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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.

rs114827156

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3631071 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.009041 (2393/264690, TOPMED)
T=0.002335 (583/249654, GnomAD_exome)
T=0.008712 (1222/140262, GnomAD) (+ 8 more)
T=0.002836 (341/120244, ExAC)
T=0.00299 (135/45090, ALFA)
T=0.00884 (115/13006, GO-ESP)
T=0.0086 (43/5008, 1000G)
T=0.002 (1/534, MGP)
T=0.009 (2/216, Qatari)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
WRAP73 : Synonymous 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.3631071C>T
GRCh37.p13 chr 1 NC_000001.10:g.3547635C>T
WRAP73 RefSeqGene NG_033937.1:g.24037G>A
Gene: WRAP73, WD repeat containing, antisense to TP73 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WRAP73 transcript NM_017818.4:c.1287G>A S [TCG] > S [TCA] Coding Sequence Variant
WD repeat-containing protein WRAP73 NP_060288.3:p.Ser429= S (Ser) > S (Ser) Synonymous Variant
WRAP73 transcript variant X1 XM_017001387.2:c.1266G>A S [TCG] > S [TCA] Coding Sequence Variant
WD repeat-containing protein WRAP73 isoform X1 XP_016856876.1:p.Ser422= S (Ser) > S (Ser) Synonymous Variant
WRAP73 transcript variant X2 XM_005244754.2:c.1152G>A S [TCG] > S [TCA] Coding Sequence Variant
WD repeat-containing protein WRAP73 isoform X2 XP_005244811.1:p.Ser384= S (Ser) > S (Ser) Synonymous Variant
WRAP73 transcript variant X3 XR_946661.3:n.1361G>A 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 45090 C=0.99701 T=0.00299
European Sub 32784 C=0.99921 T=0.00079
African Sub 3584 C=0.9766 T=0.0234
African Others Sub 122 C=0.951 T=0.049
African American Sub 3462 C=0.9775 T=0.0225
Asian Sub 172 C=1.000 T=0.000
East Asian Sub 114 C=1.000 T=0.000
Other Asian Sub 58 C=1.00 T=0.00
Latin American 1 Sub 508 C=0.990 T=0.010
Latin American 2 Sub 634 C=0.998 T=0.002
South Asian Sub 98 C=1.00 T=0.00
Other Sub 7310 C=0.9974 T=0.0026


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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.990959 T=0.009041
gnomAD - Exomes Global Study-wide 249654 C=0.997665 T=0.002335
gnomAD - Exomes European Sub 133692 C=0.999544 T=0.000456
gnomAD - Exomes Asian Sub 48994 C=0.99996 T=0.00004
gnomAD - Exomes American Sub 34576 C=0.99728 T=0.00272
gnomAD - Exomes African Sub 16208 C=0.97452 T=0.02548
gnomAD - Exomes Ashkenazi Jewish Sub 10062 C=0.99990 T=0.00010
gnomAD - Exomes Other Sub 6122 C=0.9980 T=0.0020
gnomAD - Genomes Global Study-wide 140262 C=0.991288 T=0.008712
gnomAD - Genomes European Sub 75962 C=0.99945 T=0.00055
gnomAD - Genomes African Sub 42030 C=0.97335 T=0.02665
gnomAD - Genomes American Sub 13662 C=0.99678 T=0.00322
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=0.9926 T=0.0074
ExAC Global Study-wide 120244 C=0.997164 T=0.002836
ExAC Europe Sub 72460 C=0.99957 T=0.00043
ExAC Asian Sub 25098 C=0.99996 T=0.00004
ExAC American Sub 11534 C=0.99697 T=0.00303
ExAC African Sub 10258 C=0.97339 T=0.02661
ExAC Other Sub 894 C=0.999 T=0.001
Allele Frequency Aggregator Total Global 45090 C=0.99701 T=0.00299
Allele Frequency Aggregator European Sub 32784 C=0.99921 T=0.00079
Allele Frequency Aggregator Other Sub 7310 C=0.9974 T=0.0026
Allele Frequency Aggregator African Sub 3584 C=0.9766 T=0.0234
Allele Frequency Aggregator Latin American 2 Sub 634 C=0.998 T=0.002
Allele Frequency Aggregator Latin American 1 Sub 508 C=0.990 T=0.010
Allele Frequency Aggregator Asian Sub 172 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 13006 C=0.99116 T=0.00884
GO Exome Sequencing Project European American Sub 8600 C=0.9995 T=0.0005
GO Exome Sequencing Project African American Sub 4406 C=0.9748 T=0.0252
1000Genomes Global Study-wide 5008 C=0.9914 T=0.0086
1000Genomes African Sub 1322 C=0.9705 T=0.0295
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9990 T=0.0010
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.996 T=0.004
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.998 T=0.002
Qatari Global Study-wide 216 C=0.991 T=0.009
SGDP_PRJ Global Study-wide 2 C=0.5 T=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 C= T
GRCh38.p13 chr 1 NC_000001.11:g.3631071= NC_000001.11:g.3631071C>T
GRCh37.p13 chr 1 NC_000001.10:g.3547635= NC_000001.10:g.3547635C>T
WRAP73 RefSeqGene NG_033937.1:g.24037= NG_033937.1:g.24037G>A
WRAP73 transcript NM_017818.4:c.1287= NM_017818.4:c.1287G>A
WRAP73 transcript NM_017818.3:c.1287= NM_017818.3:c.1287G>A
WRAP73 transcript variant X3 XR_946661.3:n.1361= XR_946661.3:n.1361G>A
WRAP73 transcript variant X1 XM_017001387.2:c.1266= XM_017001387.2:c.1266G>A
WRAP73 transcript variant X2 XM_005244754.2:c.1152= XM_005244754.2:c.1152G>A
WRAP73 transcript variant X2 XM_005244754.1:c.1152= XM_005244754.1:c.1152G>A
WD repeat-containing protein WRAP73 NP_060288.3:p.Ser429= NP_060288.3:p.Ser429=
WD repeat-containing protein WRAP73 isoform X1 XP_016856876.1:p.Ser422= XP_016856876.1:p.Ser422=
WD repeat-containing protein WRAP73 isoform X2 XP_005244811.1:p.Ser384= XP_005244811.1:p.Ser384=
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#.

