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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.

rs45552240

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr5:33944624 (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
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.001137 (301/264690, TOPMED)
G=0.005713 (1417/248050, GnomAD_exome)
G=0.000899 (126/140222, GnomAD) (+ 12 more)
G=0.007027 (737/104880, ExAC)
G=0.00184 (88/47708, ALFA)
G=0.00085 (11/13006, GO-ESP)
G=0.0090 (45/5008, 1000G)
G=0.0016 (7/4480, Estonian)
G=0.0013 (5/3854, ALSPAC)
G=0.0005 (2/3708, TWINSUK)
G=0.001 (1/998, GoNL)
G=0.006 (3/534, MGP)
G=0.014 (3/216, Qatari)
T=0.5 (2/4, SGDP_PRJ)
G=0.5 (2/4, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SLC45A2 : 3 Prime UTR Variant
Publications
2 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 5 NC_000005.10:g.33944624T>G
GRCh37.p13 chr 5 NC_000005.9:g.33944729T>G
SLC45A2 RefSeqGene NG_011691.2:g.45052A>C
GRCh38.p13 chr 5 alt locus HSCHR5_6_CTG1 NT_187551.1:g.145946T>G
Gene: SLC45A2, solute carrier family 45 member 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC45A2 transcript variant 1 NM_016180.5:c.*24= N/A 3 Prime UTR Variant
SLC45A2 transcript variant 2 NM_001012509.4:c. N/A Genic Downstream Transcript Variant
SLC45A2 transcript variant 3 NM_001297417.4:c. N/A Genic Downstream 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.

Allele: G (allele ID: 894090 )
ClinVar Accession Disease Names Clinical Significance
RCV001156455.1 Oculocutaneous albinism type 4 Likely-Benign

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 47708 T=0.99816 G=0.00184
European Sub 34676 T=0.99830 G=0.00170
African Sub 5532 T=0.9996 G=0.0004
African Others Sub 188 T=1.000 G=0.000
African American Sub 5344 T=0.9996 G=0.0004
Asian Sub 494 T=1.000 G=0.000
East Asian Sub 398 T=1.000 G=0.000
Other Asian Sub 96 T=1.00 G=0.00
Latin American 1 Sub 514 T=1.000 G=0.000
Latin American 2 Sub 836 T=0.999 G=0.001
South Asian Sub 162 T=0.963 G=0.037
Other Sub 5494 T=0.9964 G=0.0036


