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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.

rs116230480

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3635173 (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=0.000295 (78/264690, TOPMED)
T=0.000294 (74/251370, GnomAD_exome)
T=0.000597 (119/199246, ALFA) (+ 7 more)
T=0.000242 (34/140286, GnomAD)
T=0.000297 (36/121246, ExAC)
T=0.00017 (13/78698, PAGE_STUDY)
T=0.00031 (4/13006, GO-ESP)
T=0.0004 (2/5008, 1000G)
T=0.001 (1/998, GoNL)
T=0.002 (1/534, MGP)
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.3635173C>T
GRCh37.p13 chr 1 NC_000001.10:g.3551737C>T
WRAP73 RefSeqGene NG_033937.1:g.19935G>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.725G>A S [AGC] > N [AAC] Coding Sequence Variant
WD repeat-containing protein WRAP73 NP_060288.3:p.Ser242Asn S (Ser) > N (Asn) Missense Variant
WRAP73 transcript variant X2 XM_005244754.2:c.604-99G>A N/A Intron Variant
WRAP73 transcript variant X1 XM_017001387.2:c.725G>A S [AGC] > N [AAC] Coding Sequence Variant
WD repeat-containing protein WRAP73 isoform X1 XP_016856876.1:p.Ser242Asn S (Ser) > N (Asn) Missense Variant
WRAP73 transcript variant X3 XR_946661.3:n.791G>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 199246 C=0.999403 T=0.000597
European Sub 169908 C=0.999347 T=0.000653
African Sub 4954 C=0.9998 T=0.0002
African Others Sub 176 C=1.000 T=0.000
African American Sub 4778 C=0.9998 T=0.0002
Asian Sub 6346 C=1.0000 T=0.0000
East Asian Sub 4500 C=1.0000 T=0.0000
Other Asian Sub 1846 C=1.0000 T=0.0000
Latin American 1 Sub 796 C=0.997 T=0.003
Latin American 2 Sub 968 C=1.000 T=0.000
South Asian Sub 280 C=1.000 T=0.000
Other Sub 15994 C=0.99969 T=0.00031


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 C=0.999705 T=0.000295
gnomAD - Exomes Global Study-wide 251370 C=0.999706 T=0.000294
gnomAD - Exomes European Sub 135324 C=0.999542 T=0.000458
gnomAD - Exomes Asian Sub 49006 C=0.99992 T=0.00008
gnomAD - Exomes American Sub 34586 C=0.99988 T=0.00012
gnomAD - Exomes African Sub 16250 C=0.99994 T=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10072 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6132 C=0.9995 T=0.0005
gnomAD - Genomes Global Study-wide 140286 C=0.999758 T=0.000242
gnomAD - Genomes European Sub 75958 C=0.99967 T=0.00033
gnomAD - Genomes African Sub 42062 C=0.99990 T=0.00010
gnomAD - Genomes American Sub 13658 C=0.99971 T=0.00029
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=0.9995 T=0.0005
ExAC Global Study-wide 121246 C=0.999703 T=0.000297
ExAC Europe Sub 73230 C=0.99958 T=0.00042
ExAC Asian Sub 25162 C=1.00000 T=0.00000
ExAC American Sub 11570 C=0.99974 T=0.00026
ExAC African Sub 10380 C=0.99990 T=0.00010
ExAC Other Sub 904 C=0.999 T=0.001
The PAGE Study Global Study-wide 78698 C=0.99983 T=0.00017
The PAGE Study AfricanAmerican Sub 32514 C=0.99994 T=0.00006
The PAGE Study Mexican Sub 10810 C=0.99991 T=0.00009
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=0.9996 T=0.0004
The PAGE Study NativeHawaiian Sub 4534 C=0.9993 T=0.0007
The PAGE Study Cuban Sub 4228 C=0.9991 T=0.0009
The PAGE Study Dominican Sub 3828 C=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99969 T=0.00031
GO Exome Sequencing Project European American Sub 8600 C=0.9995 T=0.0005
GO Exome Sequencing Project African American Sub 4406 C=1.0000 T=0.0000
1000Genomes Global Study-wide 5008 C=0.9996 T=0.0004
1000Genomes African Sub 1322 C=1.0000 T=0.0000
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=0.999 T=0.001
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.999 T=0.001
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.998 T=0.002
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.3635173= NC_000001.11:g.3635173C>T
GRCh37.p13 chr 1 NC_000001.10:g.3551737= NC_000001.10:g.3551737C>T
WRAP73 RefSeqGene NG_033937.1:g.19935= NG_033937.1:g.19935G>A
WRAP73 transcript NM_017818.4:c.725= NM_017818.4:c.725G>A
WRAP73 transcript NM_017818.3:c.725= NM_017818.3:c.725G>A
WRAP73 transcript variant X3 XR_946661.3:n.791= XR_946661.3:n.791G>A
WRAP73 transcript variant X1 XM_017001387.2:c.725= XM_017001387.2:c.725G>A
WD repeat-containing protein WRAP73 NP_060288.3:p.Ser242= NP_060288.3:p.Ser242Asn
WD repeat-containing protein WRAP73 isoform X1 XP_016856876.1:p.Ser242= XP_016856876.1:p.Ser242Asn
WRAP73 transcript variant X2 XM_005244754.1:c.604-99= XM_005244754.1:c.604-99G>A
WRAP73 transcript variant X2 XM_005244754.2:c.604-99= XM_005244754.2:c.604-99G>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#.

