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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.

rs115630424

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3633445 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000744 (197/264690, TOPMED)
A=0.001876 (461/245756, GnomAD_exome)
A=0.000585 (82/140256, GnomAD) (+ 9 more)
A=0.001659 (192/115738, ExAC)
A=0.00020 (9/44790, ALFA)
A=0.00101 (17/16760, 8.3KJPN)
A=0.0048 (24/5008, 1000G)
A=0.0038 (11/2922, KOREAN)
A=0.0033 (6/1832, Korea1K)
A=0.039 (24/615, Vietnamese)
G=0.5 (2/4, SGDP_PRJ)
A=0.5 (2/4, SGDP_PRJ)
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.3633445G>A
GRCh37.p13 chr 1 NC_000001.10:g.3550009G>A
WRAP73 RefSeqGene NG_033937.1:g.21663C>T
Gene: WRAP73, WD repeat containing, antisense to TP73 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WRAP73 transcript NM_017818.4:c.875C>T P [CCG] > L [CTG] Coding Sequence Variant
WD repeat-containing protein WRAP73 NP_060288.3:p.Pro292Leu P (Pro) > L (Leu) Missense Variant
WRAP73 transcript variant X1 XM_017001387.2:c.875C>T P [CCG] > L [CTG] Coding Sequence Variant
WD repeat-containing protein WRAP73 isoform X1 XP_016856876.1:p.Pro292Leu P (Pro) > L (Leu) Missense Variant
WRAP73 transcript variant X2 XM_005244754.2:c.740C>T P [CCG] > L [CTG] Coding Sequence Variant
WD repeat-containing protein WRAP73 isoform X2 XP_005244811.1:p.Pro247Leu P (Pro) > L (Leu) Missense Variant
WRAP73 transcript variant X3 XR_946661.3:n.941C>T 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 44790 G=0.99980 A=0.00020
European Sub 32784 G=0.99997 A=0.00003
African Sub 3560 G=0.9997 A=0.0003
African Others Sub 122 G=1.000 A=0.000
African American Sub 3438 G=0.9997 A=0.0003
Asian Sub 168 G=0.958 A=0.042
East Asian Sub 112 G=0.946 A=0.054
Other Asian Sub 56 G=0.98 A=0.02
Latin American 1 Sub 500 G=1.000 A=0.000
Latin American 2 Sub 628 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 7052 G=1.0000 A=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 G=0.999256 A=0.000744
gnomAD - Exomes Global Study-wide 245756 G=0.998124 A=0.001876
gnomAD - Exomes European Sub 130974 G=0.999992 A=0.000008
gnomAD - Exomes Asian Sub 48728 G=0.99091 A=0.00909
gnomAD - Exomes American Sub 34370 G=0.99991 A=0.00009
gnomAD - Exomes African Sub 15724 G=0.99968 A=0.00032
gnomAD - Exomes Ashkenazi Jewish Sub 9910 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 6050 G=0.9985 A=0.0015
gnomAD - Genomes Global Study-wide 140256 G=0.999415 A=0.000585
gnomAD - Genomes European Sub 75948 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42044 G=0.99950 A=0.00050
gnomAD - Genomes American Sub 13660 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=0.9805 A=0.0195
gnomAD - Genomes Other Sub 2148 G=1.0000 A=0.0000
ExAC Global Study-wide 115738 G=0.998341 A=0.001659
ExAC Europe Sub 69108 G=1.00000 A=0.00000
ExAC Asian Sub 24914 G=0.99237 A=0.00763
ExAC American Sub 11424 G=1.00000 A=0.00000
ExAC African Sub 9418 G=0.9998 A=0.0002
ExAC Other Sub 874 G=1.000 A=0.000
8.3KJPN JAPANESE Study-wide 16760 G=0.99899 A=0.00101
1000Genomes Global Study-wide 5008 G=0.9952 A=0.0048
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9802 A=0.0198
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=0.996 A=0.004
1000Genomes American Sub 694 G=1.000 A=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9962 A=0.0038
Korean Genome Project KOREAN Study-wide 1832 G=0.9967 A=0.0033
A Vietnamese Genetic Variation Database Global Study-wide 615 G=0.961 A=0.039
