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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.

rs187490

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:35045022 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.340300 (90074/264690, TOPMED)
G=0.342867 (48011/140028, GnomAD)
G=0.31937 (16514/51708, ALFA) (+ 19 more)
G=0.30834 (8713/28258, 14KJPN)
G=0.30835 (5168/16760, 8.3KJPN)
G=0.3849 (2465/6404, 1000G_30x)
G=0.3830 (1918/5008, 1000G)
G=0.3179 (1424/4480, Estonian)
G=0.2901 (1118/3854, ALSPAC)
G=0.3026 (1122/3708, TWINSUK)
G=0.3171 (929/2930, KOREAN)
G=0.3496 (660/1888, HapMap)
G=0.3095 (567/1832, Korea1K)
G=0.262 (261/998, GoNL)
G=0.236 (148/626, Chileans)
G=0.385 (231/600, NorthernSweden)
A=0.381 (115/302, SGDP_PRJ)
G=0.315 (68/216, Qatari)
G=0.280 (60/214, Vietnamese)
G=0.19 (16/84, Ancient Sardinia)
G=0.17 (7/40, GENOME_DK)
A=0.39 (14/36, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AGXT2 : Intron Variant
Publications
1 citation
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 51708 A=0.68063 G=0.31937
European Sub 33772 A=0.69250 G=0.30750
African Sub 5612 A=0.5798 G=0.4202
African Others Sub 192 A=0.464 G=0.536
African American Sub 5420 A=0.5839 G=0.4161
Asian Sub 484 A=0.698 G=0.302
East Asian Sub 388 A=0.701 G=0.299
Other Asian Sub 96 A=0.69 G=0.31
Latin American 1 Sub 720 A=0.681 G=0.319
Latin American 2 Sub 7046 A=0.7100 G=0.2900
South Asian Sub 174 A=0.540 G=0.460
Other Sub 3900 A=0.6738 G=0.3262


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=0.659700 G=0.340300
gnomAD - Genomes Global Study-wide 140028 A=0.657133 G=0.342867
gnomAD - Genomes European Sub 75866 A=0.69184 G=0.30816
gnomAD - Genomes African Sub 41928 A=0.57282 G=0.42718
gnomAD - Genomes American Sub 13644 A=0.70192 G=0.29808
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.6869 G=0.3131
gnomAD - Genomes East Asian Sub 3122 A=0.7114 G=0.2886
gnomAD - Genomes Other Sub 2146 A=0.6678 G=0.3322
Allele Frequency Aggregator Total Global 51708 A=0.68063 G=0.31937
Allele Frequency Aggregator European Sub 33772 A=0.69250 G=0.30750
Allele Frequency Aggregator Latin American 2 Sub 7046 A=0.7100 G=0.2900
Allele Frequency Aggregator African Sub 5612 A=0.5798 G=0.4202
Allele Frequency Aggregator Other Sub 3900 A=0.6738 G=0.3262
Allele Frequency Aggregator Latin American 1 Sub 720 A=0.681 G=0.319
Allele Frequency Aggregator Asian Sub 484 A=0.698 G=0.302
Allele Frequency Aggregator South Asian Sub 174 A=0.540 G=0.460
14KJPN JAPANESE Study-wide 28258 A=0.69166 G=0.30834
8.3KJPN JAPANESE Study-wide 16760 A=0.69165 G=0.30835
1000Genomes_30x Global Study-wide 6404 A=0.6151 G=0.3849
1000Genomes_30x African Sub 1786 A=0.5493 G=0.4507
1000Genomes_30x Europe Sub 1266 A=0.6746 G=0.3254
1000Genomes_30x South Asian Sub 1202 A=0.5058 G=0.4942
1000Genomes_30x East Asian Sub 1170 A=0.6872 G=0.3128
1000Genomes_30x American Sub 980 A=0.706 G=0.294
1000Genomes Global Study-wide 5008 A=0.6170 G=0.3830
1000Genomes African Sub 1322 A=0.5507 G=0.4493
1000Genomes East Asian Sub 1008 A=0.6905 G=0.3095
1000Genomes Europe Sub 1006 A=0.6700 G=0.3300
1000Genomes South Asian Sub 978 A=0.513 G=0.487
1000Genomes American Sub 694 A=0.706 G=0.294
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.6821 G=0.3179
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.7099 G=0.2901
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.6974 G=0.3026
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.6829 G=0.3171
HapMap Global Study-wide 1888 A=0.6504 G=0.3496
HapMap American Sub 766 A=0.649 G=0.351
HapMap African Sub 692 A=0.617 G=0.383
HapMap Asian Sub 254 A=0.689 G=0.311
HapMap Europe Sub 176 A=0.733 G=0.267
Korean Genome Project KOREAN Study-wide 1832 A=0.6905 G=0.3095
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.738 G=0.262
Chileans Chilean Study-wide 626 A=0.764 G=0.236
Northern Sweden ACPOP Study-wide 600 A=0.615 G=0.385
SGDP_PRJ Global Study-wide 302 A=0.381 G=0.619
Qatari Global Study-wide 216 A=0.685 G=0.315
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.720 G=0.280
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 84 A=0.81 G=0.19
The Danish reference pan genome Danish Study-wide 40 A=0.82 G=0.17
Siberian Global Study-wide 36 A=0.39 G=0.61
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 5 NC_000005.10:g.35045022A>G
GRCh37.p13 chr 5 NC_000005.9:g.35045127A>G
Gene: AGXT2, alanine--glyoxylate aminotransferase 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
AGXT2 transcript variant 2 NM_001306173.2:c.88+2783T…

