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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.

rs534633106

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr20:32358683 (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 / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.015633 (4138/264690, TOPMED)
G=0.00032 (6/18710, ALFA)
G=0.04509 (755/16746, 8.3KJPN) (+ 4 more)
G=0.0174 (87/5008, 1000G)
G=0.0411 (91/2214, KOREAN)
G=0.0320 (56/1748, Korea1K)
C=0.36 (10/28, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ASXL1 : 5 Prime UTR 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 20 NC_000020.11:g.32358683C>A
GRCh38.p13 chr 20 NC_000020.11:g.32358683C>G
GRCh38.p13 chr 20 NC_000020.11:g.32358683C>T
GRCh37.p13 chr 20 NC_000020.10:g.30946486C>A
GRCh37.p13 chr 20 NC_000020.10:g.30946486C>G
GRCh37.p13 chr 20 NC_000020.10:g.30946486C>T
ASXL1 RefSeqGene (LRG_630) NG_027868.1:g.5340C>A
ASXL1 RefSeqGene (LRG_630) NG_027868.1:g.5340C>G
ASXL1 RefSeqGene (LRG_630) NG_027868.1:g.5340C>T
Gene: ASXL1, ASXL transcriptional regulator 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ASXL1 transcript variant 2 NM_001164603.1:c.-93= N/A 5 Prime UTR Variant
ASXL1 transcript variant 1 NM_015338.6:c.-93= N/A 5 Prime UTR Variant
ASXL1 transcript variant 3 NM_001363734.1:c. N/A Genic Upstream Transcript Variant
ASXL1 transcript variant X2 XM_006723727.3:c.-93= N/A 5 Prime UTR Variant
ASXL1 transcript variant X8 XM_017027706.1:c.-93= N/A 5 Prime UTR Variant
ASXL1 transcript variant X3 XM_006723728.3:c. N/A Genic Upstream Transcript Variant
ASXL1 transcript variant X7 XM_006723730.4:c. N/A Genic Upstream Transcript Variant
ASXL1 transcript variant X10 XM_006723733.1:c. N/A Genic Upstream Transcript Variant
ASXL1 transcript variant X1 XM_011528648.3:c. N/A Genic Upstream Transcript Variant
ASXL1 transcript variant X5 XM_011528652.2:c. N/A Genic Upstream Transcript Variant
ASXL1 transcript variant X4 XM_017027704.1:c. N/A Genic Upstream Transcript Variant
ASXL1 transcript variant X6 XM_017027705.1:c. 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
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 18710 C=0.99963 A=0.00005, G=0.00032, T=0.00000
European Sub 14276 C=0.99958 A=0.00007, G=0.00035, T=0.00000
African Sub 2924 C=1.0000 A=0.0000, G=0.0000, T=0.0000
African Others Sub 114 C=1.000 A=0.000, G=0.000, T=0.000
African American Sub 2810 C=1.0000 A=0.0000, G=0.0000, T=0.0000
Asian Sub 110 C=1.000 A=0.000, G=0.000, T=0.000
East Asian Sub 84 C=1.00 A=0.00, G=0.00, T=0.00
Other Asian Sub 26 C=1.00 A=0.00, G=0.00, T=0.00
Latin American 1 Sub 138 C=1.000 A=0.000, G=0.000, T=0.000
Latin American 2 Sub 490 C=1.000 A=0.000, G=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, G=0.00, T=0.00
Other Sub 674 C=0.999 A=0.000, G=0.001, T=0.000


