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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs597808

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:111535554 (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
A>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.310151 (82094/264690, TOPMED)
A=0.332849 (46543/139832, GnomAD)
A=0.00096 (27/28258, 14KJPN) (+ 15 more)
A=0.00084 (14/16760, 8.3KJPN)
A=0.38570 (6442/16702, ALFA)
A=0.1487 (952/6404, 1000G_30x)
A=0.1480 (741/5008, 1000G)
A=0.4451 (1994/4480, Estonian)
A=0.4520 (1742/3854, ALSPAC)
A=0.4914 (1822/3708, TWINSUK)
A=0.0020 (6/2930, KOREAN)
A=0.468 (467/998, GoNL)
A=0.435 (261/600, NorthernSweden)
A=0.091 (48/526, SGDP_PRJ)
A=0.194 (42/216, Qatari)
A=0.005 (1/212, Vietnamese)
A=0.13 (7/54, Siberian)
A=0.45 (18/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ATXN2 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 16702 A=0.38570 G=0.61430 0.175069 0.403664 0.421267 32
European Sub 12214 A=0.47446 G=0.52554 0.224333 0.275422 0.500246 0
African Sub 2864 A=0.0761 G=0.9239 0.011173 0.858939 0.129888 5
African Others Sub 108 A=0.000 G=1.000 0.0 1.0 0.0 N/A
African American Sub 2756 A=0.0791 G=0.9209 0.011611 0.853411 0.134978 5
Asian Sub 108 A=0.000 G=1.000 0.0 1.0 0.0 N/A
East Asian Sub 84 A=0.00 G=1.00 0.0 1.0 0.0 N/A
Other Asian Sub 24 A=0.00 G=1.00 0.0 1.0 0.0 N/A
Latin American 1 Sub 146 A=0.315 G=0.685 0.123288 0.493151 0.383562 1
Latin American 2 Sub 610 A=0.252 G=0.748 0.065574 0.560656 0.37377 0
South Asian Sub 94 A=0.11 G=0.89 0.0 0.787234 0.212766 0
Other Sub 666 A=0.329 G=0.671 0.141141 0.483483 0.375375 5


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 A=0.310151 G=0.689849
gnomAD - Genomes Global Study-wide 139832 A=0.332849 G=0.667151
gnomAD - Genomes European Sub 75672 A=0.47518 G=0.52482
gnomAD - Genomes African Sub 41934 A=0.08532 G=0.91468
gnomAD - Genomes American Sub 13634 A=0.29529 G=0.70471
gnomAD - Genomes Ashkenazi Jewish Sub 3316 A=0.6710 G=0.3290
gnomAD - Genomes East Asian Sub 3124 A=0.0006 G=0.9994
gnomAD - Genomes Other Sub 2152 A=0.3504 G=0.6496
14KJPN JAPANESE Study-wide 28258 A=0.00096 G=0.99904
8.3KJPN JAPANESE Study-wide 16760 A=0.00084 G=0.99916
Allele Frequency Aggregator Total Global 16702 A=0.38570 G=0.61430
Allele Frequency Aggregator European Sub 12214 A=0.47446 G=0.52554
Allele Frequency Aggregator African Sub 2864 A=0.0761 G=0.9239
Allele Frequency Aggregator Other Sub 666 A=0.329 G=0.671
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.252 G=0.748
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.315 G=0.685
Allele Frequency Aggregator Asian Sub 108 A=0.000 G=1.000
Allele Frequency Aggregator South Asian Sub 94 A=0.11 G=0.89
1000Genomes_30x Global Study-wide 6404 A=0.1487 G=0.8513
1000Genomes_30x African Sub 1786 A=0.0174 G=0.9826
1000Genomes_30x Europe Sub 1266 A=0.4621 G=0.5379
1000Genomes_30x South Asian Sub 1202 A=0.0616 G=0.9384
1000Genomes_30x East Asian Sub 1170 A=0.0043 G=0.9957
1000Genomes_30x American Sub 980 A=0.262 G=0.738
1000Genomes Global Study-wide 5008 A=0.1480 G=0.8520
1000Genomes African Sub 1322 A=0.0189 G=0.9811
1000Genomes East Asian Sub 1008 A=0.0040 G=0.9960
1000Genomes Europe Sub 1006 A=0.4662 G=0.5338
1000Genomes South Asian Sub 978 A=0.069 G=0.931
1000Genomes American Sub 694 A=0.254 G=0.746
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.4451 G=0.5549
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.4520 G=0.5480
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.4914 G=0.5086
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.0020 C=0.0000, G=0.9980, T=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.468 G=0.532
Northern Sweden ACPOP Study-wide 600 A=0.435 G=0.565
SGDP_PRJ Global Study-wide 526 A=0.091 G=0.909
Qatari Global Study-wide 216 A=0.194 G=0.806
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.005 G=0.995
Siberian Global Study-wide 54 A=0.13 G=0.87
The Danish reference pan genome Danish Study-wide 40 A=0.45 G=0.55
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 12 NC_000012.12:g.111535554A>C
GRCh38.p14 chr 12 NC_000012.12:g.111535554A>G
GRCh38.p14 chr 12 NC_000012.12:g.111535554A>T
GRCh37.p13 chr 12 NC_000012.11:g.111973358A>C
GRCh37.p13 chr 12 NC_000012.11:g.111973358A>G
GRCh37.p13 chr 12 NC_000012.11:g.111973358A>T
ATXN2 RefSeqGene (LRG_864) NG_011572.3:g.69123T>G
ATXN2 RefSeqGene (LRG_864) NG_011572.3:g.69123T>C
ATXN2 RefSeqGene (LRG_864) NG_011572.3:g.69123T>A
Gene: ATXN2, ataxin 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ATXN2 transcript variant 2 NM_001310121.1:c.257-1023…