NM_001306173.2:c.88+2783T>C

N/A Intron Variant
AGXT2 transcript variant 1 NM_031900.4:c.88+2783T>C N/A Intron Variant
AGXT2 transcript variant X1 XM_005248337.4:c.88+2783T…

XM_005248337.4:c.88+2783T>C

N/A Intron Variant
AGXT2 transcript variant X2 XM_005248338.4:c.88+2783T…

XM_005248338.4:c.88+2783T>C

N/A Intron Variant
AGXT2 transcript variant X3 XM_017009748.3:c.88+2783T…

XM_017009748.3:c.88+2783T>C

N/A Intron Variant
AGXT2 transcript variant X4 XM_047417534.1:c.-100+278…

XM_047417534.1:c.-100+2783T>C

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= G
GRCh38.p14 chr 5 NC_000005.10:g.35045022= NC_000005.10:g.35045022A>G
GRCh37.p13 chr 5 NC_000005.9:g.35045127= NC_000005.9:g.35045127A>G
AGXT2 transcript variant 2 NM_001306173.2:c.88+2783= NM_001306173.2:c.88+2783T>C
AGXT2 transcript variant 1 NM_031900.3:c.88+2783= NM_031900.3:c.88+2783T>C
AGXT2 transcript variant 1 NM_031900.4:c.88+2783= NM_031900.4:c.88+2783T>C
AGXT2 transcript variant X1 XM_005248337.1:c.88+2783= XM_005248337.1:c.88+2783T>C
AGXT2 transcript variant X1 XM_005248337.4:c.88+2783= XM_005248337.4:c.88+2783T>C
AGXT2 transcript variant X2 XM_005248338.1:c.88+2783= XM_005248338.1:c.88+2783T>C
AGXT2 transcript variant X2 XM_005248338.4:c.88+2783= XM_005248338.4:c.88+2783T>C
AGXT2 transcript variant X3 XM_005248339.1:c.88+2783= XM_005248339.1:c.88+2783T>C
AGXT2 transcript variant X3 XM_017009748.3:c.88+2783= XM_017009748.3:c.88+2783T>C
AGXT2 transcript variant X4 XM_047417534.1:c.-100+2783= XM_047417534.1:c.-100+2783T>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#.

