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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.

rs13005169

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:29277589 (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
T>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.226170 (59865/264690, TOPMED)
T=0.220411 (30903/140206, GnomAD)
T=0.27088 (21316/78692, PAGE_STUDY) (+ 17 more)
T=0.12980 (3668/28258, 14KJPN)
T=0.18201 (5026/27614, ALFA)
T=0.12685 (2126/16760, 8.3KJPN)
T=0.2380 (1524/6404, 1000G_30x)
T=0.2314 (1159/5008, 1000G)
T=0.0982 (440/4480, Estonian)
T=0.1287 (496/3854, ALSPAC)
T=0.1338 (496/3708, TWINSUK)
T=0.1573 (461/2930, KOREAN)
T=0.2992 (566/1892, HapMap)
T=0.130 (130/998, GoNL)
T=0.090 (54/600, NorthernSweden)
T=0.126 (65/514, SGDP_PRJ)
T=0.255 (55/216, Qatari)
T=0.187 (40/214, Vietnamese)
T=0.14 (8/56, Siberian)
T=0.10 (4/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ALK : Intron 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 27614 T=0.18201 G=0.81799
European Sub 17484 T=0.11845 G=0.88155
African Sub 5172 T=0.4346 G=0.5654
African Others Sub 156 T=0.538 G=0.462
African American Sub 5016 T=0.4314 G=0.5686
Asian Sub 194 T=0.165 G=0.835
East Asian Sub 136 T=0.118 G=0.882
Other Asian Sub 58 T=0.28 G=0.72
Latin American 1 Sub 292 T=0.202 G=0.798
Latin American 2 Sub 2770 T=0.1126 G=0.8874
South Asian Sub 116 T=0.155 G=0.845
Other Sub 1586 T=0.1803 G=0.8197


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 T=0.226170 G=0.773830
gnomAD - Genomes Global Study-wide 140206 T=0.220411 G=0.779589
gnomAD - Genomes European Sub 75948 T=0.12605 G=0.87395
gnomAD - Genomes African Sub 41992 T=0.43108 G=0.56892
gnomAD - Genomes American Sub 13658 T=0.14146 G=0.85854
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.1098 G=0.8902
gnomAD - Genomes East Asian Sub 3130 T=0.1607 G=0.8393
gnomAD - Genomes Other Sub 2154 T=0.1987 G=0.8013
The PAGE Study Global Study-wide 78692 T=0.27088 G=0.72912
The PAGE Study AfricanAmerican Sub 32510 T=0.42030 G=0.57970
The PAGE Study Mexican Sub 10810 T=0.10768 G=0.89232
The PAGE Study Asian Sub 8316 T=0.1296 G=0.8704
The PAGE Study PuertoRican Sub 7918 T=0.1934 G=0.8066
The PAGE Study NativeHawaiian Sub 4534 T=0.2545 G=0.7455
The PAGE Study Cuban Sub 4228 T=0.1710 G=0.8290
The PAGE Study Dominican Sub 3828 T=0.2704 G=0.7296
The PAGE Study CentralAmerican Sub 2450 T=0.1465 G=0.8535
The PAGE Study SouthAmerican Sub 1982 T=0.1287 G=0.8713
The PAGE Study NativeAmerican Sub 1260 T=0.1817 G=0.8183
The PAGE Study SouthAsian Sub 856 T=0.145 G=0.855
14KJPN JAPANESE Study-wide 28258 T=0.12980 G=0.87020
Allele Frequency Aggregator Total Global 27614 T=0.18201 G=0.81799
Allele Frequency Aggregator European Sub 17484 T=0.11845 G=0.88155
Allele Frequency Aggregator African Sub 5172 T=0.4346 G=0.5654
Allele Frequency Aggregator Latin American 2 Sub 2770 T=0.1126 G=0.8874
Allele Frequency Aggregator Other Sub 1586 T=0.1803 G=0.8197
Allele Frequency Aggregator Latin American 1 Sub 292 T=0.202 G=0.798
Allele Frequency Aggregator Asian Sub 194 T=0.165 G=0.835
Allele Frequency Aggregator South Asian Sub 116 T=0.155 G=0.845
