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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.

rs1569997

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:14533041 (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
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.167411 (44312/264690, TOPMED)
G=0.161639 (22644/140090, GnomAD)
G=0.21477 (6069/28258, 14KJPN) (+ 16 more)
G=0.16950 (4283/25268, ALFA)
G=0.21551 (3612/16760, 8.3KJPN)
G=0.1725 (1105/6404, 1000G_30x)
G=0.1765 (884/5008, 1000G)
G=0.1641 (735/4480, Estonian)
G=0.1943 (749/3854, ALSPAC)
G=0.1783 (661/3708, TWINSUK)
G=0.2700 (791/2930, KOREAN)
G=0.206 (206/998, GoNL)
G=0.222 (133/600, NorthernSweden)
G=0.135 (71/526, SGDP_PRJ)
G=0.162 (35/216, Qatari)
G=0.288 (61/212, Vietnamese)
G=0.30 (22/74, Ancient Sardinia)
G=0.11 (6/56, Siberian)
G=0.20 (8/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MACROD2 : 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 25362 G=0.16947 A=0.83053
European Sub 20490 G=0.17662 A=0.82338
African Sub 2946 G=0.1090 A=0.8910
African Others Sub 114 G=0.079 A=0.921
African American Sub 2832 G=0.1102 A=0.8898
Asian Sub 112 G=0.205 A=0.795
East Asian Sub 86 G=0.21 A=0.79
Other Asian Sub 26 G=0.19 A=0.81
Latin American 1 Sub 146 G=0.171 A=0.829
Latin American 2 Sub 610 G=0.203 A=0.797
South Asian Sub 98 G=0.27 A=0.73
Other Sub 960 G=0.167 A=0.833


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 G=0.167411 A=0.832589
gnomAD - Genomes Global Study-wide 140090 G=0.161639 A=0.838361
gnomAD - Genomes European Sub 75890 G=0.18197 A=0.81803
gnomAD - Genomes African Sub 41966 G=0.11385 A=0.88615
gnomAD - Genomes American Sub 13640 G=0.16474 A=0.83526
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.1784 A=0.8216
gnomAD - Genomes East Asian Sub 3126 G=0.2758 A=0.7242
gnomAD - Genomes Other Sub 2144 G=0.1651 A=0.8349
14KJPN JAPANESE Study-wide 28258 G=0.21477 A=0.78523
Allele Frequency Aggregator Total Global 25268 G=0.16950 A=0.83050
Allele Frequency Aggregator European Sub 20414 G=0.17674 A=0.82326
Allele Frequency Aggregator African Sub 2946 G=0.1090 A=0.8910
Allele Frequency Aggregator Other Sub 942 G=0.166 A=0.834
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.203 A=0.797
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.171 A=0.829
Allele Frequency Aggregator Asian Sub 112 G=0.205 A=0.795
Allele Frequency Aggregator South Asian Sub 98 G=0.27 A=0.73
8.3KJPN JAPANESE Study-wide 16760 G=0.21551 A=0.78449
1000Genomes_30x Global Study-wide 6404 G=0.1725 A=0.8275
1000Genomes_30x African Sub 1786 G=0.0873 A=0.9127
1000Genomes_30x Europe Sub 1266 G=0.1682 A=0.8318
1000Genomes_30x South Asian Sub 1202 G=0.2304 A=0.7696
1000Genomes_30x East Asian Sub 1170 G=0.2573 A=0.7427
1000Genomes_30x American Sub 980 G=0.161 A=0.839
1000Genomes Global Study-wide 5008 G=0.1765 A=0.8235
1000Genomes African Sub 1322 G=0.0877 A=0.9123
1000Genomes East Asian Sub 1008 G=0.2530 A=0.7470
1000Genomes Europe Sub 1006 G=0.1720 A=0.8280
1000Genomes South Asian Sub 978 G=0.237 A=0.763
1000Genomes American Sub 694 G=0.156 A=0.844
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.1641 A=0.8359
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.1943 A=0.8057
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.1783 A=0.8217
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.2700 A=0.7300, T=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.206 A=0.794
Northern Sweden ACPOP Study-wide 600 G=0.222 A=0.778
SGDP_PRJ Global Study-wide 526 G=0.135 A=0.865
Qatari Global Study-wide 216 G=0.162 A=0.838
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.288 A=0.712
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 74 G=0.30 A=0.70
Siberian Global Study-wide 56 G=0.11 A=0.89
The Danish reference pan genome Danish Study-wide 40 G=0.20 A=0.80
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 20 NC_000020.11:g.14533041G>A
GRCh38.p14 chr 20 NC_000020.11:g.14533041G>T
GRCh37.p13 chr 20 NC_000020.10:g.14513687G>A
GRCh37.p13 chr 20 NC_000020.10:g.14513687G>T
MACROD2 RefSeqGene NG_054905.1:g.542542G>A
MACROD2 RefSeqGene NG_054905.1:g.542542G>T
Gene: MACROD2, mono-ADP ribosylhydrolase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MACROD2 transcript variant 3 NM_001351661.2:c.301+3953…

