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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.

rs1482800155

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:3785265-3785274 (GRCh38.p14) 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
delTCCCTC
Variation Type
Indel Insertion and Deletion
Frequency
delTCCCTC=0.000015 (4/264690, TOPMED)
delTCCCTC=0.000022 (3/138398, GnomAD)
delTCCCTC=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CENPB : Inframe Deletion
CDC25B : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 14050 CCTCTCCCTC=1.00000 CCTC=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 CCTCTCCCTC=1.0000 CCTC=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 CCTCTCCCTC=1.0000 CCTC=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 CCTCTCCCTC=1.000 CCTC=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 CCTCTCCCTC=1.0000 CCTC=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 CCTCTCCCTC=1.000 CCTC=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 CCTCTCCCTC=1.00 CCTC=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 CCTCTCCCTC=1.00 CCTC=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 CCTCTCCCTC=1.000 CCTC=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 CCTCTCCCTC=1.000 CCTC=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 CCTCTCCCTC=1.00 CCTC=0.00 1.0 0.0 0.0 N/A
Other Sub 496 CCTCTCCCTC=1.000 CCTC=0.000 1.0 0.0 0.0 N/A


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 CCTCTCCCTC=0.999985 delTCCCTC=0.000015
gnomAD - Genomes Global Study-wide 138398 CCTCTCCCTC=0.999978 delTCCCTC=0.000022
gnomAD - Genomes European Sub 74946 CCTCTCCCTC=1.00000 delTCCCTC=0.00000
gnomAD - Genomes African Sub 41500 CCTCTCCCTC=0.99993 delTCCCTC=0.00007
gnomAD - Genomes American Sub 13446 CCTCTCCCTC=1.00000 delTCCCTC=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3282 CCTCTCCCTC=1.0000 delTCCCTC=0.0000
gnomAD - Genomes East Asian Sub 3092 CCTCTCCCTC=1.0000 delTCCCTC=0.0000
gnomAD - Genomes Other Sub 2132 CCTCTCCCTC=1.0000 delTCCCTC=0.0000
Allele Frequency Aggregator Total Global 14050 CCTCTCCCTC=1.00000 delTCCCTC=0.00000
Allele Frequency Aggregator European Sub 9690 CCTCTCCCTC=1.0000 delTCCCTC=0.0000
Allele Frequency Aggregator African Sub 2898 CCTCTCCCTC=1.0000 delTCCCTC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 CCTCTCCCTC=1.000 delTCCCTC=0.000
Allele Frequency Aggregator Other Sub 496 CCTCTCCCTC=1.000 delTCCCTC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 CCTCTCCCTC=1.000 delTCCCTC=0.000
Allele Frequency Aggregator Asian Sub 112 CCTCTCCCTC=1.000 delTCCCTC=0.000
Allele Frequency Aggregator South Asian Sub 98 CCTCTCCCTC=1.00 delTCCCTC=0.00
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.p14 chr 20 NC_000020.11:g.3785269_3785274del
GRCh37.p13 chr 20 NC_000020.10:g.3765916_3765921del
CDC25B RefSeqGene NG_029040.2:g.3498_3503del
Gene: CDC25B, cell division cycle 25B (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
CDC25B transcript variant 4 NM_001287516.2:c. N/A Upstream Transcript Variant
CDC25B transcript variant 5 NM_001287517.2:c. N/A Upstream Transcript Variant
CDC25B transcript variant 6 NM_001287518.2:c. N/A Upstream Transcript Variant
CDC25B transcript variant 7 NM_001287519.2:c. N/A N/A
CDC25B transcript variant 8 NM_001287520.2:c. N/A N/A
CDC25B transcript variant 9 NM_001287522.2:c. N/A N/A
CDC25B transcript variant 10 NM_001287524.2:c. N/A N/A
CDC25B transcript variant 2 NM_004358.5:c. N/A N/A
CDC25B transcript variant 3 NM_021872.4:c. N/A N/A
CDC25B transcript variant 1 NM_021873.4:c. N/A N/A
CDC25B transcript variant 12 NR_136336.2:n. N/A Upstream Transcript Variant
CDC25B transcript variant 11 NR_136335.2:n. N/A N/A
CDC25B transcript variant X1 XM_047440628.1:c. N/A N/A
Gene: CENPB, centromere protein B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CENPB transcript NM_001810.6:c.1214_1219del EGE [GGAG] > E [GAA] Coding Sequence Variant
major centromere autoantigen B NP_001801.1:p.Gly405_Glu4…

NP_001801.1:p.Gly405_Glu406del

EGE (GluGlyGlu) > E (Glu) Inframe Deletion
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
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 CCTCTCCCTC= delTCCCTC
GRCh38.p14 chr 20 NC_000020.11:g.3785265_3785274= NC_000020.11:g.3785269_3785274del
GRCh37.p13 chr 20 NC_000020.10:g.3765912_3765921= NC_000020.10:g.3765916_3765921del
CDC25B RefSeqGene NG_029040.2:g.3494_3503= NG_029040.2:g.3498_3503del
CENPB transcript NM_001810.6:c.1210_1219= NM_001810.6:c.1214_1219del
CENPB transcript NM_001810.5:c.1210_1219= NM_001810.5:c.1214_1219del
major centromere autoantigen B NP_001801.1:p.Glu404_Glu407= NP_001801.1:p.Gly405_Glu406del
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#.

3 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2750333339 Nov 08, 2017 (151)
2 GNOMAD ss2964904418 Nov 08, 2017 (151)
3 TOPMED ss5080645362 Apr 27, 2021 (155)
4 gnomAD - Genomes NC_000020.11 - 3785265 Apr 27, 2021 (155)
5 TopMed NC_000020.11 - 3785265 Apr 27, 2021 (155)
6 ALFA NC_000020.11 - 3785265 Apr 27, 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
ss2750333339, ss2964904418 NC_000020.10:3765911:CCTCTC: NC_000020.11:3785264:CCTCTCCCTC:CC…

NC_000020.11:3785264:CCTCTCCCTC:CCTC

(self)
545142735, 355754307, ss5080645362 NC_000020.11:3785264:CCTCTC: NC_000020.11:3785264:CCTCTCCCTC:CC…

NC_000020.11:3785264:CCTCTCCCTC:CCTC

(self)
6902347497 NC_000020.11:3785264:CCTCTCCCTC:CC…

NC_000020.11:3785264:CCTCTCCCTC:CCTC

NC_000020.11:3785264:CCTCTCCCTC:CC…

NC_000020.11:3785264:CCTCTCCCTC:CCTC

(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 rs1482800155

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.post820+afb47a3d