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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.

rs16823940

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3631634 (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=0.029068 (7694/264690, TOPMED)
T=0.007169 (1718/239628, GnomAD_exome)
T=0.004787 (939/196160, ALFA) (+ 13 more)
T=0.028008 (3928/140244, GnomAD)
T=0.008505 (985/115818, ExAC)
T=0.04230 (3327/78660, PAGE_STUDY)
T=0.03046 (396/13002, GO-ESP)
T=0.0276 (138/5008, 1000G)
T=0.0000 (0/3854, ALSPAC)
T=0.0003 (1/3708, TWINSUK)
T=0.0005 (1/1832, Korea1K)
T=0.0685 (105/1532, HapMap)
T=0.004 (2/534, MGP)
T=0.028 (6/216, Qatari)
C=0.50 (6/12, SGDP_PRJ)
T=0.50 (6/12, 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.3631634C>T
GRCh37.p13 chr 1 NC_000001.10:g.3548198C>T
WRAP73 RefSeqGene NG_033937.1:g.23474G>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.1072G>A V [GTC] > I [ATC] Coding Sequence Variant
WD repeat-containing protein WRAP73 NP_060288.3:p.Val358Ile V (Val) > I (Ile) Missense Variant
WRAP73 transcript variant X1 XM_017001387.2:c.1051G>A V [GTC] > I [ATC] Coding Sequence Variant
WD repeat-containing protein WRAP73 isoform X1 XP_016856876.1:p.Val351Ile V (Val) > I (Ile) Missense Variant
WRAP73 transcript variant X2 XM_005244754.2:c.937G>A V [GTC] > I [ATC] Coding Sequence Variant
WD repeat-containing protein WRAP73 isoform X2 XP_005244811.1:p.Val313Ile V (Val) > I (Ile) Missense Variant
WRAP73 transcript variant X3 XR_946661.3:n.1146G>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 196160 C=0.995213 T=0.004787
European Sub 165164 C=0.999074 T=0.000926
African Sub 7804 C=0.9162 T=0.0838
African Others Sub 248 C=0.871 T=0.129
African American Sub 7556 C=0.9177 T=0.0823
Asian Sub 3692 C=1.0000 T=0.0000
East Asian Sub 2338 C=1.0000 T=0.0000
Other Asian Sub 1354 C=1.0000 T=0.0000
Latin American 1 Sub 678 C=0.972 T=0.028
Latin American 2 Sub 2210 C=0.9937 T=0.0063
South Asian Sub 190 C=1.000 T=0.000
Other Sub 16422 C=0.99397 T=0.00603


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=0.970932 T=0.029068
gnomAD - Exomes Global Study-wide 239628 C=0.992831 T=0.007169
gnomAD - Exomes European Sub 124792 C=0.999471 T=0.000529
gnomAD - Exomes Asian Sub 48578 C=0.99990 T=0.00010
gnomAD - Exomes American Sub 34396 C=0.99465 T=0.00535
gnomAD - Exomes African Sub 15954 C=0.90993 T=0.09007
gnomAD - Exomes Ashkenazi Jewish Sub 9920 C=0.9997 T=0.0003
gnomAD - Exomes Other Sub 5988 C=0.9962 T=0.0038
gnomAD - Genomes Global Study-wide 140244 C=0.971992 T=0.028008
gnomAD - Genomes European Sub 75970 C=0.99941 T=0.00059
gnomAD - Genomes African Sub 42026 C=0.91165 T=0.08835
gnomAD - Genomes American Sub 13644 C=0.99150 T=0.00850
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2146 C=0.9748 T=0.0252