81 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss248111 Jul 12, 2000 (79)
2 SC_JCM ss461628 Jul 16, 2000 (80)
3 KWOK ss919474 Oct 04, 2000 (86)
4 TSC-CSHL ss1304703 Oct 05, 2000 (92)
5 SC_JCM ss3723536 Sep 28, 2001 (100)
6 WI_SSAHASNP ss14678218 Dec 05, 2003 (119)
7 CSHL-HAPMAP ss19643563 Feb 27, 2004 (120)
8 PERLEGEN ss24425854 Sep 20, 2004 (123)
9 ABI ss44586534 Mar 14, 2006 (126)
10 PERLEGEN ss68932158 May 17, 2007 (127)
11 AFFY ss76452150 Dec 08, 2007 (130)
12 HGSV ss78160180 Dec 06, 2007 (129)
13 HGSV ss81298088 Dec 15, 2007 (130)
14 BCMHGSC_JDW ss93058515 Mar 24, 2008 (129)
15 BGI ss104185384 Dec 01, 2009 (131)
16 KRIBB_YJKIM ss104810480 Feb 06, 2009 (130)
17 1000GENOMES ss108954015 Jan 23, 2009 (130)
18 1000GENOMES ss111684983 Jan 25, 2009 (130)
19 ILLUMINA-UK ss116564815 Feb 14, 2009 (130)
20 ENSEMBL ss143029044 Dec 01, 2009 (131)
21 GMI ss155294101 Dec 01, 2009 (131)
22 ILLUMINA ss160470130 Dec 01, 2009 (131)
23 COMPLETE_GENOMICS ss162168233 Jul 04, 2010 (132)
24 COMPLETE_GENOMICS ss164688202 Jul 04, 2010 (132)
25 BUSHMAN ss200106116 Jul 04, 2010 (132)
26 BCM-HGSC-SUB ss207088852 Jul 04, 2010 (132)
27 1000GENOMES ss221619784 Jul 14, 2010 (132)
28 1000GENOMES ss232901640 Jul 14, 2010 (132)
29 1000GENOMES ss240084640 Jul 15, 2010 (132)
30 GMI ss278243058 May 04, 2012 (137)
31 PJP ss293566801 May 09, 2011 (134)
32 ILLUMINA ss481096125 Sep 08, 2015 (146)
33 TISHKOFF ss558319433 Apr 25, 2013 (138)
34 SSMP ss652174529 Apr 25, 2013 (138)
35 EVA-GONL ss981438481 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1072535993 Aug 21, 2014 (142)
37 1000GENOMES ss1314612453 Aug 21, 2014 (142)
38 DDI ss1430306123 Apr 01, 2015 (144)
39 EVA_GENOME_DK ss1581090444 Apr 01, 2015 (144)
40 EVA_DECODE ss1590960722 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1612639367 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1655633400 Apr 01, 2015 (144)
43 EVA_SVP ss1712756482 Apr 01, 2015 (144)
44 HAMMER_LAB ss1803349265 Sep 08, 2015 (146)
45 WEILL_CORNELL_DGM ss1924701392 Feb 12, 2016 (147)
46 GENOMED ss1970061841 Jul 19, 2016 (147)
47 JJLAB ss2022953429 Sep 14, 2016 (149)
48 USC_VALOUEV ss2151104128 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2272804693 Dec 20, 2016 (150)
50 GRF ss2706640367 Nov 08, 2017 (151)
51 GNOMAD ss2823174583 Nov 08, 2017 (151)
52 SWEGEN ss2996727697 Nov 08, 2017 (151)
53 BIOINF_KMB_FNS_UNIBA ss3025262125 Nov 08, 2017 (151)
54 CSHL ss3346332300 Nov 08, 2017 (151)
55 ILLUMINA ss3636708086 Oct 12, 2018 (152)
56 EGCUT_WGS ss3664620336 Jul 13, 2019 (153)
57 EVA_DECODE ss3714455276 Jul 13, 2019 (153)
58 ACPOP ss3732251764 Jul 13, 2019 (153)
59 EVA ss3763285487 Jul 13, 2019 (153)
60 KHV_HUMAN_GENOMES ss3806461220 Jul 13, 2019 (153)
61 EVA ss3829189338 Apr 26, 2020 (154)
62 EVA ss3838063932 Apr 26, 2020 (154)
63 EVA ss3843503168 Apr 26, 2020 (154)
64 SGDP_PRJ ss3861600560 Apr 26, 2020 (154)
65 KRGDB ss3908072407 Apr 26, 2020 (154)
66 KOGIC ss3956418013 Apr 26, 2020 (154)
67 EVA ss3985134697 Apr 26, 2021 (155)
68 TOPMED ss4655680336 Apr 26, 2021 (155)
69 TOMMO_GENOMICS ss5171186139 Apr 26, 2021 (155)
70 1000G_HIGH_COVERAGE ss5263512823 Oct 13, 2022 (156)
71 EVA ss5356791353 Oct 13, 2022 (156)
72 HUGCELL_USP ss5461785290 Oct 13, 2022 (156)
73 EVA ss5507977368 Oct 13, 2022 (156)
74 1000G_HIGH_COVERAGE ss5546907544 Oct 13, 2022 (156)
75 SANFORD_IMAGENETICS ss5637559808 Oct 13, 2022 (156)
76 TOMMO_GENOMICS ss5707079013 Oct 13, 2022 (156)
77 YY_MCH ss5806181344 Oct 13, 2022 (156)
78 EVA ss5834768602 Oct 13, 2022 (156)
79 EVA ss5854765191 Oct 13, 2022 (156)