NM_001310121.1:c.257-10238T>G

 		N/A Intron Variant
ATXN2 transcript variant 3 NM_001310123.1:c.185-1023…

NM_001310123.1:c.185-10238T>G

 		N/A Intron Variant
ATXN2 transcript variant 5 NM_001372574.1:c.572-1023…

NM_001372574.1:c.572-10238T>G

 		N/A Intron Variant
ATXN2 transcript variant 1 NM_002973.4:c.572-10238T>G N/A Intron Variant
ATXN2 transcript variant 4 NR_132311.2: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 A= C G T
GRCh38.p14 chr 12 NC_000012.12:g.111535554= NC_000012.12:g.111535554A>C NC_000012.12:g.111535554A>G NC_000012.12:g.111535554A>T
GRCh37.p13 chr 12 NC_000012.11:g.111973358= NC_000012.11:g.111973358A>C NC_000012.11:g.111973358A>G NC_000012.11:g.111973358A>T
ATXN2 RefSeqGene (LRG_864) NG_011572.3:g.69123= NG_011572.3:g.69123T>G NG_011572.3:g.69123T>C NG_011572.3:g.69123T>A
ATXN2 transcript variant 2 NM_001310121.1:c.257-10238= NM_001310121.1:c.257-10238T>G NM_001310121.1:c.257-10238T>C NM_001310121.1:c.257-10238T>A
ATXN2 transcript variant 3 NM_001310123.1:c.185-10238= NM_001310123.1:c.185-10238T>G NM_001310123.1:c.185-10238T>C NM_001310123.1:c.185-10238T>A
ATXN2 transcript variant 5 NM_001372574.1:c.572-10238= NM_001372574.1:c.572-10238T>G NM_001372574.1:c.572-10238T>C NM_001372574.1:c.572-10238T>A
ATXN2 transcript variant 1 NM_002973.3:c.1052-10238= NM_002973.3:c.1052-10238T>G NM_002973.3:c.1052-10238T>C NM_002973.3:c.1052-10238T>A
ATXN2 transcript variant 1 NM_002973.4:c.572-10238= NM_002973.4:c.572-10238T>G NM_002973.4:c.572-10238T>C NM_002973.4:c.572-10238T>A
ATXN2 transcript variant X1 XM_005253924.1:c.500-10238= XM_005253924.1:c.500-10238T>G XM_005253924.1:c.500-10238T>C XM_005253924.1:c.500-10238T>A
ATXN2 transcript variant X2 XM_005253925.1:c.257-10238= XM_005253925.1:c.257-10238T>G XM_005253925.1:c.257-10238T>C XM_005253925.1:c.257-10238T>A
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#.

