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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.

rs114192897

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3635219 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000019 (5/264690, TOPMED)
C=0.000088 (22/251318, GnomAD_exome)
C=0.000116 (14/121122, ExAC) (+ 5 more)
C=0.000019 (2/102978, ALFA)
C=0.00060 (10/16760, 8.3KJPN)
C=0.0004 (2/5008, 1000G)
C=0.0024 (7/2922, KOREAN)
C=0.0022 (4/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
WRAP73 : Missense Variant
Publications
0 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 1 NC_000001.11:g.3635219T>C
GRCh37.p13 chr 1 NC_000001.10:g.3551783T>C
WRAP73 RefSeqGene NG_033937.1:g.19889A>G
Gene: WRAP73, WD repeat containing, antisense to TP73 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WRAP73 transcript NM_017818.4:c.679A>G K [AAG] > E [GAG] Coding Sequence Variant
WD repeat-containing protein WRAP73 NP_060288.3:p.Lys227Glu K (Lys) > E (Glu) Missense Variant
WRAP73 transcript variant X2 XM_005244754.2:c.604-145A…

XM_005244754.2:c.604-145A>G

N/A Intron Variant
WRAP73 transcript variant X1 XM_017001387.2:c.679A>G K [AAG] > E [GAG] Coding Sequence Variant
WD repeat-containing protein WRAP73 isoform X1 XP_016856876.1:p.Lys227Glu K (Lys) > E (Glu) Missense Variant
WRAP73 transcript variant X3 XR_946661.3:n.745A>G N/A Non Coding 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

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 102978 T=0.999981 C=0.000019
European Sub 87026 T=1.00000 C=0.00000
African Sub 3492 T=1.0000 C=0.0000
African Others Sub 116 T=1.000 C=0.000
African American Sub 3376 T=1.0000 C=0.0000
Asian Sub 3128 T=0.9994 C=0.0006
East Asian Sub 1914 T=0.9995 C=0.0005
Other Asian Sub 1214 T=0.9992 C=0.0008
Latin American 1 Sub 152 T=1.000 C=0.000
Latin American 2 Sub 632 T=1.000 C=0.000
South Asian Sub 104 T=1.000 C=0.000
Other Sub 8444 T=1.0000 C=0.0000


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=0.999981 C=0.000019
gnomAD - Exomes Global Study-wide 251318 T=0.999912 C=0.000088
gnomAD - Exomes European Sub 135276 T=1.000000 C=0.000000
gnomAD - Exomes Asian Sub 49008 T=0.99955 C=0.00045
gnomAD - Exomes American Sub 34584 T=1.00000 C=0.00000
gnomAD - Exomes African Sub 16240 T=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6134 T=1.0000 C=0.0000
ExAC Global Study-wide 121122 T=0.999884 C=0.000116
ExAC Europe Sub 73174 T=1.00000 C=0.00000
ExAC Asian Sub 25152 T=0.99944 C=0.00056
ExAC American Sub 11550 T=1.00000 C=0.00000
ExAC African Sub 10342 T=1.00000 C=0.00000
ExAC Other Sub 904 T=1.000 C=0.000
8.3KJPN JAPANESE Study-wide 16760 T=0.99940 C=0.00060
1000Genomes Global Study-wide 5008 T=0.9996 C=0.0004
1000Genomes African Sub 1322 T=1.0000 C=0.0000
1000Genomes East Asian Sub 1008 T=0.9980 C=0.0020
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=1.000 C=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9976 C=0.0024
Korean Genome Project KOREAN Study-wide 1832 T=0.9978 C=0.0022
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= C
GRCh38.p13 chr 1 NC_000001.11:g.3635219= NC_000001.11:g.3635219T>C
GRCh37.p13 chr 1 NC_000001.10:g.3551783= NC_000001.10:g.3551783T>C
WRAP73 RefSeqGene NG_033937.1:g.19889= NG_033937.1:g.19889A>G
WRAP73 transcript NM_017818.4:c.679= NM_017818.4:c.679A>G
WRAP73 transcript NM_017818.3:c.679= NM_017818.3:c.679A>G
WRAP73 transcript variant X3 XR_946661.3:n.745= XR_946661.3:n.745A>G
WRAP73 transcript variant X1 XM_017001387.2:c.679= XM_017001387.2:c.679A>G
WD repeat-containing protein WRAP73 NP_060288.3:p.Lys227= NP_060288.3:p.Lys227Glu
WD repeat-containing protein WRAP73 isoform X1 XP_016856876.1:p.Lys227= XP_016856876.1:p.Lys227Glu
WRAP73 transcript variant X2 XM_005244754.1:c.604-145= XM_005244754.1:c.604-145A>G
WRAP73 transcript variant X2 XM_005244754.2:c.604-145= XM_005244754.2:c.604-145A>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#.