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=0.984367 G=0.015633
8.3KJPN JAPANESE Study-wide 16746 C=0.95491 G=0.04509
1000Genomes Global Study-wide 5008 C=0.9826 G=0.0174
1000Genomes African Sub 1322 C=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 C=0.9891 G=0.0109
1000Genomes Europe Sub 1006 C=1.0000 G=0.0000
1000Genomes South Asian Sub 978 C=0.993 G=0.007
1000Genomes American Sub 694 C=0.901 G=0.099
KOREAN population from KRGDB KOREAN Study-wide 2214 C=0.9589 G=0.0411
Korean Genome Project KOREAN Study-wide 1748 C=0.9680 G=0.0320
SGDP_PRJ Global Study-wide 28 C=0.36 G=0.64
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 G T
GRCh38.p13 chr 20 NC_000020.11:g.32358683= NC_000020.11:g.32358683C>A NC_000020.11:g.32358683C>G NC_000020.11:g.32358683C>T
GRCh37.p13 chr 20 NC_000020.10:g.30946486= NC_000020.10:g.30946486C>A NC_000020.10:g.30946486C>G NC_000020.10:g.30946486C>T
ASXL1 RefSeqGene (LRG_630) NG_027868.1:g.5340= NG_027868.1:g.5340C>A NG_027868.1:g.5340C>G NG_027868.1:g.5340C>T
ASXL1 transcript variant 1 NM_015338.6:c.-93= NM_015338.6:c.-93C>A NM_015338.6:c.-93C>G NM_015338.6:c.-93C>T
ASXL1 transcript variant 1 NM_015338.5:c.-93= NM_015338.5:c.-93C>A NM_015338.5:c.-93C>G NM_015338.5:c.-93C>T
ASXL1 transcript variant 2 NM_001164603.1:c.-93= NM_001164603.1:c.-93C>A NM_001164603.1:c.-93C>G NM_001164603.1:c.-93C>T
ASXL1 transcript variant X2 XM_006723727.3:c.-93= XM_006723727.3:c.-93C>A XM_006723727.3:c.-93C>G XM_006723727.3:c.-93C>T
ASXL1 transcript variant X8 XM_017027706.1:c.-93= XM_017027706.1:c.-93C>A XM_017027706.1:c.-93C>G XM_017027706.1:c.-93C>T
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#.

14 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1364574562 Aug 21, 2014 (142)
2 TOPMED ss2408864217 Dec 20, 2016 (150)
3 GNOMAD ss2966850093 Nov 08, 2017 (151)
4 TOPMED ss3359132911 Nov 08, 2017 (151)
5 TOPMED ss3359132912 Nov 08, 2017 (151)
6 TOPMED ss3359132913 Nov 08, 2017 (151)
7 EVA_DECODE ss3706849208 Jul 13, 2019 (153)
8 KHV_HUMAN_GENOMES ss3821752485 Jul 13, 2019 (153)
9 SGDP_PRJ ss3889002526 Apr 27, 2020 (154)
10 KRGDB ss3939267346 Apr 27, 2020 (154)
11 KOGIC ss3982178209 Apr 27, 2020 (154)
12 EVA ss3986827317 Apr 27, 2021 (155)
13 TOPMED ss5086865793 Apr 27, 2021 (155)
14 TOMMO_GENOMICS ss5229414635 Apr 27, 2021 (155)
15 1000Genomes NC_000020.10 - 30946486 Oct 12, 2018 (152)
16 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 550397889 (NC_000020.11:32358682:C:A 1/134706)
Row 550397890 (NC_000020.11:32358682:C:G 1198/134704)

- Apr 27, 2021 (155)
17 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 550397889 (NC_000020.11:32358682:C:A 1/134706)
Row 550397890 (NC_000020.11:32358682:C:G 1198/134704)

- Apr 27, 2021 (155)
18 KOREAN population from KRGDB NC_000020.10 - 30946486 Apr 27, 2020 (154)
19 Korean Genome Project NC_000020.11 - 32358683 Apr 27, 2020 (154)
20 SGDP_PRJ NC_000020.10 - 30946486 Apr 27, 2020 (154)
21 8.3KJPN NC_000020.10 - 30946486 Apr 27, 2021 (155)
22 TopMed NC_000020.11 - 32358683 Apr 27, 2021 (155)
23 ALFA NC_000020.11 - 32358683 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
ss2966850093 NC_000020.10:30946485:C:A NC_000020.11:32358682:C:A (self)
226028199, 14987889687, ss3359132911 NC_000020.11:32358682:C:A NC_000020.11:32358682:C:A (self)
78030949, 46444740, 41019506, 87383942, ss1364574562, ss2408864217, ss2966850093, ss3889002526, ss3939267346, ss3986827317, ss5229414635 NC_000020.10:30946485:C:G NC_000020.11:32358682:C:G (self)
38556210, 226028199, 361974738, 14987889687, ss3359132912, ss3706849208, ss3821752485, ss3982178209, ss5086865793 NC_000020.11:32358682:C:G NC_000020.11:32358682:C:G (self)
226028199, 14987889687, ss3359132913 NC_000020.11:32358682:C:T NC_000020.11:32358682:C:T (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 rs534633106

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