NM_001351661.2:c.301+39533G>A

N/A Intron Variant
MACROD2 transcript variant 4 NM_001351663.2:c.301+3953…

NM_001351663.2:c.301+39533G>A

N/A Intron Variant
MACROD2 transcript variant 1 NM_080676.6:c.301+39533G>A N/A Intron Variant
MACROD2 transcript variant 2 NM_001033087.2:c. N/A Genic Upstream Transcript Variant
MACROD2 transcript variant 5 NM_001351664.2:c. N/A Genic Upstream Transcript Variant
MACROD2 transcript variant X2 XM_017027675.2:c. N/A Genic Upstream Transcript Variant
MACROD2 transcript variant X3 XM_017027676.2:c. N/A Genic Upstream Transcript Variant
MACROD2 transcript variant X1 XM_024451834.2: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
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 G= A T
GRCh38.p14 chr 20 NC_000020.11:g.14533041= NC_000020.11:g.14533041G>A NC_000020.11:g.14533041G>T
GRCh37.p13 chr 20 NC_000020.10:g.14513687= NC_000020.10:g.14513687G>A NC_000020.10:g.14513687G>T
MACROD2 RefSeqGene NG_054905.1:g.542542= NG_054905.1:g.542542G>A NG_054905.1:g.542542G>T
MACROD2 transcript variant 3 NM_001351661.2:c.301+39533= NM_001351661.2:c.301+39533G>A NM_001351661.2:c.301+39533G>T
MACROD2 transcript variant 4 NM_001351663.2:c.301+39533= NM_001351663.2:c.301+39533G>A NM_001351663.2:c.301+39533G>T
MACROD2 transcript variant 1 NM_080676.5:c.301+39533= NM_080676.5:c.301+39533G>A NM_080676.5:c.301+39533G>T
MACROD2 transcript variant 1 NM_080676.6:c.301+39533= NM_080676.6:c.301+39533G>A NM_080676.6:c.301+39533G>T
MACROD2 transcript variant X1 XM_005260667.1:c.301+39533= XM_005260667.1:c.301+39533G>A XM_005260667.1:c.301+39533G>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#.

