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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.

rs186364861

Current Build 157

Released September 3, 2024

Organism
Homo sapiens
Position
chr13:48037798 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.0003490 (482/1381102, GnomAD_exomes)
A=0.000589 (156/264690, TOPMED)
A=0.000450 (93/206498, ALFA) (+ 12 more)
A=0.000415 (62/149326, GnomAD_genomes)
A=0.00136 (107/78508, PAGE_STUDY)
A=0.00940 (728/77444, 38KJPN)
A=0.00146 (70/47898, ExAC)
A=0.0093 (67/7234, Korea4K)
A=0.0027 (17/6404, 1000G_30X)
A=0.0030 (15/5008, 1000G)
A=0.0086 (25/2922, KOREAN)
A=0.0093 (17/1832, Korea1K)
A=0.014 (11/792, PRJEB37584)
G=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
NUDT15 : Missense Variant
LOC124903172 : Non Coding Transcript 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 206498 G=0.999550 A=0.000450 0.999099 0.0 0.000901 0
European Sub 171826 G=0.999965 A=0.000035 0.99993 0.0 0.00007 0
African Sub 9354 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 360 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 8994 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 6314 G=0.9903 A=0.0097 0.980678 0.0 0.019322 0
East Asian Sub 4466 G=0.9908 A=0.0092 0.981639 0.0 0.018361 0
Other Asian Sub 1848 G=0.9892 A=0.0108 0.978355 0.0 0.021645 0
Latin American 1 Sub 796 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 968 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 274 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Sub 16966 G=0.99847 A=0.00153 0.996935 0.0 0.003065 0


