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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.

rs858

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr4:88019177 (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=0.016109 (4264/264690, TOPMED)
T=0.018271 (2559/140056, GnomAD)
T=0.02099 (488/23244, ALFA) (+ 13 more)
T=0.0118 (59/5008, 1000G)
T=0.0342 (153/4480, Estonian)
T=0.0228 (88/3854, ALSPAC)
T=0.0232 (86/3708, TWINSUK)
T=0.026 (26/998, GoNL)
T=0.030 (19/626, Chileans)
T=0.011 (7/610, HapMap)
T=0.038 (23/600, NorthernSweden)
T=0.014 (3/216, Qatari)
C=0.5 (2/4, SGDP_PRJ)
T=0.5 (2/4, SGDP_PRJ)
C=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PKD2 : Intron 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 4 NC_000004.12:g.88019177C>T
GRCh37.p13 chr 4 NC_000004.11:g.88940329C>T
PKD2 RefSeqGene NG_008604.1:g.16510C>T
Gene: PKD2, polycystin 2, transient receptor potential cation channel (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PKD2 transcript variant 1 NM_000297.4:c.596-281C>T N/A Intron Variant
PKD2 transcript variant 2 NR_156488.2:n. N/A Intron Variant
PKD2 transcript variant X1 XM_011532028.2:c.596-281C…

XM_011532028.2:c.596-281C>T

N/A Intron Variant
PKD2 transcript variant X2 XM_011532029.1:c. N/A Genic Upstream Transcript Variant
PKD2 transcript variant X3 XM_011532030.2:c. N/A Genic Upstream 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 23244 C=0.97901 T=0.02099
European Sub 17222 C=0.97422 T=0.02578
African Sub 3600 C=0.9964 T=0.0036
African Others Sub 126 C=1.000 T=0.000
African American Sub 3474 C=0.9963 T=0.0037
Asian Sub 158 C=1.000 T=0.000
East Asian Sub 100 C=1.00 T=0.00
Other Asian Sub 58 C=1.00 T=0.00
Latin American 1 Sub 212 C=0.986 T=0.014
Latin American 2 Sub 750 C=0.991 T=0.009
South Asian Sub 110 C=0.991 T=0.009
Other Sub 1192 C=0.9832 T=0.0168


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=0.983891 T=0.016109
gnomAD - Genomes Global Study-wide 140056 C=0.981729 T=0.018271
gnomAD - Genomes European Sub 75852 C=0.97295 T=0.02705
gnomAD - Genomes African Sub 41970 C=0.99547 T=0.00453
gnomAD - Genomes American Sub 13638 C=0.98248 T=0.01752
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.9855 T=0.0145
gnomAD - Genomes East Asian Sub 3128 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2148 C=0.9860 T=0.0140
1000Genomes Global Study-wide 5008 C=0.9882 T=0.0118
1000Genomes African Sub 1322 C=0.9985 T=0.0015
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9632 T=0.0368
1000Genomes South Asian Sub 978 C=0.986 T=0.014
1000Genomes American Sub 694 C=0.991 T=0.009
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9658 T=0.0342
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9772 T=0.0228
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9768 T=0.0232
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.974 T=0.026
Chileans Chilean Study-wide 626 C=0.970 T=0.030
HapMap Global Study-wide 610 C=0.989 T=0.011
HapMap African Sub 402 C=0.995 T=0.005
HapMap American Sub 120 C=0.958 T=0.042
HapMap Asian Sub 88 C=1.00 T=0.00
Northern Sweden ACPOP Study-wide 600 C=0.962 T=0.038
Qatari Global Study-wide 216 C=0.986 T=0.014
SGDP_PRJ Global Study-wide 4 C=0.5 T=0.5
Siberian 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 4 NC_000004.12:g.88019177= NC_000004.12:g.88019177C>T
GRCh37.p13 chr 4 NC_000004.11:g.88940329= NC_000004.11:g.88940329C>T
PKD2 RefSeqGene NG_008604.1:g.16510= NG_008604.1:g.16510C>T
PKD2 transcript variant 1 NM_000297.3:c.596-281= NM_000297.3:c.596-281C>T
PKD2 transcript variant 1 NM_000297.4:c.596-281= NM_000297.4:c.596-281C>T
PKD2 transcript variant X1 XM_005263065.1:c.-209-281= XM_005263065.1:c.-209-281C>T
PKD2 transcript variant X1 XM_011532028.2:c.596-281= XM_011532028.2:c.596-281C>T
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#.