70 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss769702 Aug 11, 2000 (83)
2 KWOK ss1211998 Oct 04, 2000 (86)
3 KWOK ss1953490 Oct 18, 2000 (87)
4 WI_SSAHASNP ss12198308 Jul 11, 2003 (116)
5 ABI ss40242295 Mar 13, 2006 (126)
6 HGSV ss84110463 Dec 15, 2007 (130)
7 HGSV ss86066487 Dec 15, 2007 (130)
8 BCMHGSC_JDW ss89389331 Mar 24, 2008 (129)
9 HUMANGENOME_JCVI ss97341411 Feb 06, 2009 (130)
10 BGI ss105122291 Dec 01, 2009 (131)
11 ENSEMBL ss133363633 Dec 01, 2009 (131)
12 ENSEMBL ss142881222 Dec 01, 2009 (131)
13 GMI ss157912854 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss170883227 Jul 04, 2010 (132)
15 BUSHMAN ss198695523 Jul 04, 2010 (132)
16 BL ss255347267 May 09, 2011 (134)
17 GMI ss281548945 May 04, 2012 (137)
18 GMI ss286627458 Apr 25, 2013 (138)
19 PJP ss291341163 May 09, 2011 (134)
20 1000GENOMES ss337618233 May 09, 2011 (134)
21 TISHKOFF ss563407471 Apr 25, 2013 (138)
22 SSMP ss658990354 Apr 25, 2013 (138)
23 EVA-GONL ss989963712 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1078773640 Aug 21, 2014 (142)
25 1000GENOMES ss1346655156 Aug 21, 2014 (142)
26 DDI ss1427055334 Apr 01, 2015 (144)
27 EVA_GENOME_DK ss1576528046 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1629455351 Apr 01, 2015 (144)
29 EVA_DECODE ss1642069406 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1672449384 Apr 01, 2015 (144)
31 HAMMER_LAB ss1807421856 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1933317102 Feb 12, 2016 (147)
33 GENOMED ss1967682864 Jul 19, 2016 (147)
34 JJLAB ss2027415872 Sep 14, 2016 (149)
35 USC_VALOUEV ss2155764939 Dec 20, 2016 (150)
36 HUMAN_LONGEVITY ss2193223485 Dec 20, 2016 (150)
37 SYSTEMSBIOZJU ss2628189136 Nov 08, 2017 (151)
38 GRF ss2700122603 Nov 08, 2017 (151)
39 GNOMAD ss2915225643 Nov 08, 2017 (151)
40 SWEGEN ss3010354894 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3027517924 Nov 08, 2017 (151)
42 CSHL ss3350251474 Nov 08, 2017 (151)
43 URBANLAB ss3649923320 Oct 12, 2018 (152)
44 EGCUT_WGS ss3677655472 Jul 13, 2019 (153)
45 EVA_DECODE ss3694474191 Jul 13, 2019 (153)
46 ACPOP ss3739385854 Jul 13, 2019 (153)
47 EVA ss3750970365 Jul 13, 2019 (153)
48 PACBIO ss3787336926 Jul 13, 2019 (153)
49 PACBIO ss3792419187 Jul 13, 2019 (153)
50 PACBIO ss3797302273 Jul 13, 2019 (153)
51 KHV_HUMAN_GENOMES ss3816302510 Jul 13, 2019 (153)
52 EVA ss3833328365 Apr 27, 2020 (154)
53 EVA ss3840236338 Apr 27, 2020 (154)
54 EVA ss3845724969 Apr 27, 2020 (154)
55 SGDP_PRJ ss3879121228 Apr 27, 2020 (154)
56 KRGDB ss3927863893 Apr 27, 2020 (154)
57 TOPMED ss4932916662 Apr 26, 2021 (155)
58 TOMMO_GENOMICS ss5208182441 Apr 26, 2021 (155)
59 1000G_HIGH_COVERAGE ss5292247639 Oct 16, 2022 (156)
60 HUGCELL_USP ss5486849896 Oct 16, 2022 (156)
61 EVA ss5510845524 Oct 16, 2022 (156)
62 1000G_HIGH_COVERAGE ss5590481096 Oct 16, 2022 (156)
63 SANFORD_IMAGENETICS ss5653964922 Oct 16, 2022 (156)
64 TOMMO_GENOMICS ss5758511045 Oct 16, 2022 (156)
65 YY_MCH ss5813648961 Oct 16, 2022 (156)
66 EVA ss5838519865 Oct 16, 2022 (156)
67 EVA ss5850548630 Oct 16, 2022 (156)
68 EVA ss5906038783 Oct 16, 2022 (156)
69 EVA ss5945372178 Oct 16, 2022 (156)
