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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.

rs114834790

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:11649835 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000491 (130/264690, TOPMED)
A=0.000123 (31/251190, GnomAD_exome)
A=0.000449 (63/140276, GnomAD) (+ 5 more)
A=0.000174 (21/120970, ExAC)
A=0.00004 (4/98252, ALFA)
A=0.00043 (34/78696, PAGE_STUDY)
A=0.00038 (5/13006, GO-ESP)
A=0.0004 (2/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FBXO2 : 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.11649835C>A
GRCh37.p13 chr 1 NC_000001.10:g.11709892C>A
Gene: FBXO2, F-box protein 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FBXO2 transcript NM_012168.6:c.561G>T E [GAG] > D [GAT] Coding Sequence Variant
F-box only protein 2 NP_036300.2:p.Glu187Asp E (Glu) > D (Asp) Missense 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 98252 C=0.99996 A=0.00004
European Sub 87082 C=0.99998 A=0.00002
African Sub 3492 C=0.9994 A=0.0006
African Others Sub 116 C=1.000 A=0.000
African American Sub 3376 C=0.9994 A=0.0006
Asian Sub 176 C=1.000 A=0.000
East Asian Sub 124 C=1.000 A=0.000
Other Asian Sub 52 C=1.00 A=0.00
Latin American 1 Sub 152 C=1.000 A=0.000
Latin American 2 Sub 632 C=1.000 A=0.000
South Asian Sub 104 C=1.000 A=0.000
Other Sub 6614 C=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 C=0.999509 A=0.000491
gnomAD - Exomes Global Study-wide 251190 C=0.999877 A=0.000123
gnomAD - Exomes European Sub 135174 C=0.999993 A=0.000007
gnomAD - Exomes Asian Sub 49002 C=1.00000 A=0.00000
gnomAD - Exomes American Sub 34578 C=0.99994 A=0.00006
gnomAD - Exomes African Sub 16236 C=0.99828 A=0.00172
gnomAD - Exomes Ashkenazi Jewish Sub 10064 C=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6136 C=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140276 C=0.999551 A=0.000449
gnomAD - Genomes European Sub 75960 C=1.00000 A=0.00000
gnomAD - Genomes African Sub 42054 C=0.99860 A=0.00140
gnomAD - Genomes American Sub 13660 C=0.99978 A=0.00022
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3130 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 C=0.9995 A=0.0005
ExAC Global Study-wide 120970 C=0.999826 A=0.000174
ExAC Europe Sub 73076 C=1.00000 A=0.00000
ExAC Asian Sub 25126 C=1.00000 A=0.00000
ExAC American Sub 11544 C=1.00000 A=0.00000
ExAC African Sub 10320 C=0.99797 A=0.00203
ExAC Other Sub 904 C=1.000 A=0.000
The PAGE Study Global Study-wide 78696 C=0.99957 A=0.00043
The PAGE Study AfricanAmerican Sub 32512 C=0.99902 A=0.00098
The PAGE Study Mexican Sub 10810 C=1.00000 A=0.00000
The PAGE Study Asian Sub 8318 C=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 A=0.0000
The PAGE Study Cuban Sub 4228 C=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 C=0.9997 A=0.0003
The PAGE Study CentralAmerican Sub 2450 C=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 C=0.9995 A=0.0005
The PAGE Study NativeAmerican Sub 1260 C=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99962 A=0.00038
GO Exome Sequencing Project European American Sub 8600 C=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9989 A=0.0011
1000Genomes Global Study-wide 5008 C=0.9996 A=0.0004
1000Genomes African Sub 1322 C=0.9985 A=0.0015
1000Genomes East Asian Sub 1008 C=1.0000 A=0.0000
1000Genomes Europe Sub 1006 C=1.0000 A=0.0000
1000Genomes South Asian Sub 978 C=1.000 A=0.000
1000Genomes American Sub 694 C=1.000 A=0.000
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= A
GRCh38.p13 chr 1 NC_000001.11:g.11649835= NC_000001.11:g.11649835C>A
GRCh37.p13 chr 1 NC_000001.10:g.11709892= NC_000001.10:g.11709892C>A
FBXO2 transcript NM_012168.6:c.561= NM_012168.6:c.561G>T
FBXO2 transcript NM_012168.5:c.561= NM_012168.5:c.561G>T
F-box only protein 2 NP_036300.2:p.Glu187= NP_036300.2:p.Glu187Asp
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#.