30 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217390845 Jul 14, 2010 (132)
2 1000GENOMES ss488648906 May 04, 2012 (137)
3 EXOME_CHIP ss491284974 May 04, 2012 (137)
4 ILLUMINA ss780773515 Sep 08, 2015 (146)
5 ILLUMINA ss783453306 Sep 08, 2015 (146)
6 1000GENOMES ss1289445086 Aug 21, 2014 (142)
7 EVA_EXAC ss1685260370 Apr 01, 2015 (144)
8 ILLUMINA ss1751917148 Sep 08, 2015 (146)
9 ILLUMINA ss1917721639 Feb 12, 2016 (147)
10 ILLUMINA ss1945982712 Feb 12, 2016 (147)
11 ILLUMINA ss1958234506 Feb 12, 2016 (147)
12 GNOMAD ss2731054743 Nov 08, 2017 (151)
13 AFFY ss2984842504 Nov 08, 2017 (151)
14 ILLUMINA ss3021047400 Nov 08, 2017 (151)
15 TOPMED ss3067088160 Nov 08, 2017 (151)
16 ILLUMINA ss3626011524 Oct 11, 2018 (152)
17 ILLUMINA ss3634303369 Oct 11, 2018 (152)
18 ILLUMINA ss3640010734 Oct 11, 2018 (152)
19 ILLUMINA ss3644478574 Oct 11, 2018 (152)
20 ILLUMINA ss3651370046 Oct 11, 2018 (152)
21 ILLUMINA ss3653616300 Oct 11, 2018 (152)
22 ILLUMINA ss3724990712 Jul 12, 2019 (153)
23 ILLUMINA ss3744338075 Jul 12, 2019 (153)
24 ILLUMINA ss3744604366 Jul 12, 2019 (153)
25 EVA ss3745753139 Jul 12, 2019 (153)
26 ILLUMINA ss3772106021 Jul 12, 2019 (153)
27 KRGDB ss3892926894 Apr 25, 2020 (154)
28 KOGIC ss3943689156 Apr 25, 2020 (154)
29 TOPMED ss4437255048 Apr 25, 2021 (155)
30 TOMMO_GENOMICS ss5142194539 Apr 25, 2021 (155)
31 1000Genomes NC_000001.10 - 3551783 Oct 11, 2018 (152)
32 ExAC NC_000001.10 - 3551783 Oct 11, 2018 (152)
33 gnomAD - Exomes NC_000001.10 - 3551783 Jul 12, 2019 (153)
34 KOREAN population from KRGDB NC_000001.10 - 3551783 Apr 25, 2020 (154)
35 Korean Genome Project NC_000001.11 - 3635219 Apr 25, 2020 (154)
36 8.3KJPN NC_000001.10 - 3551783 Apr 25, 2021 (155)
37 TopMed NC_000001.11 - 3635219 Apr 25, 2021 (155)
38 ALFA NC_000001.11 - 3635219 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
ss217390845 NC_000001.9:3541642:T:C NC_000001.11:3635218:T:C (self)
112914, 4436601, 69673, 104288, 163846, ss488648906, ss491284974, ss780773515, ss783453306, ss1289445086, ss1685260370, ss1751917148, ss1917721639, ss1945982712, ss1958234506, ss2731054743, ss2984842504, ss3021047400, ss3626011524, ss3634303369, ss3640010734, ss3644478574, ss3651370046, ss3653616300, ss3744338075, ss3744604366, ss3745753139, ss3772106021, ss3892926894, ss5142194539 NC_000001.10:3551782:T:C NC_000001.11:3635218:T:C (self)
67157, 535383, 861383, 9885642483, ss3067088160, ss3724990712, ss3943689156, ss4437255048 NC_000001.11:3635218:T:C NC_000001.11:3635218:T:C (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 rs114192897

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