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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.

rs397706189

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr2:29193160-29193163 (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
dupATTG
Variation Type
Indel Insertion and Deletion
Frequency
dupATTG=0.274804 (72738/264690, TOPMED)
dupATTG=0.252653 (35330/139836, GnomAD)
ATTG=0.29135 (4883/16760, 8.3KJPN) (+ 9 more)
dupATTG=0.23272 (3818/16406, ALFA)
dupATTG=0.3972 (1989/5008, 1000G)
dupATTG=0.2228 (998/4480, Estonian)
dupATTG=0.2237 (862/3854, ALSPAC)
dupATTG=0.1998 (741/3708, TWINSUK)
ATTG=0.2724 (499/1832, Korea1K)
dupATTG=0.258 (257/998, GoNL)
dupATTG=0.268 (161/600, NorthernSweden)
dupATTG=0.35 (14/40, GENOME_DK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ALK : 3 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 2 NC_000002.12:g.29193160_29193163dup
GRCh37.p13 chr 2 NC_000002.11:g.29416026_29416029dup
ALK RefSeqGene (LRG_488) NG_009445.1:g.733404_733407dup
Gene: ALK, ALK receptor tyrosine kinase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ALK transcript variant 1 NM_004304.5:c.*61_*64= N/A 3 Prime UTR Variant
ALK transcript variant 2 NM_001353765.2:c.*61_*64= N/A 3 Prime UTR Variant
ALK transcript variant X2 XM_024452778.1:c.*61_*64= N/A 3 Prime UTR Variant
ALK transcript variant X3 XM_024452779.1:c.*61_*64= N/A 3 Prime UTR Variant
ALK transcript variant X1 XR_001738688.2:n. N/A Genic Downstream 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.

Allele: dupATTG (allele ID: 288960 )
ClinVar Accession Disease Names Clinical Significance
RCV000277801.1 Neuroblastoma Susceptibility Benign

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 16406 ATTG=0.76728 ATTGATTG=0.23272
European Sub 12130 ATTG=0.78269 ATTGATTG=0.21731
African Sub 2830 ATTG=0.7986 ATTGATTG=0.2014
African Others Sub 108 ATTG=0.806 ATTGATTG=0.194
African American Sub 2722 ATTG=0.7983 ATTGATTG=0.2017
Asian Sub 108 ATTG=0.231 ATTGATTG=0.769
East Asian Sub 84 ATTG=0.21 ATTGATTG=0.79
Other Asian Sub 24 ATTG=0.29 ATTGATTG=0.71
Latin American 1 Sub 146 ATTG=0.774 ATTGATTG=0.226
Latin American 2 Sub 610 ATTG=0.480 ATTGATTG=0.520
South Asian Sub 94 ATTG=0.57 ATTGATTG=0.43
Other Sub 488 ATTG=0.715 ATTGATTG=0.285


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 -

No frequency provided

dupATTG=0.274804
gnomAD - Genomes Global Study-wide 139836 -

No frequency provided

dupATTG=0.252653
gnomAD - Genomes European Sub 75784 -

No frequency provided

dupATTG=0.23326
gnomAD - Genomes African Sub 41900 -

No frequency provided

dupATTG=0.20248
gnomAD - Genomes American Sub 13598 -

No frequency provided

dupATTG=0.41837
gnomAD - Genomes Ashkenazi Jewish Sub 3322 -

No frequency provided

dupATTG=0.1770
gnomAD - Genomes East Asian Sub 3080 -

No frequency provided

dupATTG=0.7386
gnomAD - Genomes Other Sub 2152 -

No frequency provided

dupATTG=0.2867
8.3KJPN JAPANESE Study-wide 16760 -

No frequency provided

dupATTG=0.70865
1000Genomes Global Study-wide 5008 -

No frequency provided

dupATTG=0.3972
1000Genomes African Sub 1322 -

No frequency provided

dupATTG=0.1755
1000Genomes East Asian Sub 1008 -

No frequency provided

dupATTG=0.7292
1000Genomes Europe Sub 1006 -

No frequency provided

dupATTG=0.2336
1000Genomes South Asian Sub 978 -

No frequency provided

dupATTG=0.489
1000Genomes American Sub 694 -

No frequency provided

dupATTG=0.445
Genetic variation in the Estonian population Estonian Study-wide 4480 -