SGDP_PRJ Global Study-wide 4 G=0.5 A=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 G= A
GRCh38.p13 chr 1 NC_000001.11:g.3633445= NC_000001.11:g.3633445G>A
GRCh37.p13 chr 1 NC_000001.10:g.3550009= NC_000001.10:g.3550009G>A
WRAP73 RefSeqGene NG_033937.1:g.21663= NG_033937.1:g.21663C>T
WRAP73 transcript NM_017818.4:c.875= NM_017818.4:c.875C>T
WRAP73 transcript NM_017818.3:c.875= NM_017818.3:c.875C>T
WRAP73 transcript variant X3 XR_946661.3:n.941= XR_946661.3:n.941C>T
WRAP73 transcript variant X1 XM_017001387.2:c.875= XM_017001387.2:c.875C>T
WRAP73 transcript variant X2 XM_005244754.2:c.740= XM_005244754.2:c.740C>T
WRAP73 transcript variant X2 XM_005244754.1:c.740= XM_005244754.1:c.740C>T
WD repeat-containing protein WRAP73 NP_060288.3:p.Pro292= NP_060288.3:p.Pro292Leu
WD repeat-containing protein WRAP73 isoform X1 XP_016856876.1:p.Pro292= XP_016856876.1:p.Pro292Leu
WD repeat-containing protein WRAP73 isoform X2 XP_005244811.1:p.Pro247= XP_005244811.1:p.Pro247Leu
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, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217390841 Jul 14, 2010 (132)
2 1000GENOMES ss217392072 Jul 14, 2010 (132)
3 1000GENOMES ss488648899 May 04, 2012 (137)
4 SSMP ss647535182 Apr 25, 2013 (138)
5 JMKIDD_LAB ss1067415152 Aug 21, 2014 (142)
6 1000GENOMES ss1289445029 Aug 21, 2014 (142)
7 BGI ss1558271066 Apr 01, 2015 (144)
8 EVA_EXAC ss1685260292 Apr 01, 2015 (144)
9 HUMAN_LONGEVITY ss2159561159 Dec 20, 2016 (150)
10 TOPMED ss2321716280 Dec 20, 2016 (150)
11 GNOMAD ss2731054633 Nov 08, 2017 (151)
12 GNOMAD ss2746194420 Nov 08, 2017 (151)
13 GNOMAD ss2750954651 Nov 08, 2017 (151)
14 TOPMED ss3067087809 Nov 08, 2017 (151)
15 OMUKHERJEE_ADBS ss3646220102 Oct 11, 2018 (152)
16 EVA ss3745753121 Jul 12, 2019 (153)
17 KHV_HUMAN_GENOMES ss3798774848 Jul 12, 2019 (153)
18 SGDP_PRJ ss3848065899 Apr 25, 2020 (154)
19 KRGDB ss3892926867 Apr 25, 2020 (154)
20 KOGIC ss3943689119 Apr 25, 2020 (154)
21 TOPMED ss4437254523 Apr 25, 2021 (155)
22 TOMMO_GENOMICS ss5142194469 Apr 25, 2021 (155)
23 EVA ss5236863345 Apr 25, 2021 (155)
24 1000Genomes NC_000001.10 - 3550009 Oct 11, 2018 (152)
25 ExAC NC_000001.10 - 3550009 Oct 11, 2018 (152)
26 gnomAD - Genomes NC_000001.11 - 3633445 Apr 25, 2021 (155)
27 gnomAD - Exomes NC_000001.10 - 3550009 Jul 12, 2019 (153)
28 KOREAN population from KRGDB NC_000001.10 - 3550009 Apr 25, 2020 (154)
29 Korean Genome Project NC_000001.11 - 3633445 Apr 25, 2020 (154)
30 SGDP_PRJ NC_000001.10 - 3550009 Apr 25, 2020 (154)
31 8.3KJPN NC_000001.10 - 3550009 Apr 25, 2021 (155)
32 TopMed NC_000001.11 - 3633445 Apr 25, 2021 (155)
33 A Vietnamese Genetic Variation Database NC_000001.10 - 3550009 Jul 12, 2019 (153)
34 ALFA NC_000001.11 - 3633445 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
ss217390841, ss217392072, ss1558271066 NC_000001.9:3539868:G:A NC_000001.11:3633444:G:A (self)
112856, 4436516, 69553, 104261, 82879, 163776, 10472, ss488648899, ss647535182, ss1067415152, ss1289445029, ss1685260292, ss2321716280, ss2731054633, ss2746194420, ss2750954651, ss3646220102, ss3745753121, ss3848065899, ss3892926867, ss5142194469 NC_000001.10:3550008:G:A NC_000001.11:3633444:G:A (self)
821045, 67120, 535063, 860858, 9651519760, ss2159561159, ss3067087809, ss3798774848, ss3943689119, ss4437254523, ss5236863345 NC_000001.11:3633444:G:A NC_000001.11:3633444:G: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 rs115630424

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