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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.

rs2064

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr6:20617285 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.14136 (3505/24794, ALFA)
T=0.18 (17/94, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CDKAL1 : 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 6 NC_000006.12:g.20617285A>G
GRCh38.p13 chr 6 NC_000006.12:g.20617285A>T
GRCh37.p13 chr 6 NC_000006.11:g.20617516A>G
GRCh37.p13 chr 6 NC_000006.11:g.20617516A>T
CDKAL1 RefSeqGene NG_021195.2:g.87829A>G
CDKAL1 RefSeqGene NG_021195.2:g.87829A>T
Gene: CDKAL1, CDK5 regulatory subunit associated protein 1 like 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CDKAL1 transcript NM_017774.3:c.287-32008A>G N/A Intron Variant
CDKAL1 transcript variant X7 XM_011514718.1:c.287-3200…

XM_011514718.1:c.287-32008A>G

N/A Intron Variant
CDKAL1 transcript variant X8 XM_011514719.2:c.287-3200…

XM_011514719.2:c.287-32008A>G

N/A Intron Variant
CDKAL1 transcript variant X9 XM_017010986.1:c.287-3200…

XM_017010986.1:c.287-32008A>G

N/A Intron Variant
CDKAL1 transcript variant X12 XM_017010987.1:c.-468-320…

XM_017010987.1:c.-468-32008A>G

N/A Intron Variant
CDKAL1 transcript variant X2 XM_024446481.1:c.287-3200…

XM_024446481.1:c.287-32008A>G

N/A Intron Variant
CDKAL1 transcript variant X4 XR_001743495.2:n. N/A Intron Variant
CDKAL1 transcript variant X5 XR_001743496.2:n. N/A Intron Variant
CDKAL1 transcript variant X13 XR_001743500.1:n. N/A Intron Variant
CDKAL1 transcript variant X14 XR_001743501.1:n. N/A Intron Variant
CDKAL1 transcript variant X1 XR_926265.2:n. N/A Intron Variant
CDKAL1 transcript variant X3 XR_926266.2:n. N/A Intron Variant
CDKAL1 transcript variant X6 XR_926267.2:n. N/A Intron Variant
CDKAL1 transcript variant X10 XR_001743498.2:n. N/A Genic Upstream Transcript Variant
CDKAL1 transcript variant X11 XR_001743499.2: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
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 22691 A=0.84553 G=0.15447, T=0.00000
European Sub 18519 A=0.83390 G=0.16610, T=0.00000
African Sub 2285 A=0.9873 G=0.0127, T=0.0000
African Others Sub 104 A=1.000 G=0.000, T=0.000
African American Sub 2181 A=0.9867 G=0.0133, T=0.0000
Asian Sub 39 A=0.79 G=0.21, T=0.00
East Asian Sub 34 A=0.79 G=0.21, T=0.00
Other Asian Sub 5 A=0.8 G=0.2, T=0.0
Latin American 1 Sub 92 A=0.96 G=0.04, T=0.00
Latin American 2 Sub 284 A=0.923 G=0.077, T=0.000
South Asian Sub 55 A=0.91 G=0.09, T=0.00
Other Sub 1417 A=0.7452 G=0.2548, T=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
SGDP_PRJ Global Study-wide 94 A=0.05 G=0.77, T=0.18
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 A= G T
GRCh38.p13 chr 6 NC_000006.12:g.20617285= NC_000006.12:g.20617285A>G NC_000006.12:g.20617285A>T
GRCh37.p13 chr 6 NC_000006.11:g.20617516= NC_000006.11:g.20617516A>G NC_000006.11:g.20617516A>T
CDKAL1 RefSeqGene NG_021195.2:g.87829= NG_021195.2:g.87829A>G NG_021195.2:g.87829A>T
CDKAL1 transcript NM_017774.3:c.287-32008= NM_017774.3:c.287-32008A>G NM_017774.3:c.287-32008A>T
CDKAL1 transcript variant X1 XM_005249201.1:c.287-32008= XM_005249201.1:c.287-32008A>G XM_005249201.1:c.287-32008A>T
CDKAL1 transcript variant X2 XM_005249202.1:c.77-32008= XM_005249202.1:c.77-32008A>G XM_005249202.1:c.77-32008A>T
CDKAL1 transcript variant X3 XM_005249203.1:c.287-32008= XM_005249203.1:c.287-32008A>G XM_005249203.1:c.287-32008A>T
CDKAL1 transcript variant X7 XM_011514718.1:c.287-32008= XM_011514718.1:c.287-32008A>G XM_011514718.1:c.287-32008A>T
CDKAL1 transcript variant X8 XM_011514719.2:c.287-32008= XM_011514719.2:c.287-32008A>G XM_011514719.2:c.287-32008A>T
CDKAL1 transcript variant X9 XM_017010986.1:c.287-32008= XM_017010986.1:c.287-32008A>G XM_017010986.1:c.287-32008A>T
CDKAL1 transcript variant X12 XM_017010987.1:c.-468-32008= XM_017010987.1:c.-468-32008A>G XM_017010987.1:c.-468-32008A>T
CDKAL1 transcript variant X2 XM_024446481.1:c.287-32008= XM_024446481.1:c.287-32008A>G XM_024446481.1:c.287-32008A>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#.

