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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.

rs28645341

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr14:29704872 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.315467 (83501/264690, TOPMED)
C=0.312828 (43779/139946, GnomAD)
C=0.30783 (5815/18890, ALFA) (+ 14 more)
C=0.26563 (4452/16760, 8.3KJPN)
C=0.3251 (1628/5008, 1000G)
C=0.3138 (1406/4480, Estonian)
C=0.3054 (1177/3854, ALSPAC)
C=0.3252 (1206/3708, TWINSUK)
C=0.2263 (663/2930, KOREAN)
C=0.2249 (412/1832, Korea1K)
C=0.318 (317/998, GoNL)
C=0.293 (176/600, NorthernSweden)
T=0.345 (111/322, SGDP_PRJ)
C=0.296 (64/216, Qatari)
C=0.136 (29/214, Vietnamese)
C=0.33 (13/40, GENOME_DK)
T=0.38 (13/34, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRKD1 : 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 14 NC_000014.9:g.29704872T>C
GRCh37.p13 chr 14 NC_000014.8:g.30174078T>C
PRKD1 RefSeqGene NG_052879.1:g.227822A>G
Gene: PRKD1, protein kinase D1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRKD1 transcript variant 1 NM_001330069.2:c.403+2066…

NM_001330069.2:c.403+20664A>G

N/A Intron Variant
PRKD1 transcript variant 3 NM_001348390.1:c.115+2066…

NM_001348390.1:c.115+20664A>G

N/A Intron Variant
PRKD1 transcript variant 2 NM_002742.3:c.403+20664A>G N/A Intron Variant
PRKD1 transcript variant X1 XM_011536965.2:c.115+2066…

XM_011536965.2:c.115+20664A>G

N/A Intron Variant
PRKD1 transcript variant X3 XM_017021462.1:c.-93+1959…

XM_017021462.1:c.-93+19598A>G

N/A Intron Variant
PRKD1 transcript variant X2 XR_943493.2:n. N/A Intron 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 18890 T=0.69217 C=0.30783
European Sub 14286 T=0.69670 C=0.30330
African Sub 2946 T=0.6785 C=0.3215
African Others Sub 114 T=0.667 C=0.333
African American Sub 2832 T=0.6790 C=0.3210
Asian Sub 112 T=0.777 C=0.223
East Asian Sub 86 T=0.80 C=0.20
Other Asian Sub 26 T=0.69 C=0.31
Latin American 1 Sub 146 T=0.699 C=0.301
Latin American 2 Sub 610 T=0.636 C=0.364
South Asian Sub 98 T=0.56 C=0.44
Other Sub 692 T=0.710 C=0.290