83 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2414393 Oct 23, 2000 (88)
2 TSC-CSHL ss5196866 Oct 08, 2002 (108)
3 SC_SNP ss8340572 Apr 21, 2003 (114)
4 CSHL-HAPMAP ss19477183 Feb 27, 2004 (120)
5 SSAHASNP ss21772299 Apr 05, 2004 (121)
6 ABI ss41378665 Mar 14, 2006 (126)
7 HGSV ss78411903 Dec 07, 2007 (129)
8 HGSV ss80068328 Dec 15, 2007 (130)
9 BCMHGSC_JDW ss91648275 Mar 24, 2008 (129)
10 HUMANGENOME_JCVI ss96186996 Feb 06, 2009 (130)
11 BGI ss106180409 Feb 06, 2009 (130)
12 1000GENOMES ss111769064 Jan 25, 2009 (130)
13 1000GENOMES ss113120727 Jan 25, 2009 (130)
14 IGMI-SNU ss115463308 Feb 06, 2009 (130)
15 ILLUMINA-UK ss117494309 Feb 14, 2009 (130)
16 ENSEMBL ss135760069 Dec 01, 2009 (131)
17 ENSEMBL ss138214855 Dec 01, 2009 (131)
18 GMI ss156200352 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss167862552 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss169159231 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss171932906 Jul 04, 2010 (132)
22 BUSHMAN ss203840147 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss208601634 Jul 04, 2010 (132)
24 1000GENOMES ss228272713 Jul 14, 2010 (132)
25 1000GENOMES ss237775435 Jul 15, 2010 (132)
26 1000GENOMES ss243958588 Jul 15, 2010 (132)
27 GMI ss283311514 May 04, 2012 (137)
28 GMI ss287427857 Apr 25, 2013 (138)
29 PJP ss292617558 May 09, 2011 (134)
30 TISHKOFF ss566154719 Apr 25, 2013 (138)
31 SSMP ss662027626 Apr 25, 2013 (138)
32 EVA-GONL ss994571877 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1082097106 Aug 21, 2014 (142)
34 1000GENOMES ss1364182351 Aug 21, 2014 (142)
35 DDI ss1429005695 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1579450074 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1638476682 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1681470715 Apr 01, 2015 (144)
39 EVA_DECODE ss1698628201 Apr 01, 2015 (144)
40 HAMMER_LAB ss1809435618 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1938080182 Feb 12, 2016 (147)
42 GENOMED ss1969098557 Jul 19, 2016 (147)
43 JJLAB ss2029821034 Sep 14, 2016 (149)
44 USC_VALOUEV ss2158374810 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2241573471 Dec 20, 2016 (150)
46 SYSTEMSBIOZJU ss2629406813 Nov 08, 2017 (151)
47 GRF ss2704048560 Nov 08, 2017 (151)
48 GNOMAD ss2965766347 Nov 08, 2017 (151)
49 AFFY ss2985210394 Nov 08, 2017 (151)
50 AFFY ss2985831395 Nov 08, 2017 (151)
51 SWEGEN ss3017916149 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3028743891 Nov 08, 2017 (151)
53 CSHL ss3352433752 Nov 08, 2017 (151)
54 URBANLAB ss3650978198 Oct 12, 2018 (152)
55 ILLUMINA ss3653978907 Oct 12, 2018 (152)
56 EGCUT_WGS ss3684635295 Jul 13, 2019 (153)
57 EVA_DECODE ss3706617814 Jul 13, 2019 (153)
58 ACPOP ss3743275643 Jul 13, 2019 (153)
59 EVA ss3758459219 Jul 13, 2019 (153)
60 PACBIO ss3788607515 Jul 13, 2019 (153)
61 PACBIO ss3793506544 Jul 13, 2019 (153)
62 PACBIO ss3798393693 Jul 13, 2019 (153)
63 KHV_HUMAN_GENOMES ss3821631035 Jul 13, 2019 (153)
64 EVA ss3835603532 Apr 27, 2020 (154)
65 EVA ss3841427136 Apr 27, 2020 (154)
66 EVA ss3846934995 Apr 27, 2020 (154)
67 SGDP_PRJ ss3888793627 Apr 27, 2020 (154)
68 KRGDB ss3938988624 Apr 27, 2020 (154)
69 EVA ss3985869745 Apr 27, 2021 (155)
70 TOPMED ss5083314992 Apr 27, 2021 (155)
71 TOMMO_GENOMICS ss5228972226 Apr 27, 2021 (155)
72 1000G_HIGH_COVERAGE ss5308187707 Oct 13, 2022 (156)
73 EVA ss5436451156 Oct 13, 2022 (156)
74 HUGCELL_USP ss5500578452 Oct 13, 2022 (156)
75 EVA ss5512165069 Oct 13, 2022 (156)
76 1000G_HIGH_COVERAGE ss5614324310 Oct 13, 2022 (156)
77 SANFORD_IMAGENETICS ss5662923757 Oct 13, 2022 (156)
78 TOMMO_GENOMICS ss5787996054 Oct 13, 2022 (156)
79 YY_MCH ss5817841787 Oct 13, 2022 (156)
80 EVA ss5845486389 Oct 13, 2022 (156)
81 EVA ss5853081276 Oct 13, 2022 (156)
82 EVA ss5922793971 Oct 13, 2022 (156)
83 EVA ss5957829684 Oct 13, 2022 (156)
84 1000Genomes NC_000020.10 - 14513687 Oct 12, 2018 (152)
85 1000Genomes_30x NC_000020.11 - 14533041 Oct 13, 2022 (156)
86 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 14513687 Oct 12, 2018 (152)
87 Genetic variation in the Estonian population NC_000020.10 - 14513687 Oct 12, 2018 (152)
88 The Danish reference pan genome NC_000020.10 - 14513687 Apr 27, 2020 (154)
89 gnomAD - Genomes NC_000020.11 - 14533041 Apr 27, 2021 (155)
90 Genome of the Netherlands Release 5 NC_000020.10 - 14513687 Apr 27, 2020 (154)
91 KOREAN population from KRGDB NC_000020.10 - 14513687 Apr 27, 2020 (154)
92 Northern Sweden NC_000020.10 - 14513687 Jul 13, 2019 (153)
93 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000020.10 - 14513687 Apr 27, 2021 (155)
94 Qatari NC_000020.10 - 14513687 Apr 27, 2020 (154)
95 SGDP_PRJ NC_000020.10 - 14513687 Apr 27, 2020 (154)
96 Siberian NC_000020.10 - 14513687 Apr 27, 2020 (154)
97 8.3KJPN NC_000020.10 - 14513687 Apr 27, 2021 (155)
98 14KJPN NC_000020.11 - 14533041 Oct 13, 2022 (156)
99 TopMed NC_000020.11 - 14533041 Apr 27, 2021 (155)
100 UK 10K study - Twins NC_000020.10 - 14513687 Oct 12, 2018 (152)
101 A Vietnamese Genetic Variation Database NC_000020.10 - 14513687 Jul 13, 2019 (153)
102 ALFA NC_000020.11 - 14533041 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).