33 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217405862 Jul 14, 2010 (132)
2 NHLBI-ESP ss341932876 May 09, 2011 (134)
3 1000GENOMES ss488651931 May 04, 2012 (137)
4 EXOME_CHIP ss491286195 May 04, 2012 (137)
5 ILLUMINA ss780747641 Sep 08, 2015 (146)
6 ILLUMINA ss783425468 Sep 08, 2015 (146)
7 1000GENOMES ss1289696545 Aug 21, 2014 (142)
8 EVA_EXAC ss1685301705 Apr 01, 2015 (144)
9 ILLUMINA ss1751865781 Sep 08, 2015 (146)
10 ILLUMINA ss1917722666 Feb 12, 2016 (147)
11 ILLUMINA ss1945984695 Feb 12, 2016 (147)
12 ILLUMINA ss1958241445 Feb 12, 2016 (147)
13 HUMAN_LONGEVITY ss2160076975 Dec 20, 2016 (150)
14 TOPMED ss2322234681 Dec 20, 2016 (150)
15 GNOMAD ss2731117034 Nov 08, 2017 (151)
16 GNOMAD ss2746214259 Nov 08, 2017 (151)
17 GNOMAD ss2751661182 Nov 08, 2017 (151)
18 AFFY ss2984845246 Nov 08, 2017 (151)
19 ILLUMINA ss3021054490 Nov 08, 2017 (151)
20 TOPMED ss3068682713 Nov 08, 2017 (151)
21 ILLUMINA ss3626026719 Oct 11, 2018 (152)
22 ILLUMINA ss3634306929 Oct 11, 2018 (152)
23 ILLUMINA ss3640014293 Oct 11, 2018 (152)
24 ILLUMINA ss3644480549 Oct 11, 2018 (152)
25 ILLUMINA ss3651378438 Oct 11, 2018 (152)
26 ILLUMINA ss3653618878 Oct 11, 2018 (152)
27 ILLUMINA ss3724996586 Jul 12, 2019 (153)
28 ILLUMINA ss3744339274 Jul 12, 2019 (153)
29 ILLUMINA ss3744607911 Jul 12, 2019 (153)
30 PAGE_CC ss3770785634 Jul 12, 2019 (153)
31 ILLUMINA ss3772109523 Jul 12, 2019 (153)
32 EVA ss3823559773 Apr 25, 2020 (154)
33 TOPMED ss4439338550 Apr 25, 2021 (155)
34 1000Genomes NC_000001.10 - 11709892 Oct 11, 2018 (152)
35 ExAC NC_000001.10 - 11709892 Oct 11, 2018 (152)
36 gnomAD - Genomes NC_000001.11 - 11649835 Apr 25, 2021 (155)
37 gnomAD - Exomes NC_000001.10 - 11709892 Jul 12, 2019 (153)
38 GO Exome Sequencing Project NC_000001.10 - 11709892 Oct 11, 2018 (152)
39 The PAGE Study NC_000001.11 - 11649835 Jul 12, 2019 (153)
40 TopMed NC_000001.11 - 11649835 Apr 25, 2021 (155)
41 ALFA NC_000001.11 - 11649835 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
ss217405862 NC_000001.9:11632478:C:A NC_000001.11:11649834:C:A (self)
373078, 4480974, 133357, 18501, ss341932876, ss488651931, ss491286195, ss780747641, ss783425468, ss1289696545, ss1685301705, ss1751865781, ss1917722666, ss1945984695, ss1958241445, ss2322234681, ss2731117034, ss2746214259, ss2751661182, ss2984845246, ss3021054490, ss3626026719, ss3634306929, ss3640014293, ss3644480549, ss3651378438, ss3653618878, ss3744339274, ss3744607911, ss3772109523, ss3823559773 NC_000001.10:11709891:C:A NC_000001.11:11649834:C:A (self)
2597195, 7103, 1852918, 2944885, 3190131291, ss2160076975, ss3068682713, ss3724996586, ss3770785634, ss4439338550 NC_000001.11:11649834:C:A NC_000001.11:11649834:C: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 rs114834790

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