC_000015.10:47918522: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.

1 citation for rs45552332
PMID Title Author Year Journal
17999355 A genomewide association study of skin pigmentation in a South Asian population. Stokowski RP et al. 2007 American journal of human genetics
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