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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.

rs200338097

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr15:38349573 (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>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.195172 (51660/264690, TOPMED)
T=0.001595 (189/118472, GnomAD_exome)
A=0.24513 (19284/78668, PAGE_STUDY) (+ 8 more)
T=0.00553 (197/35620, ExAC)
A=0.2339 (685/2928, KOREAN)
G=0.0000 (0/1730, ALFA)
T=0.0000 (0/1730, ALFA)
T=0.0020 (2/1010, 1000G)
A=0.165 (83/502, SGDP_PRJ)
T=0.449 (97/216, Qatari)
A=0.0 (0/6, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SPRED1 : Intron Variant
Publications
1 citation
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 15 NC_000015.10:g.38349573A>G
GRCh38.p13 chr 15 NC_000015.10:g.38349573A>T
GRCh37.p13 chr 15 NC_000015.9:g.38641774A>G
GRCh37.p13 chr 15 NC_000015.9:g.38641774A>T
SPRED1 RefSeqGene NG_008980.1:g.101723A>G
SPRED1 RefSeqGene NG_008980.1:g.101723A>T
Gene: SPRED1, sprouty related EVH1 domain containing 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SPRED1 transcript NM_152594.3:c.684+50A>G N/A Intron Variant
SPRED1 transcript variant X1 XM_005254202.3:c.720+50A>G N/A Intron Variant
SPRED1 transcript variant X2 XM_011521289.3:c.621+50A>G 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.

Allele: T (allele ID: 49892 )
ClinVar Accession Disease Names Clinical Significance
RCV000034342.5 not provided Uncertain-Significance

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 1694 A=1.0000 G=0.0000, T=0.0000
European Sub 879 A=1.000 G=0.000, T=0.000
African Sub 441 A=1.000 G=0.000, T=0.000
African Others Sub 19 A=1.00 G=0.00, T=0.00
African American Sub 422 A=1.000 G=0.000, T=0.000
Asian Sub 20 A=1.00 G=0.00, T=0.00
East Asian Sub 11 A=1.00 G=0.00, T=0.00
Other Asian Sub 9 A=1.0 G=0.0, T=0.0
Latin American 1 Sub 4 A=1.0 G=0.0, T=0.0
Latin American 2 Sub 12 A=1.00 G=0.00, T=0.00
South Asian Sub 2 A=1.0 G=0.0, T=0.0
Other Sub 336 A=1.000 G=0.000, T=0.000


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=0.195172 T=0.804828
gnomAD - Exomes Global Study-wide 118472 A=0.998405 T=0.001595
gnomAD - Exomes European Sub 63020 A=0.99857 T=0.00143
gnomAD - Exomes Asian Sub 22640 A=0.99859 T=0.00141
gnomAD - Exomes American Sub 15256 A=0.99777 T=0.00223
gnomAD - Exomes African Sub 7482 A=0.9963 T=0.0037
gnomAD - Exomes Ashkenazi Jewish Sub 6878 A=0.9997 T=0.0003
gnomAD - Exomes Other Sub 3196 A=0.9991 T=0.0009
The PAGE Study Global Study-wide 78668 A=0.24513 T=0.75487
The PAGE Study AfricanAmerican Sub 32504 A=0.33522 T=0.66478
The PAGE Study Mexican Sub 10798 A=0.16272 T=0.83728
The PAGE Study Asian Sub 8316 A=0.2138 T=0.7862
The PAGE Study PuertoRican Sub 7916 A=0.1843 T=0.8157
The PAGE Study NativeHawaiian Sub 4530 A=0.1826 T=0.8174
The PAGE Study Cuban Sub 4230 A=0.1596 T=0.8404
The PAGE Study Dominican Sub 3826 A=0.2279 T=0.7721
The PAGE Study CentralAmerican Sub 2450 A=0.1686 T=0.8314
The PAGE Study SouthAmerican Sub 1982 A=0.1509 T=0.8491
The PAGE Study NativeAmerican Sub 1260 A=0.1460 T=0.8540
The PAGE Study SouthAsian Sub 856 A=0.145 T=0.855
ExAC Global Study-wide 35620 A=0.99447 T=0.00553
ExAC Europe Sub 19674 A=0.99522 T=0.00478
ExAC Asian Sub 9402 A=0.9968 T=0.0032
ExAC African Sub 4232 A=0.9917 T=0.0083
ExAC American Sub 1964 A=0.9827 T=0.0173
ExAC Other Sub 348 A=0.989 T=0.011
KOREAN population from KRGDB KOREAN Study-wide 2928 A=0.2339 T=0.7661
1000Genomes Global Study-wide 1010 A=0.9980 T=0.0020
1000Genomes African Sub 467 A=0.998 T=0.002
1000Genomes East Asian Sub 199 A=0.995 T=0.005
1000Genomes South Asian Sub 131 A=1.000 T=0.000
1000Genomes American Sub 113 A=1.000 T=0.000
1000Genomes Europe Sub 100 A=1.00 T=0.00
SGDP_PRJ Global Study-wide 502 A=0.165 T=0.835
Qatari Global Study-wide 216 A=0.551 T=0.449
Siberian Global Study-wide 6 A=0.0 T=1.0
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= G T
GRCh38.p13 chr 15 NC_000015.10:g.38349573= NC_000015.10:g.38349573A>G NC_000015.10:g.38349573A>T
GRCh37.p13 chr 15 NC_000015.9:g.38641774= NC_000015.9:g.38641774A>G NC_000015.9:g.38641774A>T
SPRED1 RefSeqGene NG_008980.1:g.101723= NG_008980.1:g.101723A>G NG_008980.1:g.101723A>T
SPRED1 transcript NM_152594.2:c.684+50= NM_152594.2:c.684+50A>G NM_152594.2:c.684+50A>T
SPRED1 transcript NM_152594.3:c.684+50= NM_152594.3:c.684+50A>G NM_152594.3:c.684+50A>T
SPRED1 transcript variant X1 XM_005254202.1:c.720+50= XM_005254202.1:c.720+50A>G XM_005254202.1:c.720+50A>T
SPRED1 transcript variant X1 XM_005254202.3:c.720+50= XM_005254202.3:c.720+50A>G XM_005254202.3:c.720+50A>T
SPRED1 transcript variant X2 XM_005254203.1:c.462+50= XM_005254203.1:c.462+50A>G XM_005254203.1:c.462+50A>T
SPRED1 transcript variant X2 XM_011521289.3:c.621+50= XM_011521289.3:c.621+50A>G XM_011521289.3:c.621+50A>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#.