No frequency provided

dupATTG=0.2228
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 -

No frequency provided

dupATTG=0.2237
UK 10K study - Twins TWIN COHORT Study-wide 3708 -

No frequency provided

dupATTG=0.1998
Korean Genome Project KOREAN Study-wide 1832 -

No frequency provided

dupATTG=0.7276
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 -

No frequency provided

dupATTG=0.258
Northern Sweden ACPOP Study-wide 600 -

No frequency provided

dupATTG=0.268
The Danish reference pan genome Danish Study-wide 40 -

No frequency provided

dupATTG=0.35
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 ATTG= dupATTG
GRCh38.p13 chr 2 NC_000002.12:g.29193160_29193163= NC_000002.12:g.29193160_29193163dup
GRCh37.p13 chr 2 NC_000002.11:g.29416026_29416029= NC_000002.11:g.29416026_29416029dup
ALK RefSeqGene (LRG_488) NG_009445.1:g.733404_733407= NG_009445.1:g.733404_733407dup
ALK transcript variant 1 NM_004304.5:c.*61_*64= NM_004304.5:c.*61_*64dup
ALK transcript variant 1 NM_004304.4:c.*61_*64= NM_004304.4:c.*61_*64dup
ALK transcript variant 2 NM_001353765.2:c.*61_*64= NM_001353765.2:c.*61_*64dup
ALK transcript variant 2 NM_001353765.1:c.*61_*64= NM_001353765.1:c.*61_*64dup
ALK transcript variant X3 XM_024452779.1:c.*61_*64= XM_024452779.1:c.*61_*64dup
ALK transcript variant X2 XM_024452778.1:c.*61_*64= XM_024452778.1:c.*61_*64dup
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#.