8.3KJPN JAPANESE Study-wide 16760 T=0.12685 G=0.87315
1000Genomes_30x Global Study-wide 6404 T=0.2380 G=0.7620
1000Genomes_30x African Sub 1786 T=0.4910 G=0.5090
1000Genomes_30x Europe Sub 1266 T=0.1382 G=0.8618
1000Genomes_30x South Asian Sub 1202 T=0.1339 G=0.8661
1000Genomes_30x East Asian Sub 1170 T=0.1684 G=0.8316
1000Genomes_30x American Sub 980 T=0.116 G=0.884
1000Genomes Global Study-wide 5008 T=0.2314 G=0.7686
1000Genomes African Sub 1322 T=0.4803 G=0.5197
1000Genomes East Asian Sub 1008 T=0.1667 G=0.8333
1000Genomes Europe Sub 1006 T=0.1382 G=0.8618
1000Genomes South Asian Sub 978 T=0.139 G=0.861
1000Genomes American Sub 694 T=0.117 G=0.883
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.0982 G=0.9018
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.1287 G=0.8713
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.1338 G=0.8662
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.1573 A=0.0000, C=0.0000, G=0.8427
HapMap Global Study-wide 1892 T=0.2992 G=0.7008
HapMap American Sub 770 T=0.179 G=0.821
HapMap African Sub 692 T=0.529 G=0.471
HapMap Asian Sub 254 T=0.142 G=0.858
HapMap Europe Sub 176 T=0.148 G=0.852
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.130 G=0.870
Northern Sweden ACPOP Study-wide 600 T=0.090 G=0.910
SGDP_PRJ Global Study-wide 514 T=0.126 G=0.874
Qatari Global Study-wide 216 T=0.255 G=0.745
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.187 G=0.813
Siberian Global Study-wide 56 T=0.14 G=0.86
The Danish reference pan genome Danish Study-wide 40 T=0.10 G=0.90
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 2 NC_000002.12:g.29277589T>A
GRCh38.p14 chr 2 NC_000002.12:g.29277589T>C
GRCh38.p14 chr 2 NC_000002.12:g.29277589T>G
GRCh37.p13 chr 2 NC_000002.11:g.29500455T>A
GRCh37.p13 chr 2 NC_000002.11:g.29500455T>C
GRCh37.p13 chr 2 NC_000002.11:g.29500455T>G
ALK RefSeqGene (LRG_488) NG_009445.1:g.648978A>T
ALK RefSeqGene (LRG_488) NG_009445.1:g.648978A>G
ALK RefSeqGene (LRG_488) NG_009445.1:g.648978A>C
Gene: ALK, ALK receptor tyrosine kinase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ALK transcript variant 1 NM_004304.5:c.1818-2093A>T N/A Intron Variant
ALK transcript variant 2 NM_001353765.2:c. N/A Genic Upstream Transcript Variant
ALK transcript variant X1 XR_001738688.3:n. N/A Intron 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
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 T= A C G
GRCh38.p14 chr 2 NC_000002.12:g.29277589= NC_000002.12:g.29277589T>A NC_000002.12:g.29277589T>C NC_000002.12:g.29277589T>G
GRCh37.p13 chr 2 NC_000002.11:g.29500455= NC_000002.11:g.29500455T>A NC_000002.11:g.29500455T>C NC_000002.11:g.29500455T>G
ALK RefSeqGene (LRG_488) NG_009445.1:g.648978= NG_009445.1:g.648978A>T NG_009445.1:g.648978A>G NG_009445.1:g.648978A>C
ALK transcript variant 1 NM_004304.4:c.1818-2093= NM_004304.4:c.1818-2093A>T NM_004304.4:c.1818-2093A>G NM_004304.4:c.1818-2093A>C
ALK transcript variant 1 NM_004304.5:c.1818-2093= NM_004304.5:c.1818-2093A>T NM_004304.5:c.1818-2093A>G NM_004304.5:c.1818-2093A>C
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#.