23 SubSNP, 10 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GMI ss282220721 May 04, 2012 (137)
2 BILGI_BIOE ss538655374 Apr 25, 2013 (138)
3 SSMP ss660142871 Apr 25, 2013 (138)
4 EGL ss836188029 Oct 18, 2013 (136)
5 1000GENOMES ss1353088095 Aug 21, 2014 (142)
6 EVA_EXAC ss1691746435 Apr 01, 2015 (144)
7 WEILL_CORNELL_DGM ss1935098008 Feb 12, 2016 (147)
8 ILLUMINA ss1959603236 Feb 12, 2016 (147)
9 USC_VALOUEV ss2156725624 Dec 20, 2016 (150)
10 TOPMED ss2370639165 Dec 20, 2016 (150)
11 GRF ss2701191297 Nov 08, 2017 (151)
12 ILLUMINA ss3021622641 Nov 08, 2017 (151)
13 TOPMED ss3225124800 Nov 08, 2017 (151)
14 TOPMED ss3225124801 Nov 08, 2017 (151)
15 CSHL ss3351076044 Nov 08, 2017 (151)
16 ILLUMINA ss3652022362 Oct 12, 2018 (152)
17 EVA_DECODE ss3697713075 Jul 13, 2019 (153)
18 ILLUMINA ss3725490211 Jul 13, 2019 (153)
19 PAGE_CC ss3771822700 Jul 13, 2019 (153)
20 SGDP_PRJ ss3882722633 Apr 27, 2020 (154)
21 KRGDB ss3931855102 Apr 27, 2020 (154)
22 FSA-LAB ss3984069772 Apr 26, 2021 (155)
23 TOPMED ss4988029254 Apr 26, 2021 (155)
24 1000Genomes NC_000015.9 - 38641774 Oct 12, 2018 (152)
25 ExAC NC_000015.9 - 38641774 Oct 12, 2018 (152)
26 gnomAD - Exomes NC_000015.9 - 38641774 Jul 13, 2019 (153)
27 KOREAN population from KRGDB NC_000015.9 - 38641774 Apr 27, 2020 (154)
28 The PAGE Study NC_000015.10 - 38349573 Jul 13, 2019 (153)
29 Qatari NC_000015.9 - 38641774 Apr 27, 2020 (154)
30 SGDP_PRJ NC_000015.9 - 38641774 Apr 27, 2020 (154)
31 Siberian NC_000015.9 - 38641774 Apr 27, 2020 (154)
32 TopMed NC_000015.10 - 38349573 Apr 26, 2021 (155)
33 ALFA NC_000015.10 - 38349573 Apr 26, 2021 (155)
34 ClinVar RCV000034342.5 Oct 12, 2018 (152)
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
2672898455, ss3225124800 NC_000015.10:38349572:A:G NC_000015.10:38349572:A:G (self)
ss282220721 NC_000015.8:36429065:A:T NC_000015.10:38349572:A:T (self)
66146064, 2113464, 10377818, 39032496, 17139938, 34739613, 9241978, ss538655374, ss660142871, ss1353088095, ss1691746435, ss1935098008, ss1959603236, ss2156725624, ss2370639165, ss2701191297, ss3021622641, ss3351076044, ss3652022362, ss3882722633, ss3931855102, ss3984069772 NC_000015.9:38641773:A:T NC_000015.10:38349572:A:T (self)
RCV000034342.5, 1044169, 203574914, 2672898455, ss836188029, ss3225124801, ss3697713075, ss3725490211, ss3771822700, ss4988029254 NC_000015.10:38349572:A:T NC_000015.10:38349572: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.

1 citation for rs200338097
PMID Title Author Year Journal
23757202 Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Bean LJ et al. 2013 Human mutation
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