ExAC Global Study-wide 115818 C=0.991495 T=0.008505
ExAC Europe Sub 70466 C=0.99957 T=0.00043
ExAC Asian Sub 23248 C=0.99983 T=0.00017
ExAC American Sub 11356 C=0.99516 T=0.00484
ExAC African Sub 9896 C=0.9099 T=0.0901
ExAC Other Sub 852 C=0.995 T=0.005
The PAGE Study Global Study-wide 78660 C=0.95770 T=0.04230
The PAGE Study AfricanAmerican Sub 32480 C=0.91521 T=0.08479
The PAGE Study Mexican Sub 10810 C=0.99473 T=0.00527
The PAGE Study Asian Sub 8316 C=0.9999 T=0.0001
The PAGE Study PuertoRican Sub 7918 C=0.9744 T=0.0256
The PAGE Study NativeHawaiian Sub 4534 C=0.9985 T=0.0015
The PAGE Study Cuban Sub 4228 C=0.9844 T=0.0156
The PAGE Study Dominican Sub 3828 C=0.9545 T=0.0455
The PAGE Study CentralAmerican Sub 2450 C=0.9853 T=0.0147
The PAGE Study SouthAmerican Sub 1982 C=0.9919 T=0.0081
The PAGE Study NativeAmerican Sub 1258 C=0.9897 T=0.0103
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13002 C=0.96954 T=0.03046
GO Exome Sequencing Project European American Sub 8596 C=0.9993 T=0.0007
GO Exome Sequencing Project African American Sub 4406 C=0.9115 T=0.0885
1000Genomes Global Study-wide 5008 C=0.9724 T=0.0276
1000Genomes African Sub 1322 C=0.8986 T=0.1014
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
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=1.0000 T=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9997 T=0.0003
Korean Genome Project KOREAN Study-wide 1832 C=0.9995 T=0.0005
HapMap Global Study-wide 1532 C=0.9315 T=0.0685
HapMap African Sub 688 C=0.872 T=0.128
HapMap American Sub 592 C=0.975 T=0.025
HapMap Asian Sub 252 C=0.992 T=0.008
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.996 T=0.004
Qatari Global Study-wide 216 C=0.972 T=0.028
SGDP_PRJ Global Study-wide 12 C=0.50 T=0.50
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.3631634= NC_000001.11:g.3631634C>T
GRCh37.p13 chr 1 NC_000001.10:g.3548198= NC_000001.10:g.3548198C>T
WRAP73 RefSeqGene NG_033937.1:g.23474= NG_033937.1:g.23474G>A
WRAP73 transcript NM_017818.4:c.1072= NM_017818.4:c.1072G>A
WRAP73 transcript NM_017818.3:c.1072= NM_017818.3:c.1072G>A
WRAP73 transcript variant X3 XR_946661.3:n.1146= XR_946661.3:n.1146G>A
WRAP73 transcript variant X1 XM_017001387.2:c.1051= XM_017001387.2:c.1051G>A
WRAP73 transcript variant X2 XM_005244754.2:c.937= XM_005244754.2:c.937G>A
WRAP73 transcript variant X2 XM_005244754.1:c.937= XM_005244754.1:c.937G>A
WD repeat-containing protein WRAP73 NP_060288.3:p.Val358= NP_060288.3:p.Val358Ile
WD repeat-containing protein WRAP73 isoform X1 XP_016856876.1:p.Val351= XP_016856876.1:p.Val351Ile
WD repeat-containing protein WRAP73 isoform X2 XP_005244811.1:p.Val313= XP_005244811.1:p.Val313Ile
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#.