31 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF ss880 Sep 19, 2000 (36)
2 PERLEGEN ss24297197 Sep 20, 2004 (123)
3 AFFY ss76550709 Dec 07, 2007 (129)
4 KRIBB_YJKIM ss104807689 Feb 05, 2009 (130)
5 1000GENOMES ss232485186 Jul 14, 2010 (132)
6 EVA-GONL ss980362153 Aug 21, 2014 (142)
7 JMKIDD_LAB ss1071723430 Aug 21, 2014 (142)
8 1000GENOMES ss1310664625 Aug 21, 2014 (142)
9 DDI ss1429958834 Apr 01, 2015 (144)
10 EVA_DECODE ss1589864247 Apr 01, 2015 (144)
11 EVA_UK10K_ALSPAC ss1610568995 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1653563028 Apr 01, 2015 (144)
13 EVA_SVP ss1712688160 Apr 01, 2015 (144)
14 WEILL_CORNELL_DGM ss1923606625 Feb 12, 2016 (147)
15 JJLAB ss2022388375 Sep 14, 2016 (149)
16 USC_VALOUEV ss2150517711 Dec 20, 2016 (150)
17 HUMAN_LONGEVITY ss2264755366 Dec 20, 2016 (150)
18 TOPMED ss2432558215 Dec 20, 2016 (150)
19 GNOMAD ss2811944387 Nov 08, 2017 (151)
20 AFFY ss2985297466 Nov 08, 2017 (151)
21 AFFY ss2985921545 Nov 08, 2017 (151)
22 SWEGEN ss2995080669 Nov 08, 2017 (151)
23 CSHL ss3345826935 Nov 08, 2017 (151)
24 TOPMED ss3435141491 Nov 08, 2017 (151)
25 ILLUMINA ss3654069121 Oct 12, 2018 (152)
26 EGCUT_WGS ss3662967113 Jul 13, 2019 (153)
27 EVA_DECODE ss3712502803 Jul 13, 2019 (153)
28 ACPOP ss3731353238 Jul 13, 2019 (153)
29 KHV_HUMAN_GENOMES ss3805222467 Jul 13, 2019 (153)
30 SGDP_PRJ ss3859446030 Apr 26, 2020 (154)
31 TOPMED ss4621828449 Apr 26, 2021 (155)
32 1000Genomes NC_000004.11 - 88940329 Oct 12, 2018 (152)
33 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 88940329 Oct 12, 2018 (152)
34 Chileans NC_000004.11 - 88940329 Apr 26, 2020 (154)
35 Genetic variation in the Estonian population NC_000004.11 - 88940329 Oct 12, 2018 (152)
36 gnomAD - Genomes NC_000004.12 - 88019177 Apr 26, 2021 (155)
37 Genome of the Netherlands Release 5 NC_000004.11 - 88940329 Apr 26, 2020 (154)
38 HapMap NC_000004.12 - 88019177 Apr 26, 2020 (154)
39 Northern Sweden NC_000004.11 - 88940329 Jul 13, 2019 (153)
40 Qatari NC_000004.11 - 88940329 Apr 26, 2020 (154)
41 SGDP_PRJ NC_000004.11 - 88940329 Apr 26, 2020 (154)
42 Siberian NC_000004.11 - 88940329 Apr 26, 2020 (154)
43 TopMed NC_000004.12 - 88019177 Apr 26, 2021 (155)
44 UK 10K study - Twins NC_000004.11 - 88940329 Oct 12, 2018 (152)
45 ALFA NC_000004.12 - 88019177 Apr 26, 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).

Associated ID History Updated (Build)
rs17729772 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss76550709, ss1589864247, ss1712688160 NC_000004.10:89159352:C:T NC_000004.12:88019176:C:T (self)
22094526, 12289180, 320988, 8705361, 5427565, 4638103, 5648555, 11463010, 3034065, 12289180, ss232485186, ss980362153, ss1071723430, ss1310664625, ss1429958834, ss1610568995, ss1653563028, ss1923606625, ss2022388375, ss2150517711, ss2432558215, ss2811944387, ss2985297466, ss2985921545, ss2995080669, ss3345826935, ss3654069121, ss3662967113, ss3731353238, ss3859446030 NC_000004.11:88940328:C:T NC_000004.12:88019176:C:T (self)
156494845, 2656522, 287045237, 459206005, 2826618580, ss2264755366, ss3435141491, ss3712502803, ss3805222467, ss4621828449 NC_000004.12:88019176:C:T NC_000004.12:88019176:C:T (self)
ss880, ss24297197, ss104807689 NT_016354.19:13488049:C:T NC_000004.12:88019176: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 rs858

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