26 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217405779 Jul 14, 2010 (132)
2 1000GENOMES ss217410931 Jul 14, 2010 (132)
3 1000GENOMES ss328375654 May 09, 2011 (134)
4 NHLBI-ESP ss341927325 May 09, 2011 (134)
5 1000GENOMES ss489716371 May 04, 2012 (137)
6 CLINSEQ_SNP ss491582816 May 04, 2012 (137)
7 ILLUMINA ss534958377 Sep 08, 2015 (146)
8 JMKIDD_LAB ss1067415146 Aug 21, 2014 (142)
9 1000GENOMES ss1289444912 Aug 21, 2014 (142)
10 EVA_EXAC ss1685260112 Apr 01, 2015 (144)
11 EVA_MGP ss1710885464 Apr 01, 2015 (144)
12 WEILL_CORNELL_DGM ss1917990132 Feb 12, 2016 (147)
13 HUMAN_LONGEVITY ss2159560973 Dec 20, 2016 (150)
14 TOPMED ss2321716070 Dec 20, 2016 (150)
15 GNOMAD ss2731054389 Nov 08, 2017 (151)
16 GNOMAD ss2746194340 Nov 08, 2017 (151)
17 GNOMAD ss2750954411 Nov 08, 2017 (151)
18 SWEGEN ss2986198743 Nov 08, 2017 (151)
19 TOPMED ss3067087262 Nov 08, 2017 (151)
20 ILLUMINA ss3626011508 Oct 11, 2018 (152)
21 EVA_DECODE ss3686043975 Jul 12, 2019 (153)
22 EVA ss3823550212 Apr 25, 2020 (154)
23 EVA ss3825551126 Apr 25, 2020 (154)
24 SGDP_PRJ ss3848065841 Apr 25, 2020 (154)
25 EVA ss3986095070 Apr 25, 2021 (155)
26 TOPMED ss4437253792 Apr 25, 2021 (155)
27 1000Genomes NC_000001.10 - 3547635 Oct 11, 2018 (152)
28 ExAC NC_000001.10 - 3547635 Oct 11, 2018 (152)
29 gnomAD - Genomes NC_000001.11 - 3631071 Apr 25, 2021 (155)
30 gnomAD - Exomes NC_000001.10 - 3547635 Jul 12, 2019 (153)
31 GO Exome Sequencing Project NC_000001.10 - 3547635 Oct 11, 2018 (152)
32 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 3547635 Apr 25, 2020 (154)
33 Qatari NC_000001.10 - 3547635 Apr 25, 2020 (154)
34 SGDP_PRJ NC_000001.10 - 3547635 Apr 25, 2020 (154)
35 TopMed NC_000001.11 - 3631071 Apr 25, 2021 (155)
36 ALFA NC_000001.11 - 3631071 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
ss217405779, ss217410931, ss491582816 NC_000001.9:3537494:C:T NC_000001.11:3631070:C:T (self)
112735, 4436327, 69278, 8946, 2216, 32062, 82821, ss328375654, ss341927325, ss489716371, ss534958377, ss1067415146, ss1289444912, ss1685260112, ss1710885464, ss1917990132, ss2321716070, ss2731054389, ss2746194340, ss2750954411, ss2986198743, ss3626011508, ss3823550212, ss3825551126, ss3848065841, ss3986095070 NC_000001.10:3547634:C:T NC_000001.11:3631070:C:T (self)
820482, 534582, 860127, 1154889216, ss2159560973, ss3067087262, ss3686043975, ss4437253792 NC_000001.11:3631070:C:T NC_000001.11:3631070:C:T (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 rs114827156

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