70 EVA ss5980761523 Oct 16, 2022 (156)
71 1000Genomes NC_000012.11 - 111973358 Oct 12, 2018 (152)
72 1000Genomes_30x NC_000012.12 - 111535554 Oct 16, 2022 (156)
73 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 111973358 Oct 12, 2018 (152)
74 Genetic variation in the Estonian population NC_000012.11 - 111973358 Oct 12, 2018 (152)
75 The Danish reference pan genome NC_000012.11 - 111973358 Apr 27, 2020 (154)
76 gnomAD - Genomes NC_000012.12 - 111535554 Apr 26, 2021 (155)
77 Genome of the Netherlands Release 5 NC_000012.11 - 111973358 Apr 27, 2020 (154)
78 KOREAN population from KRGDB NC_000012.11 - 111973358 Apr 27, 2020 (154)
79 Northern Sweden NC_000012.11 - 111973358 Jul 13, 2019 (153)
80 Qatari NC_000012.11 - 111973358 Apr 27, 2020 (154)
81 SGDP_PRJ NC_000012.11 - 111973358 Apr 27, 2020 (154)
82 Siberian NC_000012.11 - 111973358 Apr 27, 2020 (154)
83 8.3KJPN NC_000012.11 - 111973358 Apr 26, 2021 (155)
84 14KJPN NC_000012.12 - 111535554 Oct 16, 2022 (156)
85 TopMed NC_000012.12 - 111535554 Apr 26, 2021 (155)
86 UK 10K study - Twins NC_000012.11 - 111973358 Oct 12, 2018 (152)
87 A Vietnamese Genetic Variation Database NC_000012.11 - 111973358 Jul 13, 2019 (153)
88 ALFA NC_000012.12 - 111535554 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)
rs60279802 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
35041287, ss3927863893 NC_000012.11:111973357:A:C NC_000012.12:111535553:A:C (self)
ss84110463, ss86066487 NC_000012.9:110436077:A:G NC_000012.12:111535553:A:G (self)
ss89389331, ss170883227, ss198695523, ss255347267, ss281548945, ss286627458, ss291341163, ss1642069406 NC_000012.10:110457740:A:G NC_000012.12:111535553:A:G (self)
59466534, 33027052, 23393720, 3129120, 14732175, 35041287, 12670719, 15359032, 31138208, 8281293, 66151748, 33027052, 7328338, ss337618233, ss563407471, ss658990354, ss989963712, ss1078773640, ss1346655156, ss1427055334, ss1576528046, ss1629455351, ss1672449384, ss1807421856, ss1933317102, ss1967682864, ss2027415872, ss2155764939, ss2628189136, ss2700122603, ss2915225643, ss3010354894, ss3350251474, ss3677655472, ss3739385854, ss3750970365, ss3787336926, ss3792419187, ss3797302273, ss3833328365, ss3840236338, ss3879121228, ss3927863893, ss5208182441, ss5510845524, ss5653964922, ss5838519865, ss5945372178, ss5980761523 NC_000012.11:111973357:A:G NC_000012.12:111535553:A:G (self)
78007031, 419455854, 92348149, 148462319, 13554574877, ss2193223485, ss3027517924, ss3649923320, ss3694474191, ss3816302510, ss3845724969, ss4932916662, ss5292247639, ss5486849896, ss5590481096, ss5758511045, ss5813648961, ss5850548630, ss5906038783 NC_000012.12:111535553:A:G NC_000012.12:111535553:A:G (self)
ss12198308 NT_009775.13:760236:A:G NC_000012.12:111535553:A:G (self)
ss769702, ss1211998, ss1953490, ss40242295, ss97341411, ss105122291, ss133363633, ss142881222, ss157912854 NT_009775.17:2549887:A:G NC_000012.12:111535553:A:G (self)
35041287, ss3927863893 NC_000012.11:111973357:A:T NC_000012.12:111535553:A: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 rs597808

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