83 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23157538 Sep 20, 2004 (123)
2 PERLEGEN ss68756650 May 17, 2007 (127)
3 ILLUMINA ss74886633 Dec 07, 2007 (129)
4 ILLUMINA ss160383162 Dec 01, 2009 (131)
5 ILLUMINA ss172617254 Jul 04, 2010 (132)
6 1000GENOMES ss217405802 Jul 14, 2010 (132)
7 1000GENOMES ss217410949 Jul 14, 2010 (132)
8 1000GENOMES ss218202388 Jul 14, 2010 (132)
9 NHLBI-ESP ss341927356 May 09, 2011 (134)
10 ILLUMINA ss480065706 May 04, 2012 (137)
11 ILLUMINA ss480074478 May 04, 2012 (137)
12 ILLUMINA ss480749880 Sep 08, 2015 (146)
13 ILLUMINA ss484830759 May 04, 2012 (137)
14 1000GENOMES ss489716383 May 04, 2012 (137)
15 EXOME_CHIP ss491284967 May 04, 2012 (137)
16 CLINSEQ_SNP ss491582822 May 04, 2012 (137)
17 ILLUMINA ss536906161 Sep 08, 2015 (146)
18 ILLUMINA ss778816544 Sep 08, 2015 (146)
19 ILLUMINA ss780873516 Sep 08, 2015 (146)
20 ILLUMINA ss782861949 Sep 08, 2015 (146)
21 ILLUMINA ss783558715 Sep 08, 2015 (146)
22 ILLUMINA ss783826251 Sep 08, 2015 (146)
23 ILLUMINA ss832115983 Sep 08, 2015 (146)
24 ILLUMINA ss834276855 Sep 08, 2015 (146)
25 JMKIDD_LAB ss1067415150 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1067626225 Aug 21, 2014 (142)
27 1000GENOMES ss1289444945 Aug 21, 2014 (142)
28 DDI ss1425692422 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1599424085 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1642418118 Apr 01, 2015 (144)
31 EVA_EXAC ss1685260194 Apr 01, 2015 (144)
32 EVA_MGP ss1710885466 Apr 01, 2015 (144)
33 ILLUMINA ss1751917129 Sep 08, 2015 (146)
34 ILLUMINA ss1751917130 Sep 08, 2015 (146)
35 HAMMER_LAB ss1793782492 Sep 08, 2015 (146)
36 ILLUMINA ss1917721634 Feb 12, 2016 (147)
37 WEILL_CORNELL_DGM ss1917990140 Feb 12, 2016 (147)
38 ILLUMINA ss1945982707 Feb 12, 2016 (147)
39 ILLUMINA ss1958234495 Feb 12, 2016 (147)
40 HUMAN_LONGEVITY ss2159561017 Dec 20, 2016 (150)
41 TOPMED ss2321716118 Dec 20, 2016 (150)
42 ILLUMINA ss2632468437 Nov 08, 2017 (151)
43 GNOMAD ss2731054505 Nov 08, 2017 (151)
44 GNOMAD ss2746194378 Nov 08, 2017 (151)
45 GNOMAD ss2750954464 Nov 08, 2017 (151)
46 AFFY ss2984842497 Nov 08, 2017 (151)
47 SWEGEN ss2986198750 Nov 08, 2017 (151)
48 ILLUMINA ss3021047391 Nov 08, 2017 (151)
49 TOPMED ss3067087383 Nov 08, 2017 (151)
50 ILLUMINA ss3626011511 Oct 11, 2018 (152)
51 ILLUMINA ss3626011512 Oct 11, 2018 (152)
52 ILLUMINA ss3630507805 Oct 11, 2018 (152)
53 ILLUMINA ss3632878514 Oct 11, 2018 (152)
54 ILLUMINA ss3633572125 Oct 11, 2018 (152)
55 ILLUMINA ss3634303363 Oct 11, 2018 (152)
56 ILLUMINA ss3634303364 Oct 11, 2018 (152)
57 ILLUMINA ss3635266305 Oct 11, 2018 (152)
58 ILLUMINA ss3635979691 Oct 11, 2018 (152)
59 ILLUMINA ss3637016655 Oct 11, 2018 (152)
60 ILLUMINA ss3637733670 Oct 11, 2018 (152)
61 ILLUMINA ss3640010728 Oct 11, 2018 (152)
62 ILLUMINA ss3640010729 Oct 11, 2018 (152)
63 ILLUMINA ss3642747881 Oct 11, 2018 (152)
64 ILLUMINA ss3644478569 Oct 11, 2018 (152)
65 ILLUMINA ss3651370037 Oct 11, 2018 (152)
66 ILLUMINA ss3653616293 Oct 11, 2018 (152)
67 EVA_DECODE ss3686043988 Jul 12, 2019 (153)
68 ILLUMINA ss3724990705 Jul 12, 2019 (153)
69 ILLUMINA ss3744338070 Jul 12, 2019 (153)