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 T=0.998863 G=0.001137
gnomAD - Exomes Global Study-wide 248050 T=0.994287 G=0.005713
gnomAD - Exomes European Sub 133084 T=0.998512 G=0.001488
gnomAD - Exomes Asian Sub 48556 T=0.97658 G=0.02342
gnomAD - Exomes American Sub 34406 T=0.99898 G=0.00102
gnomAD - Exomes African Sub 15942 T=0.99975 G=0.00025
gnomAD - Exomes Ashkenazi Jewish Sub 9998 T=0.9994 G=0.0006
gnomAD - Exomes Other Sub 6064 T=0.9939 G=0.0061
gnomAD - Genomes Global Study-wide 140222 T=0.999101 G=0.000899
gnomAD - Genomes European Sub 75938 T=0.99884 G=0.00116
gnomAD - Genomes African Sub 42028 T=0.99964 G=0.00036
gnomAD - Genomes American Sub 13652 T=0.99868 G=0.00132
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.9997 G=0.0003
gnomAD - Genomes East Asian Sub 3132 T=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2150 T=0.9981 G=0.0019
ExAC Global Study-wide 104880 T=0.992973 G=0.007027
ExAC Europe Sub 63770 T=0.99818 G=0.00182
ExAC Asian Sub 21844 T=0.97276 G=0.02724
ExAC American Sub 9866 T=0.9986 G=0.0014
ExAC African Sub 8622 T=0.9997 G=0.0003
ExAC Other Sub 778 T=0.988 G=0.012
Allele Frequency Aggregator Total Global 47708 T=0.99816 G=0.00184
Allele Frequency Aggregator European Sub 34676 T=0.99830 G=0.00170
Allele Frequency Aggregator African Sub 5532 T=0.9996 G=0.0004
Allele Frequency Aggregator Other Sub 5494 T=0.9964 G=0.0036
Allele Frequency Aggregator Latin American 2 Sub 836 T=0.999 G=0.001
Allele Frequency Aggregator Latin American 1 Sub 514 T=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 494 T=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 162 T=0.963 G=0.037
GO Exome Sequencing Project Global Study-wide 13006 T=0.99915 G=0.00085
GO Exome Sequencing Project European American Sub 8600 T=0.9988 G=0.0012
GO Exome Sequencing Project African American Sub 4406 T=0.9998 G=0.0002
1000Genomes Global Study-wide 5008 T=0.9910 G=0.0090
1000Genomes African Sub 1322 T=0.9992 G=0.0008
1000Genomes East Asian Sub 1008 T=1.0000 G=0.0000
1000Genomes Europe Sub 1006 T=0.9990 G=0.0010
1000Genomes South Asian Sub 978 T=0.957 G=0.043
1000Genomes American Sub 694 T=0.999 G=0.001
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9984 G=0.0016
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9987 G=0.0013
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9995 G=0.0005
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.999 G=0.001
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.994 G=0.006
Qatari Global Study-wide 216 T=0.986 G=0.014
SGDP_PRJ Global Study-wide 4 T=0.5 G=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 T= G
GRCh38.p13 chr 5 NC_000005.10:g.33944624= NC_000005.10:g.33944624T>G
GRCh37.p13 chr 5 NC_000005.9:g.33944729= NC_000005.9:g.33944729T>G
SLC45A2 RefSeqGene NG_011691.2:g.45052= NG_011691.2:g.45052A>C
SLC45A2 transcript variant 1 NM_016180.5:c.*24= NM_016180.5:c.*24A>C
SLC45A2 transcript variant 1 NM_016180.4:c.*24= NM_016180.4:c.*24A>C
SLC45A2 transcript variant 1 NM_016180.3:c.*24= NM_016180.3:c.*24A>C
GRCh38.p13 chr 5 alt locus HSCHR5_6_CTG1 NT_187551.1:g.145946= NT_187551.1:g.145946T>G
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, 14 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss69374774 May 17, 2007 (127)
2 ILLUMINA ss160687280 Dec 01, 2009 (131)
3 ILLUMINA ss481963207 Sep 08, 2015 (146)
4 SSMP ss652168420 Apr 25, 2013 (138)
5 NHLBI-ESP ss712635556 Apr 25, 2013 (138)
6 EVA-GONL ss981430533 Aug 21, 2014 (142)
7 1000GENOMES ss1314582846 Aug 21, 2014 (142)
8 EVA_UK10K_ALSPAC ss1612626942 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1655620975 Apr 01, 2015 (144)
10 EVA_EXAC ss1687774458 Apr 01, 2015 (144)
11 EVA_MGP ss1711083755 Apr 01, 2015 (144)
12 WEILL_CORNELL_DGM ss1924692283 Feb 12, 2016 (147)
13 HUMAN_LONGEVITY ss2272760316 Dec 20, 2016 (150)
14 TOPMED ss2440792152 Dec 20, 2016 (150)
15 GNOMAD ss2734944538 Nov 08, 2017 (151)
16 GNOMAD ss2747368492 Nov 08, 2017 (151)
17 GNOMAD ss2823086392 Nov 08, 2017 (151)
18 TOPMED ss3460629126 Nov 08, 2017 (151)
19 ILLUMINA ss3636707662 Oct 12, 2018 (152)
20 OMUKHERJEE_ADBS ss3646317962 Oct 12, 2018 (152)
21 EGCUT_WGS ss3664610827 Jul 13, 2019 (153)
22 KHV_HUMAN_GENOMES ss3806451615 Jul 13, 2019 (153)
23 EVA ss3824075375 Apr 26, 2020 (154)
24 SGDP_PRJ ss3861582956 Apr 26, 2020 (154)
25 FSA-LAB ss3984303649 Apr 26, 2021 (155)
26 EVA ss3986304056 Apr 26, 2021 (155)
27 TOPMED ss4655428973 Apr 26, 2021 (155)
28 1000Genomes NC_000005.9 - 33944729 Oct 12, 2018 (152)
29 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 33944729 Oct 12, 2018 (152)
30 Genetic variation in the Estonian population NC_000005.9 - 33944729 Oct 12, 2018 (152)
31 ExAC NC_000005.9 - 33944729 Oct 12, 2018 (152)
32 gnomAD - Genomes NC_000005.10 - 33944624 Apr 26, 2021 (155)
33 gnomAD - Exomes NC_000005.9 - 33944729 Jul 13, 2019 (153)
34 GO Exome Sequencing Project NC_000005.9 - 33944729 Oct 12, 2018 (152)
35 Genome of the Netherlands Release 5 NC_000005.9 - 33944729 Apr 26, 2020 (154)
36 Medical Genome Project healthy controls from Spanish population NC_000005.9 - 33944729 Apr 26, 2020 (154)
37 Qatari NC_000005.9 - 33944729 Apr 26, 2020 (154)
38 SGDP_PRJ NC_000005.9 - 33944729 Apr 26, 2020 (154)
39 TopMed NC_000005.10 - 33944624 Apr 26, 2021 (155)
40 UK 10K study - Twins NC_000005.9 - 33944729 Oct 12, 2018 (152)
41 ALFA NC_000005.10 - 33944624 Apr 26, 2021 (155)
42 ClinVar RCV001156455.1 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss160687280 NC_000005.8:33980485:T:G NC_000005.10:33944623:T:G (self)
26165006, 14554377, 10349075, 7762193, 4060971, 533528, 6466889, 199515, 6734213, 13599936, 14554377, ss481963207, ss652168420, ss712635556, ss981430533, ss1314582846, ss1612626942, ss1655620975, ss1687774458, ss1711083755, ss1924692283, ss2440792152, ss2734944538, ss2747368492, ss2823086392, ss3636707662, ss3646317962, ss3664610827, ss3824075375, ss3861582956, ss3984303649, ss3986304056 NC_000005.9:33944728:T:G NC_000005.10:33944623:T:G (self)
RCV001156455.1, 184855132, 308119567, 492806530, 1342088726, ss2272760316, ss3460629126, ss3806451615, ss4655428973 NC_000005.10:33944623:T:G NC_000005.10:33944623:T:G (self)
ss69374774 NT_006576.16:33934728:T:G NC_000005.10:33944623:T:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs45552240
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
20806075 Spectrum of candidate gene mutations associated with Indian familial oculocutaneous and ocular albinism. Renugadevi K et al. 2010 Molecular vision
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