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 T=0.684533 C=0.315467
gnomAD - Genomes Global Study-wide 139946 T=0.687172 C=0.312828
gnomAD - Genomes European Sub 75804 T=0.69302 C=0.30698
gnomAD - Genomes African Sub 41926 T=0.67192 C=0.32808
gnomAD - Genomes American Sub 13618 T=0.65090 C=0.34910
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.7571 C=0.2429
gnomAD - Genomes East Asian Sub 3126 T=0.8167 C=0.1833
gnomAD - Genomes Other Sub 2150 T=0.7116 C=0.2884
8.3KJPN JAPANESE Study-wide 16760 T=0.73437 C=0.26563
1000Genomes Global Study-wide 5008 T=0.6749 C=0.3251
1000Genomes African Sub 1322 T=0.6452 C=0.3548
1000Genomes East Asian Sub 1008 T=0.8105 C=0.1895
1000Genomes Europe Sub 1006 T=0.6968 C=0.3032
1000Genomes South Asian Sub 978 T=0.574 C=0.426
1000Genomes American Sub 694 T=0.646 C=0.354
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.6862 C=0.3138
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.6946 C=0.3054
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.6748 C=0.3252
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.7737 C=0.2263
Korean Genome Project KOREAN Study-wide 1832 T=0.7751 C=0.2249
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.682 C=0.318
Northern Sweden ACPOP Study-wide 600 T=0.707 C=0.293
SGDP_PRJ Global Study-wide 322 T=0.345 C=0.655
Qatari Global Study-wide 216 T=0.704 C=0.296
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.864 C=0.136
The Danish reference pan genome Danish Study-wide 40 T=0.68 C=0.33
Siberian Global Study-wide 34 T=0.38 C=0.62
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 T= C
GRCh38.p13 chr 14 NC_000014.9:g.29704872= NC_000014.9:g.29704872T>C
GRCh37.p13 chr 14 NC_000014.8:g.30174078= NC_000014.8:g.30174078T>C
PRKD1 RefSeqGene NG_052879.1:g.227822= NG_052879.1:g.227822A>G
PRKD1 transcript variant 1 NM_001330069.2:c.403+20664= NM_001330069.2:c.403+20664A>G
PRKD1 transcript variant 3 NM_001348390.1:c.115+20664= NM_001348390.1:c.115+20664A>G
PRKD1 transcript variant 2 NM_002742.2:c.403+20664= NM_002742.2:c.403+20664A>G
PRKD1 transcript variant 2 NM_002742.3:c.403+20664= NM_002742.3:c.403+20664A>G
PRKD1 transcript variant X1 XM_005267859.1:c.403+20664= XM_005267859.1:c.403+20664A>G
PRKD1 transcript variant X1 XM_011536965.2:c.115+20664= XM_011536965.2:c.115+20664A>G
PRKD1 transcript variant X3 XM_017021462.1:c.-93+19598= XM_017021462.1:c.-93+19598A>G
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#.