Associated ID History Updated (Build)
rs60724328 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78411903, ss80068328, ss91648275, ss111769064, ss113120727, ss117494309, ss167862552, ss169159231, ss171932906, ss203840147, ss208601634, ss283311514, ss287427857, ss292617558, ss1698628201 NC_000020.9:14461686:G:A NC_000020.11:14533040:G:A (self)
77626113, 42975647, 30373543, 5615013, 19149450, 46166018, 16560508, 1095672, 20122104, 40810607, 10891164, 86941533, 42975647, 9488199, ss228272713, ss237775435, ss243958588, ss566154719, ss662027626, ss994571877, ss1082097106, ss1364182351, ss1429005695, ss1579450074, ss1638476682, ss1681470715, ss1809435618, ss1938080182, ss1969098557, ss2029821034, ss2158374810, ss2629406813, ss2704048560, ss2965766347, ss2985210394, ss2985831395, ss3017916149, ss3352433752, ss3653978907, ss3684635295, ss3743275643, ss3758459219, ss3788607515, ss3793506544, ss3798393693, ss3835603532, ss3841427136, ss3888793627, ss3938988624, ss3985869745, ss5228972226, ss5436451156, ss5512165069, ss5662923757, ss5845486389, ss5957829684 NC_000020.10:14513686:G:A NC_000020.11:14533040:G:A (self)
101850245, 547336463, 121833158, 358423937, 9654706734, ss2241573471, ss3028743891, ss3650978198, ss3706617814, ss3821631035, ss3846934995, ss5083314992, ss5308187707, ss5500578452, ss5614324310, ss5787996054, ss5817841787, ss5853081276, ss5922793971 NC_000020.11:14533040:G:A NC_000020.11:14533040:G:A (self)
ss2414393, ss5196866, ss8340572, ss19477183, ss21772299, ss41378665, ss96186996, ss106180409, ss115463308, ss135760069, ss138214855, ss156200352 NT_011387.8:14453686:G:A NC_000020.11:14533040:G:A (self)
46166018, ss3938988624 NC_000020.10:14513686:G:T NC_000020.11:14533040:G: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 rs1569997

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