50 SubSNP, 12 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ABI ss41731301 Mar 14, 2006 (136)
2 HGSV ss80935596 Dec 03, 2013 (138)
3 HUMANGENOME_JCVI ss95268010 Feb 03, 2009 (136)
4 HUMANGENOME_JCVI ss96720886 Feb 04, 2009 (136)
5 BCMHGSC_JDW ss103851162 Dec 06, 2013 (138)
6 GMI ss288145085 May 04, 2012 (136)
7 1000GENOMES ss326182377 May 09, 2011 (136)
8 1000GENOMES ss326190948 May 09, 2011 (136)
9 1000GENOMES ss326249385 May 09, 2011 (136)
10 LUNTER ss551063341 Apr 25, 2013 (136)
11 LUNTER ss551105119 Apr 25, 2013 (136)
12 LUNTER ss552878978 Apr 25, 2013 (136)
13 TISHKOFF ss555152981 Apr 25, 2013 (136)
14 SSMP ss663300855 Apr 01, 2015 (136)
15 BILGI_BIOE ss666142568 Apr 25, 2013 (136)
16 EVA-GONL ss976626504 Aug 21, 2014 (136)
17 1000GENOMES ss1368154685 Aug 21, 2014 (136)
18 DDI ss1536282405 Apr 01, 2015 (136)
19 EVA_GENOME_DK ss1575374999 Apr 01, 2015 (136)
20 EVA_DECODE ss1586032347 Apr 01, 2015 (136)
21 EVA_UK10K_ALSPAC ss1702349561 Apr 01, 2015 (136)
22 EVA_UK10K_TWINSUK ss1702349587 Apr 01, 2015 (136)
23 HAMMER_LAB ss1796471067 Sep 08, 2015 (136)
24 GENOMED ss1968724228 Jul 19, 2016 (136)
25 JJLAB ss2030403519 Sep 14, 2016 (136)
26 SYSTEMSBIOZJU ss2624744036 Nov 08, 2017 (151)
27 GNOMAD ss2771238231 Nov 08, 2017 (151)
28 SWEGEN ss2989191961 Nov 08, 2017 (151)
29 MCHAISSO ss3063930531 Nov 08, 2017 (151)
30 MCHAISSO ss3064781493 Nov 08, 2017 (151)
31 TOPMED ss3302769210 Nov 08, 2017 (151)
32 BEROUKHIMLAB ss3644088632 Oct 11, 2018 (152)
33 BIOINF_KMB_FNS_UNIBA ss3645542490 Oct 11, 2018 (152)
34 URBANLAB ss3646993766 Oct 11, 2018 (152)
35 EGCUT_WGS ss3657147217 Jul 13, 2019 (153)
36 EVA_DECODE ss3703512960 Jul 13, 2019 (153)
37 ACPOP ss3728266724 Jul 13, 2019 (153)
38 KHV_HUMAN_GENOMES ss3800897381 Jul 13, 2019 (153)
39 EVA ss3826886647 Apr 25, 2020 (154)
40 EVA ss3836850612 Apr 25, 2020 (154)
41 EVA ss3842265282 Apr 25, 2020 (154)
42 KOGIC ss3947379464 Apr 25, 2020 (154)
43 FSA-LAB ss3984172288 Apr 26, 2021 (155)
44 FSA-LAB ss3984172290 Apr 26, 2021 (155)
45 FSA-LAB ss3984172291 Apr 26, 2021 (155)
46 EVA ss3986017148 Apr 26, 2021 (155)
47 EVA ss3986175777 Apr 26, 2021 (155)
48 TOPMED ss4498797205 Apr 26, 2021 (155)
49 TOMMO_GENOMICS ss5150474399 Apr 26, 2021 (155)
50 CPQ_GEN_INCA ss5236858768 Apr 26, 2021 (155)
51 1000Genomes NC_000002.11 - 29416026 Oct 11, 2018 (152)
52 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 29416026 Oct 11, 2018 (152)
53 Genetic variation in the Estonian population NC_000002.11 - 29416026 Oct 11, 2018 (152)
54 The Danish reference pan genome NC_000002.11 - 29416026 Apr 25, 2020 (154)
55 gnomAD - Genomes NC_000002.12 - 29193160 Apr 26, 2021 (155)
56 Genome of the Netherlands Release 5 NC_000002.11 - 29416026 Apr 25, 2020 (154)
57 Korean Genome Project NC_000002.12 - 29193160 Apr 25, 2020 (154)
58 Northern Sweden NC_000002.11 - 29416026 Jul 13, 2019 (153)
59 8.3KJPN NC_000002.11 - 29416026 Apr 26, 2021 (155)
60 TopMed NC_000002.12 - 29193160 Apr 26, 2021 (155)
61 UK 10K study - Twins NC_000002.11 - 29416026 Oct 11, 2018 (152)
62 ALFA NC_000002.12 - 29193160 Apr 26, 2021 (155)
63 ClinVar RCV000277801.1 Oct 11, 2018 (152)
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)
rs10625834 Feb 27, 2017 (136)
rs10686493 May 15, 2013 (138)
rs56993508 May 23, 2008 (130)
rs138695218 Sep 17, 2011 (135)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss326182377, ss326190948, ss326249385, ss551063341, ss551105119, ss552878978, ss1586032347 NC_000002.10:29269529::ATTG NC_000002.12:29193159:ATTG:ATTGATTG (self)
ss288145085 NC_000002.10:29269533::ATTG NC_000002.12:29193159:ATTG:ATTGATTG (self)
7364036, 4088185, 2885465, 656390, 1795425, 1551589, 8443706, 4088185, ss663300855, ss666142568, ss976626504, ss1368154685, ss1536282405, ss1575374999, ss1702349561, ss1702349587, ss1796471067, ss1968724228, ss2030403519, ss2624744036, ss2771238231, ss2989191961, ss3644088632, ss3657147217, ss3728266724, ss3826886647, ss3836850612, ss3984172288, ss3986017148, ss3986175777, ss5150474399, ss5236858768 NC_000002.11:29416025::ATTG NC_000002.12:29193159:ATTG:ATTGATTG (self)
ss555152981, ss3984172290, ss3984172291 NC_000002.11:29416029::ATTG NC_000002.12:29193159:ATTG:ATTGATTG (self)
52331241, 3757465, 302620084, ss3063930531, ss3064781493, ss3302769210, ss3645542490, ss3646993766, ss3703512960, ss3800897381, ss3842265282, ss3947379464, ss4498797205 NC_000002.12:29193159::ATTG NC_000002.12:29193159:ATTG:ATTGATTG (self)
RCV000277801.1, 3031694541 NC_000002.12:29193159:ATTG:ATTGATTG NC_000002.12:29193159:ATTG:ATTGATTG (self)
ss96720886 NT_022184.15:8237912::ATTG NC_000002.12:29193159:ATTG:ATTGATTG (self)
ss41731301, ss80935596, ss95268010, ss103851162 NT_022184.15:8237916::ATTG NC_000002.12:29193159:ATTG:ATTGATTG (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 rs397706189

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