54 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35422742 May 24, 2005 (125)
2 EGP_SNPS ss70452672 May 17, 2007 (127)
3 BCMHGSC_JDW ss89894057 Mar 24, 2008 (129)
4 BGI ss103173013 Dec 01, 2009 (131)
5 1000GENOMES ss108211707 Jan 23, 2009 (130)
6 1000GENOMES ss113091238 Jan 25, 2009 (130)
7 ILLUMINA-UK ss118395276 Feb 14, 2009 (130)
8 ENSEMBL ss133894488 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss167757171 Jul 04, 2010 (132)
10 COMPLETE_GENOMICS ss169036012 Jul 04, 2010 (132)
11 BCM-HGSC-SUB ss206892581 Jul 04, 2010 (132)
12 1000GENOMES ss226485560 Jul 14, 2010 (132)
13 1000GENOMES ss236479217 Jul 15, 2010 (132)
14 1000GENOMES ss242926119 Jul 15, 2010 (132)
15 GMI ss281940269 May 04, 2012 (137)
16 GMI ss286812502 Apr 25, 2013 (138)
17 PJP ss291692348 May 09, 2011 (134)
18 TISHKOFF ss563996991 Apr 25, 2013 (138)
19 SSMP ss659660025 Apr 25, 2013 (138)
20 EVA-GONL ss990976189 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1079525450 Aug 21, 2014 (142)
22 1000GENOMES ss1350368662 Aug 21, 2014 (142)
23 DDI ss1427372139 Apr 01, 2015 (144)
24 EVA_GENOME_DK ss1577146227 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1631400657 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1674394690 Apr 01, 2015 (144)
27 EVA_DECODE ss1694967658 Apr 01, 2015 (144)
28 HAMMER_LAB ss1807850552 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1934352372 Feb 12, 2016 (147)
30 GENOMED ss1967924882 Jul 19, 2016 (147)
31 JJLAB ss2027950543 Sep 14, 2016 (149)
32 USC_VALOUEV ss2156322345 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2200666505 Dec 20, 2016 (150)
34 TOPMED ss2364967655 Dec 20, 2016 (150)
35 SYSTEMSBIOZJU ss2628464143 Nov 08, 2017 (151)
36 GRF ss2700738400 Nov 08, 2017 (151)
37 GNOMAD ss2925882071 Nov 08, 2017 (151)
38 SWEGEN ss3011941040 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3027798182 Nov 08, 2017 (151)
40 TOPMED ss3207021100 Nov 08, 2017 (151)
41 CSHL ss3350730708 Nov 08, 2017 (151)
42 EGCUT_WGS ss3679182523 Jul 13, 2019 (153)
43 EVA_DECODE ss3696364452 Jul 13, 2019 (153)
44 ACPOP ss3740239795 Jul 13, 2019 (153)
45 EVA ss3752128928 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3817460623 Jul 13, 2019 (153)
47 EVA ss3833834481 Apr 27, 2020 (154)
48 EVA ss3840509975 Apr 27, 2020 (154)
49 EVA ss3845997898 Apr 27, 2020 (154)
50 SGDP_PRJ ss3881167943 Apr 27, 2020 (154)
51 KRGDB ss3930146026 Apr 27, 2020 (154)
52 KOGIC ss3974618056 Apr 27, 2020 (154)
53 TOPMED ss4965131067 Apr 26, 2021 (155)
54 TOMMO_GENOMICS ss5212514938 Apr 26, 2021 (155)
55 1000Genomes NC_000014.8 - 30174078 Oct 12, 2018 (152)
56 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 30174078 Oct 12, 2018 (152)
57 Genetic variation in the Estonian population NC_000014.8 - 30174078 Oct 12, 2018 (152)
58 The Danish reference pan genome NC_000014.8 - 30174078 Apr 27, 2020 (154)
59 gnomAD - Genomes NC_000014.9 - 29704872 Apr 26, 2021 (155)
60 Genome of the Netherlands Release 5 NC_000014.8 - 30174078 Apr 27, 2020 (154)
61 KOREAN population from KRGDB NC_000014.8 - 30174078 Apr 27, 2020 (154)
62 Korean Genome Project NC_000014.9 - 29704872 Apr 27, 2020 (154)
63 Northern Sweden NC_000014.8 - 30174078 Jul 13, 2019 (153)
64 Qatari NC_000014.8 - 30174078 Apr 27, 2020 (154)
65 SGDP_PRJ NC_000014.8 - 30174078 Apr 27, 2020 (154)
66 Siberian NC_000014.8 - 30174078 Apr 27, 2020 (154)
67 8.3KJPN NC_000014.8 - 30174078 Apr 26, 2021 (155)
68 TopMed NC_000014.9 - 29704872 Apr 26, 2021 (155)
69 UK 10K study - Twins NC_000014.8 - 30174078 Oct 12, 2018 (152)
70 A Vietnamese Genetic Variation Database NC_000014.8 - 30174078 Jul 13, 2019 (153)
71 ALFA NC_000014.9 - 29704872 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35422742, ss89894057, ss108211707, ss113091238, ss118395276, ss167757171, ss169036012, ss206892581, ss281940269, ss286812502, ss291692348, ss1694967658 NC_000014.7:29243828:T:C NC_000014.9:29704871:T:C (self)
63324238, 35174776, 24920771, 3535373, 15712008, 37323420, 13524660, 16394302, 33184923, 8838699, 70484245, 35174776, 7823912, ss226485560, ss236479217, ss242926119, ss563996991, ss659660025, ss990976189, ss1079525450, ss1350368662, ss1427372139, ss1577146227, ss1631400657, ss1674394690, ss1807850552, ss1934352372, ss1967924882, ss2027950543, ss2156322345, ss2364967655, ss2628464143, ss2700738400, ss2925882071, ss3011941040, ss3350730708, ss3679182523, ss3740239795, ss3752128928, ss3833834481, ss3840509975, ss3881167943, ss3930146026, ss5212514938 NC_000014.8:30174077:T:C NC_000014.9:29704871:T:C (self)
446553278, 30996057, 113024478, 180676726, 4636437629, ss2200666505, ss3027798182, ss3207021100, ss3696364452, ss3817460623, ss3845997898, ss3974618056, ss4965131067 NC_000014.9:29704871:T:C NC_000014.9:29704871:T:C (self)
ss70452672, ss103173013, ss133894488 NT_026437.12:11174077:T:C NC_000014.9:29704871:T:C (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 rs28645341

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