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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.

rs60561655

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1075708-1075712 (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
delG
Variation Type
Indel Insertion and Deletion
Frequency
(G)5=0.466912 (58026/124276, GnomAD)
(G)5=0.19189 (3145/16390, 8.3KJPN)
delG=0.47942 (7781/16230, ALFA) (+ 4 more)
(G)5=0.4587 (2297/5008, 1000G)
(G)5=0.4071 (1569/3854, ALSPAC)
(G)5=0.4150 (1539/3708, TWINSUK)
(G)5=0.473 (278/588, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RNF223 : 2KB Upstream 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.1075712del
GRCh37.p13 chr 1 NC_000001.10:g.1011092del
Gene: RNF223, ring finger protein 223 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
RNF223 transcript NM_001205252.2:c. N/A 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 16230 GGGGG=0.52058 GGGG=0.47942
European Sub 11978 GGGGG=0.48990 GGGG=0.51010
African Sub 2816 GGGGG=0.6928 GGGG=0.3072
African Others Sub 108 GGGGG=0.713 GGGG=0.287
African American Sub 2708 GGGGG=0.6920 GGGG=0.3080
Asian Sub 108 GGGGG=0.324 GGGG=0.676
East Asian Sub 84 GGGGG=0.30 GGGG=0.70
Other Asian Sub 24 GGGGG=0.42 GGGG=0.58
Latin American 1 Sub 146 GGGGG=0.507 GGGG=0.493
Latin American 2 Sub 610 GGGGG=0.379 GGGG=0.621
South Asian Sub 94 GGGGG=0.39 GGGG=0.61
Other Sub 478 GGGGG=0.529 GGGG=0.471


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
gnomAD - Genomes Global Study-wide 124276 (G)5=0.466912 delG=0.533088
gnomAD - Genomes European Sub 70220 (G)5=0.42904 delG=0.57096
gnomAD - Genomes African Sub 33230 (G)5=0.63250 delG=0.36750
gnomAD - Genomes American Sub 12702 (G)5=0.32404 delG=0.67596
gnomAD - Genomes Ashkenazi Jewish Sub 3210 (G)5=0.3966 delG=0.6034
gnomAD - Genomes East Asian Sub 2992 (G)5=0.2226 delG=0.7774
gnomAD - Genomes Other Sub 1922 (G)5=0.4298 delG=0.5702
8.3KJPN JAPANESE Study-wide 16390 (G)5=0.19189 delG=0.80811
1000Genomes Global Study-wide 5008 (G)5=0.4587 delG=0.5413
1000Genomes African Sub 1322 (G)5=0.7345 delG=0.2655
1000Genomes East Asian Sub 1008 (G)5=0.2083 delG=0.7917
1000Genomes Europe Sub 1006 (G)5=0.4354 delG=0.5646
1000Genomes South Asian Sub 978 (G)5=0.455 delG=0.545
1000Genomes American Sub 694 (G)5=0.336 delG=0.664
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 (G)5=0.4071 delG=0.5929
UK 10K study - Twins TWIN COHORT Study-wide 3708 (G)5=0.4150 delG=0.5850
Northern Sweden ACPOP Study-wide 588 (G)5=0.473 delG=0.527
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)5= delG
GRCh38.p13 chr 1 NC_000001.11:g.1075708_1075712= NC_000001.11:g.1075712del
GRCh37.p13 chr 1 NC_000001.10:g.1011088_1011092= NC_000001.10:g.1011092del
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#.

