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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.

rs202245468

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:263836-263837 (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
delCT
Variation Type
Deletion
Frequency
delCT=0.05747 (4160/72388, GnomAD)
delCT=0.14241 (2335/16396, 8.3KJPN)
delCT=0.05637 (920/16322, ALFA) (+ 2 more)
delCT=0.028 (17/600, NorthernSweden)
delCT=0.03 (1/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC100996442 : 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 1 NC_000001.11:g.263836_263837del
GRCh37.p13 chr 1 NC_000001.10:g.233587_233588del
Gene: LOC100996442, uncharacterized LOC100996442 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC100996442 transcript variant X12 XR_001737582.2:n. N/A Intron Variant
LOC100996442 transcript variant X4 XR_001737578.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X5 XR_001737579.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X8 XR_001737580.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X11 XR_001737581.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X13 XR_001737583.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X14 XR_001737584.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X1 XR_002958514.1:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X2 XR_002958515.1:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X3 XR_002958516.1:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X6 XR_002958517.1:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X7 XR_002958518.1:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X9 XR_002958519.1:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X10 XR_002958520.1:n. 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 (New)
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 16322 CT=0.94363 =0.05637
European Sub 12070 CT=0.94126 =0.05874
African Sub 2816 CT=0.9585 =0.0415
African Others Sub 108 CT=0.981 =0.019
African American Sub 2708 CT=0.9575 =0.0425
Asian Sub 108 CT=0.954 =0.046
East Asian Sub 84 CT=0.94 =0.06
Other Asian Sub 24 CT=1.00 =0.00
Latin American 1 Sub 146 CT=0.932 =0.068
Latin American 2 Sub 610 CT=0.948 =0.052
South Asian Sub 94 CT=0.78 =0.22
Other Sub 478 CT=0.946 =0.054


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 72388 CT=0.94253 delCT=0.05747
gnomAD - Genomes European Sub 42944 CT=0.93813 delCT=0.06187
gnomAD - Genomes African Sub 18742 CT=0.95902 delCT=0.04098
gnomAD - Genomes American Sub 6046 CT=0.9337 delCT=0.0663
gnomAD - Genomes Ashkenazi Jewish Sub 2216 CT=0.9549 delCT=0.0451
gnomAD - Genomes East Asian Sub 1434 CT=0.8891 delCT=0.1109
gnomAD - Genomes Other Sub 1006 CT=0.9254 delCT=0.0746
8.3KJPN JAPANESE Study-wide 16396 CT=0.85759 delCT=0.14241
Northern Sweden ACPOP Study-wide 600 CT=0.972 delCT=0.028
The Danish reference pan genome Danish Study-wide 40 CT=0.97 delCT=0.03
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 CT= delCT
GRCh38.p13 chr 1 NC_000001.11:g.263836_263837= NC_000001.11:g.263836_263837del
GRCh37.p13 chr 1 NC_000001.10:g.233587_233588= NC_000001.10:g.233587_233588del
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#.

10 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss498763772 May 04, 2012 (137)
2 EVA_GENOME_DK ss1573867139 Apr 01, 2015 (144)
3 EVA_DECODE ss1584129273 Apr 01, 2015 (144)
4 JJLAB ss2030297681 Sep 14, 2016 (149)
5 GNOMAD ss2750613893 Nov 08, 2017 (151)
6 SWEGEN ss2986143974 Nov 08, 2017 (151)
7 TOPMED ss3066346314 Nov 08, 2017 (151)
8 EVA_DECODE ss3685991038 Jul 12, 2019 (153)
9 ACPOP ss3726715480 Jul 12, 2019 (153)
10 TOMMO_GENOMICS ss5142038978 Apr 25, 2021 (155)
11 The Danish reference pan genome NC_000001.10 - 233587 Apr 25, 2020 (154)
12 gnomAD - Genomes NC_000001.11 - 263836 Apr 25, 2021 (155)
13 Northern Sweden NC_000001.10 - 233587 Jul 12, 2019 (153)
14 8.3KJPN NC_000001.10 - 233587 Apr 25, 2021 (155)
15 ALFA NC_000001.11 - 263836 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
ss1584129273 NC_000001.9:223449:CT: NC_000001.11:263835:CT: (self)
120160, 345, 8285, ss498763772, ss1573867139, ss2030297681, ss2750613893, ss2986143974, ss3726715480, ss5142038978 NC_000001.10:233586:CT: NC_000001.11:263835:CT: (self)
24253, 7488666164, ss3066346314, ss3685991038 NC_000001.11:263835:CT: NC_000001.11:263835:CT: (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 rs202245468

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