91 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss21632304 Apr 05, 2004 (121)
2 PERLEGEN ss23233755 Sep 20, 2004 (123)
3 ABI ss44336305 Mar 14, 2006 (126)
4 AFFY ss66225413 Nov 30, 2006 (127)
5 PERLEGEN ss68807895 May 17, 2007 (127)
6 AFFY ss76371602 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss83027559 Dec 15, 2007 (130)
8 HGSV ss83732736 Dec 15, 2007 (130)
9 BCMHGSC_JDW ss91100651 Mar 24, 2008 (129)
10 HUMANGENOME_JCVI ss97023348 Feb 05, 2009 (130)
11 BGI ss106077981 Feb 05, 2009 (130)
12 1000GENOMES ss109360192 Jan 24, 2009 (130)
13 ILLUMINA-UK ss117636963 Feb 14, 2009 (130)
14 ENSEMBL ss132948629 Dec 01, 2009 (131)
15 ENSEMBL ss138411976 Dec 01, 2009 (131)
16 GMI ss156845487 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss164072201 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss166336341 Jul 04, 2010 (132)
19 ILLUMINA ss172301510 Jul 04, 2010 (132)
20 AFFY ss173406833 Jul 04, 2010 (132)
21 BUSHMAN ss200207646 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss205671950 Jul 04, 2010 (132)
23 1000GENOMES ss210852525 Jul 14, 2010 (132)
24 1000GENOMES ss219140440 Jul 14, 2010 (132)
25 1000GENOMES ss231090878 Jul 14, 2010 (132)
26 1000GENOMES ss238663256 Jul 15, 2010 (132)
27 BL ss252996737 May 09, 2011 (134)
28 GMI ss276398681 May 04, 2012 (137)
29 GMI ss284314832 Apr 25, 2013 (138)
30 PJP ss292534280 May 09, 2011 (134)
31 TISHKOFF ss555440380 Apr 25, 2013 (138)
32 SSMP ss649020730 Apr 25, 2013 (138)
33 EVA-GONL ss976627172 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1068961628 Aug 21, 2014 (142)
35 1000GENOMES ss1296446514 Aug 21, 2014 (142)
36 DDI ss1428518069 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1578795308 Apr 01, 2015 (144)
38 EVA_DECODE ss1586033087 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1603094971 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1646089004 Apr 01, 2015 (144)
41 EVA_SVP ss1712441099 Apr 01, 2015 (144)
42 HAMMER_LAB ss1796472504 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1919859473 Feb 12, 2016 (147)
44 ILLUMINA ss1958402187 Feb 12, 2016 (147)
45 GENOMED ss1968724357 Jul 19, 2016 (147)
46 JJLAB ss2020458331 Sep 14, 2016 (149)
47 USC_VALOUEV ss2148502904 Dec 20, 2016 (150)
48 HUMAN_LONGEVITY ss2228634915 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2624744163 Nov 08, 2017 (151)
50 GRF ss2703064036 Nov 08, 2017 (151)
51 GNOMAD ss2771245270 Nov 08, 2017 (151)
52 SWEGEN ss2989192966 Nov 08, 2017 (151)
53 ILLUMINA ss3021954508 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3023995573 Nov 08, 2017 (151)
55 CSHL ss3344135852 Nov 08, 2017 (151)
56 ILLUMINA ss3638249703 Oct 11, 2018 (152)
57 URBANLAB ss3646993887 Oct 11, 2018 (152)
58 ILLUMINA ss3652383928 Oct 11, 2018 (152)
59 EGCUT_WGS ss3657148214 Jul 13, 2019 (153)
60 EVA_DECODE ss3703514220 Jul 13, 2019 (153)
61 ILLUMINA ss3725769816 Jul 13, 2019 (153)
62 ACPOP ss3728267309 Jul 13, 2019 (153)
63 EVA ss3756518905 Jul 13, 2019 (153)
64 PAGE_CC ss3770906739 Jul 13, 2019 (153)
65 PACBIO ss3783814451 Jul 13, 2019 (153)
66 PACBIO ss3789409748 Jul 13, 2019 (153)
67 PACBIO ss3794282521 Jul 13, 2019 (153)
68 KHV_HUMAN_GENOMES ss3800898234 Jul 13, 2019 (153)
69 EVA ss3826887058 Apr 25, 2020 (154)
70 EVA ss3836850784 Apr 25, 2020 (154)
71 EVA ss3842265456 Apr 25, 2020 (154)
72 SGDP_PRJ ss3851868557 Apr 25, 2020 (154)
73 KRGDB ss3897286247 Apr 25, 2020 (154)
74 EVA ss4016986487 Apr 26, 2021 (155)
75 TOPMED ss4498818566 Apr 26, 2021 (155)
76 TOMMO_GENOMICS ss5150477076 Apr 26, 2021 (155)
77 1000G_HIGH_COVERAGE ss5247382737 Oct 17, 2022 (156)
78 EVA ss5327675295 Oct 17, 2022 (156)
79 HUGCELL_USP ss5447648307 Oct 17, 2022 (156)
80 1000G_HIGH_COVERAGE ss5522243435 Oct 17, 2022 (156)
81 SANFORD_IMAGENETICS ss5624440157 Oct 17, 2022 (156)
82 SANFORD_IMAGENETICS ss5628357215 Oct 17, 2022 (156)