35 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217314389 Jul 14, 2010 (132)
2 1000GENOMES ss488648905 May 04, 2012 (137)
3 EXOME_CHIP ss491284973 May 04, 2012 (137)
4 NHLBI-ESP ss712267175 Apr 25, 2013 (138)
5 ILLUMINA ss780873842 Sep 08, 2015 (146)
6 ILLUMINA ss783559110 Sep 08, 2015 (146)
7 EVA-GONL ss974794685 Aug 21, 2014 (142)
8 1000GENOMES ss1289445084 Aug 21, 2014 (142)
9 EVA_EXAC ss1685260363 Apr 01, 2015 (144)
10 EVA_MGP ss1710885479 Apr 01, 2015 (144)
11 ILLUMINA ss1751917147 Sep 08, 2015 (146)
12 ILLUMINA ss1917721638 Feb 12, 2016 (147)
13 ILLUMINA ss1945982711 Feb 12, 2016 (147)
14 ILLUMINA ss1958234504 Feb 12, 2016 (147)
15 HUMAN_LONGEVITY ss2159561294 Dec 20, 2016 (150)
16 TOPMED ss2321716428 Dec 20, 2016 (150)
17 GNOMAD ss2746194453 Nov 08, 2017 (151)
18 GNOMAD ss2750954800 Nov 08, 2017 (151)
19 AFFY ss2984842503 Nov 08, 2017 (151)
20 ILLUMINA ss3021047399 Nov 08, 2017 (151)
21 TOPMED ss3067088157 Nov 08, 2017 (151)
22 ILLUMINA ss3626011523 Oct 11, 2018 (152)
23 ILLUMINA ss3634303368 Oct 11, 2018 (152)
24 ILLUMINA ss3640010733 Oct 11, 2018 (152)
25 ILLUMINA ss3644478573 Oct 11, 2018 (152)
26 ILLUMINA ss3651370045 Oct 11, 2018 (152)
27 ILLUMINA ss3653616299 Oct 11, 2018 (152)
28 ILLUMINA ss3724990711 Jul 12, 2019 (153)
29 ILLUMINA ss3744338074 Jul 12, 2019 (153)
30 ILLUMINA ss3744604365 Jul 12, 2019 (153)
31 PAGE_CC ss3770780665 Jul 12, 2019 (153)
32 ILLUMINA ss3772106020 Jul 12, 2019 (153)
33 EVA ss3823550281 Apr 25, 2020 (154)
34 EVA ss3986095093 Apr 25, 2021 (155)
35 TOPMED ss4437255039 Apr 25, 2021 (155)
36 1000Genomes NC_000001.10 - 3551737 Oct 11, 2018 (152)
37 ExAC NC_000001.10 - 3551737 Oct 11, 2018 (152)
38 gnomAD - Genomes NC_000001.11 - 3635173 Apr 25, 2021 (155)
39 gnomAD - Exomes NC_000001.10 - 3551737 Jul 12, 2019 (153)
40 GO Exome Sequencing Project NC_000001.10 - 3551737 Oct 11, 2018 (152)
41 Genome of the Netherlands Release 5 NC_000001.10 - 3551737 Apr 25, 2020 (154)
42 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 3551737 Apr 25, 2020 (154)
43 The PAGE Study NC_000001.11 - 3635173 Jul 12, 2019 (153)
44 TopMed NC_000001.11 - 3635173 Apr 25, 2021 (155)
45 ALFA NC_000001.11 - 3635173 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
ss217314389 NC_000001.9:3541596:C:T NC_000001.11:3635172:C:T (self)
112912, 4436593, 69663, 9015, 21501, 2231, ss488648905, ss491284973, ss712267175, ss780873842, ss783559110, ss974794685, ss1289445084, ss1685260363, ss1710885479, ss1751917147, ss1917721638, ss1945982711, ss1958234504, ss2321716428, ss2746194453, ss2750954800, ss2984842503, ss3021047399, ss3626011523, ss3634303368, ss3640010733, ss3644478573, ss3651370045, ss3653616299, ss3744338074, ss3744604365, ss3772106020, ss3823550281, ss3986095093 NC_000001.10:3551736:C:T NC_000001.11:3635172:C:T (self)
821446, 2134, 535380, 861374, 11189760167, ss2159561294, ss3067088157, ss3724990711, ss3770780665, ss4437255039 NC_000001.11:3635172:C:T NC_000001.11:3635172: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 rs116230480

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