80 EVA ss5893700664 Oct 13, 2022 (156)
81 EVA ss5965974725 Oct 13, 2022 (156)
82 1000Genomes NC_000005.9 - 35045127 Oct 12, 2018 (152)
83 1000Genomes_30x NC_000005.10 - 35045022 Oct 13, 2022 (156)
84 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 35045127 Oct 12, 2018 (152)
85 Chileans NC_000005.9 - 35045127 Apr 26, 2020 (154)
86 Genetic variation in the Estonian population NC_000005.9 - 35045127 Oct 12, 2018 (152)
87 The Danish reference pan genome NC_000005.9 - 35045127 Apr 26, 2020 (154)
88 gnomAD - Genomes NC_000005.10 - 35045022 Apr 26, 2021 (155)
89 Genome of the Netherlands Release 5 NC_000005.9 - 35045127 Apr 26, 2020 (154)
90 HapMap NC_000005.10 - 35045022 Apr 26, 2020 (154)
91 KOREAN population from KRGDB NC_000005.9 - 35045127 Apr 26, 2020 (154)
92 Korean Genome Project NC_000005.10 - 35045022 Apr 26, 2020 (154)
93 Northern Sweden NC_000005.9 - 35045127 Jul 13, 2019 (153)
94 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000005.9 - 35045127 Apr 26, 2021 (155)
95 Qatari NC_000005.9 - 35045127 Apr 26, 2020 (154)
96 SGDP_PRJ NC_000005.9 - 35045127 Apr 26, 2020 (154)
97 Siberian NC_000005.9 - 35045127 Apr 26, 2020 (154)
98 8.3KJPN NC_000005.9 - 35045127 Apr 26, 2021 (155)
99 14KJPN NC_000005.10 - 35045022 Oct 13, 2022 (156)
100 TopMed NC_000005.10 - 35045022 Apr 26, 2021 (155)
101 UK 10K study - Twins NC_000005.9 - 35045127 Oct 12, 2018 (152)
102 A Vietnamese Genetic Variation Database NC_000005.9 - 35045127 Jul 13, 2019 (153)
103 ALFA NC_000005.10 - 35045022 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)
rs879102 Jan 18, 2001 (92)
rs17306459 Oct 08, 2004 (123)
rs56563765 May 26, 2008 (130)
rs60759165 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78160180, ss81298088, ss93058515, ss108954015, ss111684983, ss116564815, ss160470130, ss162168233, ss164688202, ss200106116, ss207088852, ss278243058, ss293566801, ss1590960722, ss1712756482 NC_000005.8:35080883:A:G NC_000005.10:35045021:A:G (self)
26195796, 14568314, 343369, 10358584, 7255383, 6474500, 15249801, 5536629, 360624, 6743322, 13617540, 3620482, 29155446, 14568314, 3238829, ss221619784, ss232901640, ss240084640, ss481096125, ss558319433, ss652174529, ss981438481, ss1072535993, ss1314612453, ss1430306123, ss1581090444, ss1612639367, ss1655633400, ss1803349265, ss1924701392, ss1970061841, ss2022953429, ss2151104128, ss2706640367, ss2823174583, ss2996727697, ss3346332300, ss3636708086, ss3664620336, ss3732251764, ss3763285487, ss3829189338, ss3838063932, ss3861600560, ss3908072407, ss3985134697, ss5171186139, ss5356791353, ss5507977368, ss5637559808, ss5834768602, ss5965974725 NC_000005.9:35045126:A:G NC_000005.10:35045021:A:G (self)
34433479, 185067968, 2844314, 12796014, 40916117, 493057893, 3816231303, ss2272804693, ss3025262125, ss3714455276, ss3806461220, ss3843503168, ss3956418013, ss4655680336, ss5263512823, ss5461785290, ss5546907544, ss5707079013, ss5806181344, ss5854765191, ss5893700664 NC_000005.10:35045021:A:G NC_000005.10:35045021:A:G (self)
ss14678218, ss19643563 NT_006576.14:17497232:A:G NC_000005.10:35045021:A:G (self)
ss248111, ss461628, ss919474, ss1304703, ss3723536, ss24425854, ss44586534, ss68932158, ss76452150, ss104185384, ss104810480, ss143029044, ss155294101 NT_006576.16:35035126:A:G NC_000005.10:35045021:A:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs187490
PMID Title Author Year Journal
20547007 No association between oxytocin or prolactin gene variants and childhood-onset mood disorders. Strauss JS et al. 2010 Psychoneuroendocrinology
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