34 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss81579218 Sep 08, 2015 (146)
2 BUSHMAN ss193082063 Jul 04, 2010 (137)
3 BL ss255892847 May 09, 2011 (137)
4 1000GENOMES ss325997184 May 09, 2011 (137)
5 1000GENOMES ss325997308 May 09, 2011 (137)
6 1000GENOMES ss325997748 May 09, 2011 (137)
7 1000GENOMES ss498763978 May 04, 2012 (137)
8 LUNTER ss550899269 Apr 25, 2013 (138)
9 LUNTER ss550903259 Apr 25, 2013 (138)
10 LUNTER ss552739233 Apr 25, 2013 (138)
11 TISHKOFF ss553708591 Apr 25, 2013 (138)
12 SSMP ss663103706 Apr 01, 2015 (144)
13 1000GENOMES ss1367645797 Aug 21, 2014 (142)
14 DDI ss1536213979 Apr 01, 2015 (144)
15 EVA_UK10K_ALSPAC ss1700145896 Apr 01, 2015 (144)
16 EVA_UK10K_TWINSUK ss1700154863 Apr 01, 2015 (144)
17 HAMMER_LAB ss1793716333 Sep 08, 2015 (146)
18 JJLAB ss2030297866 Sep 14, 2016 (149)
19 SYSTEMSBIOZJU ss2624265423 Nov 08, 2017 (151)
20 MCHAISSO ss3063573622 Nov 08, 2017 (151)
21 MCHAISSO ss3064386191 Nov 08, 2017 (151)
22 TOPMED ss3066462020 Nov 08, 2017 (151)
23 BEROUKHIMLAB ss3644051581 Oct 11, 2018 (152)
24 EVA_DECODE ss3685997196 Jul 12, 2019 (153)
25 ACPOP ss3726718380 Jul 12, 2019 (153)
26 PACBIO ss3783302979 Jul 12, 2019 (153)
27 PACBIO ss3788980714 Jul 12, 2019 (153)
28 PACBIO ss3793853258 Jul 12, 2019 (153)
29 KHV_HUMAN_GENOMES ss3798746460 Jul 12, 2019 (153)
30 EVA ss3825982451 Apr 25, 2020 (154)
31 EVA ss3836378978 Apr 25, 2020 (154)
32 EVA ss3841783008 Apr 25, 2020 (154)
33 GNOMAD ss3986964230 Apr 25, 2021 (155)
34 TOMMO_GENOMICS ss5142064823 Apr 25, 2021 (155)
35 1000Genomes NC_000001.10 - 1011088 Oct 11, 2018 (152)
36 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1011088 Oct 11, 2018 (152)
37 gnomAD - Genomes NC_000001.11 - 1075708 Apr 25, 2021 (155)
38 Northern Sweden NC_000001.10 - 1011088 Jul 12, 2019 (153)
39 8.3KJPN NC_000001.10 - 1011088 Apr 25, 2021 (155)
40 UK 10K study - Twins NC_000001.10 - 1011088 Oct 11, 2018 (152)
41 ALFA NC_000001.11 - 1075708 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).

Associated ID History Updated (Build)
rs112602142 May 11, 2012 (137)
rs149405692 May 04, 2012 (137)
rs372977333 May 15, 2013 (138)
rs375545205 May 13, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81579218 NC_000001.8:1051014:G: NC_000001.11:1075707:GGGGG:GGGG (self)
ss255892847, ss325997184, ss325997308, ss325997748, ss550899269, ss550903259, ss552739233 NC_000001.9:1000950:G: NC_000001.11:1075707:GGGGG:GGGG (self)
13827, 4161, 3245, 34130, 4161, ss498763978, ss663103706, ss1367645797, ss1536213979, ss1700145896, ss1700154863, ss1793716333, ss2030297866, ss2624265423, ss3644051581, ss3726718380, ss3783302979, ss3788980714, ss3793853258, ss3825982451, ss3836378978, ss5142064823 NC_000001.10:1011087:G: NC_000001.11:1075707:GGGGG:GGGG (self)
ss553708591 NC_000001.10:1011091:G: NC_000001.11:1075707:GGGGG:GGGG (self)
131330, ss3063573622, ss3064386191, ss3066462020, ss3685997196, ss3798746460, ss3841783008, ss3986964230 NC_000001.11:1075707:G: NC_000001.11:1075707:GGGGG:GGGG (self)
5748178753 NC_000001.11:1075707:GGGGG:GGGG NC_000001.11:1075707:GGGGG:GGGG
ss193082063 NT_032977.10:489719:G: NC_000001.11:1075707:GGGGG:GGGG (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 rs60561655

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