70 ILLUMINA ss3744604360 Jul 12, 2019 (153)
71 ILLUMINA ss3744604361 Jul 12, 2019 (153)
72 PAGE_CC ss3770780657 Jul 12, 2019 (153)
73 ILLUMINA ss3772106015 Jul 12, 2019 (153)
74 ILLUMINA ss3772106016 Jul 12, 2019 (153)
75 KHV_HUMAN_GENOMES ss3798774824 Jul 12, 2019 (153)
76 EVA ss3823550237 Apr 25, 2020 (154)
77 EVA ss3825551131 Apr 25, 2020 (154)
78 SGDP_PRJ ss3848065858 Apr 25, 2020 (154)
79 KOGIC ss3943689073 Apr 25, 2020 (154)
80 FSA-LAB ss3983912915 Apr 25, 2021 (155)
81 EVA ss3986095081 Apr 25, 2021 (155)
82 EVA ss4016890027 Apr 25, 2021 (155)
83 TOPMED ss4437253957 Apr 25, 2021 (155)
84 1000Genomes NC_000001.10 - 3548198 Oct 11, 2018 (152)
85 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3548198 Oct 11, 2018 (152)
86 ExAC NC_000001.10 - 3548198 Oct 11, 2018 (152)
87 gnomAD - Genomes NC_000001.11 - 3631634 Apr 25, 2021 (155)
88 gnomAD - Exomes NC_000001.10 - 3548198 Jul 12, 2019 (153)
89 GO Exome Sequencing Project NC_000001.10 - 3548198 Oct 11, 2018 (152)
90 HapMap NC_000001.11 - 3631634 Apr 25, 2020 (154)
91 Korean Genome Project NC_000001.11 - 3631634 Apr 25, 2020 (154)
92 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 3548198 Apr 25, 2020 (154)
93 The PAGE Study NC_000001.11 - 3631634 Jul 12, 2019 (153)
94 Qatari NC_000001.10 - 3548198 Apr 25, 2020 (154)
95 SGDP_PRJ NC_000001.10 - 3548198 Apr 25, 2020 (154)
96 TopMed NC_000001.11 - 3631634 Apr 25, 2021 (155)
97 UK 10K study - Twins NC_000001.10 - 3548198 Oct 11, 2018 (152)
98 ALFA NC_000001.11 - 3631634 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
ss217405802, ss217410949, ss480065706, ss491582822, ss3642747881 NC_000001.9:3538057:C:T NC_000001.11:3631633:C:T (self)
112768, 50064, 4436415, 69403, 8971, 2218, 32070, 82838, 50064, ss218202388, ss341927356, ss480074478, ss480749880, ss484830759, ss489716383, ss491284967, ss536906161, ss778816544, ss780873516, ss782861949, ss783558715, ss783826251, ss832115983, ss834276855, ss1067415150, ss1067626225, ss1289444945, ss1425692422, ss1599424085, ss1642418118, ss1685260194, ss1710885466, ss1751917129, ss1751917130, ss1793782492, ss1917721634, ss1917990140, ss1945982707, ss1958234495, ss2321716118, ss2632468437, ss2731054505, ss2746194378, ss2750954464, ss2984842497, ss2986198750, ss3021047391, ss3626011511, ss3626011512, ss3630507805, ss3632878514, ss3633572125, ss3634303363, ss3634303364, ss3635266305, ss3635979691, ss3637016655, ss3637733670, ss3640010728, ss3640010729, ss3644478569, ss3651370037, ss3653616293, ss3744338070, ss3744604360, ss3744604361, ss3772106015, ss3772106016, ss3823550237, ss3825551131, ss3848065858, ss3983912915, ss3986095081, ss4016890027 NC_000001.10:3548197:C:T NC_000001.11:3631633:C:T (self)
820611, 2594, 67074, 2126, 534693, 860292, 5034838689, ss2159561017, ss3067087383, ss3686043988, ss3724990705, ss3770780657, ss3798774824, ss3943689073, ss4437253957 NC_000001.11:3631633:C:T NC_000001.11:3631633:C:T (self)
ss23157538, ss68756650, ss74886633, ss160383162, ss172617254 NT_004350.19:3026829:C:T NC_000001.11:3631633: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 rs16823940

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