17 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF ss2090 Sep 19, 2000 (36)
2 GMI ss278679179 May 04, 2012 (136)
3 ILLUMINA ss410860789 Sep 17, 2011 (136)
4 ILLUMINA ss482836513 May 04, 2012 (136)
5 ILLUMINA ss485212665 May 04, 2012 (136)
6 ILLUMINA ss534789764 Sep 08, 2015 (146)
7 ILLUMINA ss780081005 Aug 21, 2014 (142)
8 ILLUMINA ss781893890 Aug 21, 2014 (142)
9 ILLUMINA ss835563009 Aug 21, 2014 (142)
10 ILLUMINA ss2094948910 Dec 20, 2016 (150)
11 ILLUMINA ss2095170931 Dec 20, 2016 (150)
12 ILLUMINA ss2634409634 Nov 08, 2017 (151)
13 ILLUMINA ss3629460204 Oct 12, 2018 (152)
14 ILLUMINA ss3632329407 Oct 12, 2018 (152)
15 ILLUMINA ss3642478411 Oct 12, 2018 (152)
16 ILLUMINA ss3653090231 Oct 12, 2018 (152)
17 SGDP_PRJ ss3864061369 Apr 26, 2020 (154)
18 SGDP_PRJ NC_000006.11 - 20617516 Apr 26, 2020 (154)
19 ALFA NC_000006.12 - 20617285 Apr 26, 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)
rs361529 Sep 19, 2000 (85)
rs59427534 May 25, 2008 (130)
rs184012394 Jan 11, 2013 (136)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss278679179, ss410860789, ss485212665, ss2094948910 NC_000006.10:20725494:A:G NC_000006.12:20617284:A:G (self)
16078349, ss482836513, ss534789764, ss780081005, ss781893890, ss835563009, ss2095170931, ss2634409634, ss3629460204, ss3632329407, ss3642478411, ss3653090231, ss3864061369 NC_000006.11:20617515:A:G NC_000006.12:20617284:A:G (self)
8497124609 NC_000006.12:20617284:A:G NC_000006.12:20617284:A:G (self)
ss2090 NT_007592.15:20557515:A:G NC_000006.12:20617284:A:G (self)
ss278679179 NC_000006.10:20725494:A:T NC_000006.12:20617284:A:T (self)
16078349, ss3864061369 NC_000006.11:20617515:A:T NC_000006.12:20617284:A:T (self)
8497124609 NC_000006.12:20617284:A:T NC_000006.12:20617284:A:T
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 rs2064

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