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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.

rs188270533

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:24986947 (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
T>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.002992 (792/264690, TOPMED)
A=0.002580 (598/231822, GnomAD_exome)
A=0.003223 (452/140242, GnomAD) (+ 12 more)
A=0.002990 (337/112722, ExAC)
A=0.00380 (106/27878, ALFA)
A=0.0006 (4/6404, 1000G_30x)
A=0.0016 (9/5734, GO-ESP)
A=0.0006 (3/5008, 1000G)
A=0.0123 (55/4480, Estonian)
A=0.0034 (13/3854, ALSPAC)
A=0.0051 (19/3708, TWINSUK)
A=0.005 (5/998, GoNL)
A=0.005 (3/600, NorthernSweden)
T=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PWAR5 : Non Coding Transcript Variant
SNORD108 : Non Coding Transcript Variant
SNHG14 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 27878 T=0.99620 A=0.00380 0.992467 7.2e-05 0.007461 2
European Sub 20348 T=0.99523 A=0.00477 0.990564 0.000098 0.009338 2
African Sub 3540 T=0.9994 A=0.0006 0.99887 0.0 0.00113 0
African Others Sub 122 T=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 3418 T=0.9994 A=0.0006 0.99883 0.0 0.00117 0
Asian Sub 168 T=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 112 T=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 56 T=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 T=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 T=0.997 A=0.003 0.993443 0.0 0.006557 0
South Asian Sub 98 T=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 2968 T=0.9983 A=0.0017 0.996631 0.0 0.003369 0