83 TOMMO_GENOMICS ss5678846674 Oct 17, 2022 (156)
84 YY_MCH ss5802038729 Oct 17, 2022 (156)
85 EVA ss5819835893 Oct 17, 2022 (156)
86 EVA ss5847184326 Oct 17, 2022 (156)
87 EVA ss5847861407 Oct 17, 2022 (156)
88 EVA ss5852444202 Oct 17, 2022 (156)
89 EVA ss5929570889 Oct 17, 2022 (156)
90 EVA ss5954561161 Oct 17, 2022 (156)
91 EVA ss5979560817 Oct 17, 2022 (156)
92 1000Genomes NC_000002.11 - 29500455 Oct 11, 2018 (152)
93 1000Genomes_30x NC_000002.12 - 29277589 Oct 17, 2022 (156)
94 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 29500455 Oct 11, 2018 (152)
95 Genetic variation in the Estonian population NC_000002.11 - 29500455 Oct 11, 2018 (152)
96 The Danish reference pan genome NC_000002.11 - 29500455 Apr 25, 2020 (154)
97 gnomAD - Genomes NC_000002.12 - 29277589 Apr 26, 2021 (155)
98 Genome of the Netherlands Release 5 NC_000002.11 - 29500455 Apr 25, 2020 (154)
99 HapMap NC_000002.12 - 29277589 Apr 25, 2020 (154)
100 KOREAN population from KRGDB NC_000002.11 - 29500455 Apr 25, 2020 (154)
101 Northern Sweden NC_000002.11 - 29500455 Jul 13, 2019 (153)
102 The PAGE Study NC_000002.12 - 29277589 Jul 13, 2019 (153)
103 Qatari NC_000002.11 - 29500455 Apr 25, 2020 (154)
104 SGDP_PRJ NC_000002.11 - 29500455 Apr 25, 2020 (154)
105 Siberian NC_000002.11 - 29500455 Apr 25, 2020 (154)
106 8.3KJPN NC_000002.11 - 29500455 Apr 26, 2021 (155)
107 14KJPN NC_000002.12 - 29277589 Oct 17, 2022 (156)
108 TopMed NC_000002.12 - 29277589 Apr 26, 2021 (155)
109 UK 10K study - Twins NC_000002.11 - 29500455 Oct 11, 2018 (152)
110 A Vietnamese Genetic Variation Database NC_000002.11 - 29500455 Jul 13, 2019 (153)
111 ALFA NC_000002.12 - 29277589 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)
rs58770686 May 24, 2008 (130)
rs59776654 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
4463641, ss3897286247 NC_000002.11:29500454:T:A NC_000002.12:29277588:T:A (self)
4463641, ss3897286247 NC_000002.11:29500454:T:C NC_000002.12:29277588:T:C (self)
ss83732736 NC_000002.9:29412105:T:G NC_000002.12:29277588:T:G (self)
ss91100651, ss109360192, ss117636963, ss164072201, ss166336341, ss200207646, ss205671950, ss210852525, ss252996737, ss276398681, ss284314832, ss292534280, ss1586033087, ss1712441099 NC_000002.10:29353958:T:G NC_000002.12:29277588:T:G (self)
7366824, 4089809, 2886462, 4971203, 1796082, 4463641, 1552174, 1901403, 3885537, 1019258, 8446383, 4089809, 890304, ss219140440, ss231090878, ss238663256, ss555440380, ss649020730, ss976627172, ss1068961628, ss1296446514, ss1428518069, ss1578795308, ss1603094971, ss1646089004, ss1796472504, ss1919859473, ss1958402187, ss1968724357, ss2020458331, ss2148502904, ss2624744163, ss2703064036, ss2771245270, ss2989192966, ss3021954508, ss3344135852, ss3638249703, ss3652383928, ss3657148214, ss3728267309, ss3756518905, ss3783814451, ss3789409748, ss3794282521, ss3826887058, ss3836850784, ss3851868557, ss3897286247, ss4016986487, ss5150477076, ss5327675295, ss5624440157, ss5628357215, ss5819835893, ss5847184326, ss5847861407, ss5954561161, ss5979560817 NC_000002.11:29500454:T:G NC_000002.12:29277588:T:G (self)
9769370, 52349148, 1760788, 128208, 12683778, 302641445, 992046551, ss2228634915, ss3023995573, ss3646993887, ss3703514220, ss3725769816, ss3770906739, ss3800898234, ss3842265456, ss4498818566, ss5247382737, ss5447648307, ss5522243435, ss5678846674, ss5802038729, ss5852444202, ss5929570889 NC_000002.12:29277588:T:G NC_000002.12:29277588:T:G (self)
ss21632304 NT_022184.13:8316387:T:G NC_000002.12:29277588:T:G (self)
ss23233755, ss44336305, ss66225413, ss68807895, ss76371602, ss83027559, ss97023348, ss106077981, ss132948629, ss138411976, ss156845487, ss172301510, ss173406833 NT_022184.15:8322341:T:G NC_000002.12:29277588:T:G (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 rs13005169

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.post761+d5e8e07