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=0.997008 A=0.002992
gnomAD - Exomes Global Study-wide 231822 T=0.997420 A=0.002580
gnomAD - Exomes European Sub 119922 T=0.995697 A=0.004303
gnomAD - Exomes Asian Sub 47904 T=0.99971 A=0.00029
gnomAD - Exomes American Sub 34310 T=0.99863 A=0.00137
gnomAD - Exomes African Sub 13956 T=0.99950 A=0.00050
gnomAD - Exomes Ashkenazi Jewish Sub 9854 T=1.0000 A=0.0000
gnomAD - Exomes Other Sub 5876 T=0.9976 A=0.0024
gnomAD - Genomes Global Study-wide 140242 T=0.996777 A=0.003223
gnomAD - Genomes European Sub 75948 T=0.99459 A=0.00541
gnomAD - Genomes African Sub 42032 T=0.99948 A=0.00052
gnomAD - Genomes American Sub 13656 T=0.99912 A=0.00088
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3130 T=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 T=0.9967 A=0.0033
ExAC Global Study-wide 112722 T=0.997010 A=0.002990
ExAC Europe Sub 67976 T=0.99553 A=0.00447
ExAC Asian Sub 24416 T=0.99959 A=0.00041
ExAC American Sub 11342 T=0.99868 A=0.00132
ExAC African Sub 8146 T=0.9993 A=0.0007
ExAC Other Sub 842 T=0.998 A=0.002
Allele Frequency Aggregator Total Global 27878 T=0.99620 A=0.00380
Allele Frequency Aggregator European Sub 20348 T=0.99523 A=0.00477
Allele Frequency Aggregator African Sub 3540 T=0.9994 A=0.0006
Allele Frequency Aggregator Other Sub 2968 T=0.9983 A=0.0017
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.997 A=0.003
Allele Frequency Aggregator Asian Sub 168 T=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 T=1.00 A=0.00
1000Genomes_30x Global Study-wide 6404 T=0.9994 A=0.0006
1000Genomes_30x African Sub 1786 T=0.9989 A=0.0011
1000Genomes_30x Europe Sub 1266 T=0.9992 A=0.0008
1000Genomes_30x South Asian Sub 1202 T=0.9992 A=0.0008
1000Genomes_30x East Asian Sub 1170 T=1.0000 A=0.0000
1000Genomes_30x American Sub 980 T=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 5734 T=0.9984 A=0.0016
GO Exome Sequencing Project European American Sub 3982 T=0.9980 A=0.0020
GO Exome Sequencing Project African American Sub 1752 T=0.9994 A=0.0006
1000Genomes Global Study-wide 5008 T=0.9994 A=0.0006
1000Genomes African Sub 1322 T=0.9992 A=0.0008
1000Genomes East Asian Sub 1008 T=1.0000 A=0.0000
1000Genomes Europe Sub 1006 T=0.9990 A=0.0010
1000Genomes South Asian Sub 978 T=0.999 A=0.001
1000Genomes American Sub 694 T=1.000 A=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9877 A=0.0123
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9966 A=0.0034
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9949 A=0.0051
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.995 A=0.005
Northern Sweden ACPOP Study-wide 600 T=0.995 A=0.005
SGDP_PRJ Global Study-wide 2 T=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.24986947T>A
GRCh37.p13 chr 15 NC_000015.9:g.25232094T>A
PWSAS genomic region NG_002690.1:g.206038T>A
Gene: PWAR5, Prader Willi/Angelman region RNA 5 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PWAR5 transcript NR_022008.1:n.2088T>A N/A Non Coding Transcript Variant
Gene: SNORD108, small nucleolar RNA, C/D box 108 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SNORD108 transcript NR_001292.2:n.23T>A N/A Non Coding Transcript Variant
Gene: SNHG14, small nucleolar RNA host gene 14 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SNHG14 transcript NR_146177.1: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 T= A
GRCh38.p14 chr 15 NC_000015.10:g.24986947= NC_000015.10:g.24986947T>A
GRCh37.p13 chr 15 NC_000015.9:g.25232094= NC_000015.9:g.25232094T>A
PWSAS genomic region NG_002690.1:g.206038= NG_002690.1:g.206038T>A
SNORD108 transcript NR_001292.2:n.23= NR_001292.2:n.23T>A
PWAR5 transcript NR_022008.1:n.2088= NR_022008.1:n.2088T>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, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss464059116 Sep 17, 2011 (135)
2 CLINSEQ_SNP ss491696147 May 04, 2012 (137)
3 NHLBI-ESP ss713212888 Apr 25, 2013 (138)
4 EVA-GONL ss991599458 Aug 21, 2014 (142)
5 1000GENOMES ss1352726085 Aug 21, 2014 (142)
6 EVA_UK10K_ALSPAC ss1632621350 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1675615383 Apr 01, 2015 (144)
8 EVA_EXAC ss1691710041 Apr 01, 2015 (144)
9 EVA_DECODE ss1695609385 Apr 01, 2015 (144)
10 HUMAN_LONGEVITY ss2205335104 Dec 20, 2016 (150)
11 GNOMAD ss2741055554 Nov 08, 2017 (151)
12 GNOMAD ss2749246245 Nov 08, 2017 (151)
13 GNOMAD ss2932731016 Nov 08, 2017 (151)
14 SWEGEN ss3012969673 Nov 08, 2017 (151)
15 EGCUT_WGS ss3680137745 Jul 13, 2019 (153)
16 EVA_DECODE ss3697538104 Jul 13, 2019 (153)
17 ACPOP ss3740766076 Jul 13, 2019 (153)
18 EVA ss3824895532 Apr 27, 2020 (154)
19 EVA ss3825854473 Apr 27, 2020 (154)
20 SGDP_PRJ ss3882501850 Apr 27, 2020 (154)
21 TOPMED ss4984928346 Apr 27, 2021 (155)
22 1000G_HIGH_COVERAGE ss5297777625 Oct 16, 2022 (156)
23 EVA ss5418042048 Oct 16, 2022 (156)
24 HUGCELL_USP ss5491599342 Oct 16, 2022 (156)
25 1000G_HIGH_COVERAGE ss5598846771 Oct 16, 2022 (156)
26 SANFORD_IMAGENETICS ss5657126088 Oct 16, 2022 (156)
27 EVA ss5827950865 Oct 16, 2022 (156)
28 EVA ss5848396022 Oct 16, 2022 (156)
29 EVA ss5875153189 Oct 16, 2022 (156)
30 EVA ss5948535774 Oct 16, 2022 (156)
31 1000Genomes NC_000015.9 - 25232094 Oct 12, 2018 (152)
32 1000Genomes_30x NC_000015.10 - 24986947 Oct 16, 2022 (156)
33 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 25232094 Oct 12, 2018 (152)
34 Genetic variation in the Estonian population NC_000015.9 - 25232094 Oct 12, 2018 (152)
35 ExAC NC_000015.9 - 25232094 Oct 12, 2018 (152)
36 gnomAD - Genomes NC_000015.10 - 24986947 Apr 27, 2021 (155)
37 gnomAD - Exomes NC_000015.9 - 25232094 Jul 13, 2019 (153)
38 GO Exome Sequencing Project NC_000015.9 - 25232094 Oct 12, 2018 (152)
39 Genome of the Netherlands Release 5 NC_000015.9 - 25232094 Apr 27, 2020 (154)
40 Northern Sweden NC_000015.9 - 25232094 Jul 13, 2019 (153)
41 SGDP_PRJ NC_000015.9 - 25232094 Apr 27, 2020 (154)
42 TopMed NC_000015.10 - 24986947 Apr 27, 2021 (155)
43 UK 10K study - Twins NC_000015.9 - 25232094 Oct 12, 2018 (152)
44 ALFA NC_000015.10 - 24986947 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
ss491696147, ss1695609385 NC_000015.8:22783186:T:A NC_000015.10:24986946:T:A (self)
65769608, 36520318, 25875993, 2074349, 10318220, 1352829, 16313850, 14050941, 34518830, 36520318, ss464059116, ss713212888, ss991599458, ss1352726085, ss1632621350, ss1675615383, ss1691710041, ss2741055554, ss2749246245, ss2932731016, ss3012969673, ss3680137745, ss3740766076, ss3824895532, ss3825854473, ss3882501850, ss5418042048, ss5657126088, ss5827950865, ss5848396022, ss5948535774 NC_000015.9:25232093:T:A NC_000015.10:24986946:T:A (self)
86372706, 463621863, 200474006, 13153081320, ss2205335104, ss3697538104, ss4984928346, ss5297777625, ss5491599342, ss5598846771, ss5875153189 NC_000015.10:24986946:T:A NC_000015.10:24986946:T: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 rs188270533

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.post820+afb47a3d