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
gnomAD v4 - Exomes Global Study-wide 1381102 G=0.9996510 A=0.0003490
gnomAD v4 - Exomes European Sub 1155928 G=0.9999879 A=0.0000121
gnomAD v4 - Exomes South Asian Sub 82712 G=0.99965 A=0.00035
gnomAD v4 - Exomes American Sub 40036 G=1.00000 A=0.00000
gnomAD v4 - Exomes East Asian Sub 39000 G=0.98895 A=0.01105
gnomAD v4 - Exomes African Sub 33356 G=0.99994 A=0.00006
gnomAD v4 - Exomes Ashkenazi Jewish Sub 25578 G=0.99977 A=0.00023
gnomAD v4 - Exomes Middle Eastern sub 4492 G=1.0000 A=0.0000
TopMed Global Study-wide 264690 G=0.999411 A=0.000589
Allele Frequency Aggregator Total Global 206498 G=0.999550 A=0.000450
Allele Frequency Aggregator European Sub 171826 G=0.999965 A=0.000035
Allele Frequency Aggregator Other Sub 16966 G=0.99847 A=0.00153
Allele Frequency Aggregator African Sub 9354 G=1.0000 A=0.0000
Allele Frequency Aggregator Asian Sub 6314 G=0.9903 A=0.0097
Allele Frequency Aggregator Latin American 2 Sub 968 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 796 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 274 G=1.000 A=0.000
gnomAD v4 - Genomes Global Study-wide 149326 G=0.999585 A=0.000415
gnomAD v4 - Genomes European Sub 78662 G=0.99999 A=0.00001
gnomAD v4 - Genomes African Sub 41590 G=1.00000 A=0.00000
gnomAD v4 - Genomes American Sub 15312 G=1.00000 A=0.00000
gnomAD v4 - Genomes East Asian Sub 5164 G=0.9892 A=0.0108
gnomAD v4 - Genomes South Asian Sub 4832 G=0.9992 A=0.0008
gnomAD v4 - Genomes Ashkenazi Jewish Sub 3472 G=0.9997 A=0.0003
gnomAD v4 - Genomes Middle Eastern sub 294 G=1.000 A=0.000
The PAGE Study Global Study-wide 78508 G=0.99864 A=0.00136
The PAGE Study AfricanAmerican Sub 32374 G=0.99981 A=0.00019
The PAGE Study Mexican Sub 10804 G=0.99981 A=0.00019
The PAGE Study Asian Sub 8316 G=0.9900 A=0.0100
The PAGE Study PuertoRican Sub 7914 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4500 G=0.9971 A=0.0029
The PAGE Study Cuban Sub 4228 G=0.9995 A=0.0005
The PAGE Study Dominican Sub 3828 G=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2448 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1980 G=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=0.999 A=0.001
38KJPN JAPANESE Study-wide 77444 G=0.99060 A=0.00940
ExAC Global Study-wide 47898 G=0.99854 A=0.00146
ExAC Europe Sub 26914 G=0.99996 A=0.00004
ExAC Asian Sub 13856 G=0.99502 A=0.00498
ExAC African Sub 5092 G=1.0000 A=0.0000
ExAC American Sub 1710 G=1.0000 A=0.0000
ExAC Other Sub 326 G=1.000 A=0.000
Korean Genome Project 4K KOREAN Study-wide 7234 G=0.9907 A=0.0093
1000Genomes_30X Global Study-wide 6404 G=0.9973 A=0.0027
1000Genomes_30X African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30X Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30X South Asian Sub 1202 G=0.9992 A=0.0008
1000Genomes_30X East Asian Sub 1170 G=0.9863 A=0.0137
1000Genomes_30X American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9970 A=0.0030
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9861 A=0.0139
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=0.999 A=0.001
1000Genomes American Sub 694 G=1.000 A=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9914 A=0.0086
Korean Genome Project KOREAN Study-wide 1832 G=0.9907 A=0.0093
CNV burdens in cranial meningiomas Global Study-wide 792 G=0.986 A=0.014
CNV burdens in cranial meningiomas CRM Sub 792 G=0.986 A=0.014
SGDP_PRJ Global Study-wide 2 G=0.5 A=0.5
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 13 NC_000013.11:g.48037798G>A
GRCh37.p13 chr 13 NC_000013.10:g.48611934G>A
NUDT15 RefSeqGene NG_047021.1:g.5232G>A
LOC127826269 genomic region NG_127776.1:g.1045G>A
LOC127826270 genomic region NG_127777.1:g.168G>A
Gene: NUDT15, nudix hydrolase 15 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NUDT15 transcript variant 1 NM_018283.4:c.52G>A V [GTC] > I [ATC] Coding Sequence Variant
nucleotide triphosphate diphosphatase NUDT15 isoform 1 NP_060753.1:p.Val18Ile V (Val) > I (Ile) Missense Variant
NUDT15 transcript variant 2 NM_001304745.2:c.52G>A V [GTC] > I [ATC] Coding Sequence Variant
nucleotide triphosphate diphosphatase NUDT15 isoform 2 NP_001291674.1:p.Val18Ile V (Val) > I (Ile) Missense Variant
NUDT15 transcript variant 4 NR_136688.2:n.73G>A N/A Non Coding Transcript Variant
NUDT15 transcript variant 3 NR_136687.2:n.73G>A N/A Non Coding Transcript Variant
Gene: LOC124903172, uncharacterized LOC124903172 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124903172 transcript XR_007063788.1:n.195C>T N/A Non Coding 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: A (allele ID: 227131 )
ClinVar Accession Disease Names Clinical Significance
RCV000210850.2 Thiopurines, poor metabolism of, 2 Drug-Response
RCV003937795.1 NUDT15-related disorder Likely-Benign
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
GRCh38.p14 chr 13 NC_000013.11:g.48037798= NC_000013.11:g.48037798G>A
GRCh37.p13 chr 13 NC_000013.10:g.48611934= NC_000013.10:g.48611934G>A
NUDT15 RefSeqGene NG_047021.1:g.5232= NG_047021.1:g.5232G>A
NUDT15 transcript variant 1 NM_018283.4:c.52= NM_018283.4:c.52G>A
NUDT15 transcript variant 1 NM_018283.3:c.52= NM_018283.3:c.52G>A
NUDT15 transcript variant 1 NM_018283.2:c.52= NM_018283.2:c.52G>A
NUDT15 transcript NM_018283.1:c.52= NM_018283.1:c.52G>A
NUDT15 transcript variant 3 NR_136687.2:n.73= NR_136687.2:n.73G>A
NUDT15 transcript variant 3 NR_136687.1:n.232= NR_136687.1:n.232G>A
NUDT15 transcript variant 4 NR_136688.2:n.73= NR_136688.2:n.73G>A
NUDT15 transcript variant 4 NR_136688.1:n.232= NR_136688.1:n.232G>A
NUDT15 transcript variant 2 NM_001304745.2:c.52= NM_001304745.2:c.52G>A
NUDT15 transcript variant 2 NM_001304745.1:c.52= NM_001304745.1:c.52G>A
LOC127826269 genomic region NG_127776.1:g.1045= NG_127776.1:g.1045G>A
LOC127826270 genomic region NG_127777.1:g.168= NG_127777.1:g.168G>A
LOC124903172 transcript XR_007063788.1:n.195= XR_007063788.1:n.195C>T
nucleotide triphosphate diphosphatase NUDT15 isoform 1 NP_060753.1:p.Val18= NP_060753.1:p.Val18Ile
nucleotide triphosphate diphosphatase NUDT15 isoform 2 NP_001291674.1:p.Val18= NP_001291674.1:p.Val18Ile
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#.

55 SubSNP, 14 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss463351466 Sep 17, 2011 (135)
2 1000GENOMES ss491059964 May 04, 2012 (137)
3 EXOME_CHIP ss491478994 May 04, 2012 (137)
4 ILLUMINA ss780773477 Sep 08, 2015 (146)
5 ILLUMINA ss783453266 Sep 08, 2015 (146)
6 1000GENOMES ss1348162918 Aug 21, 2014 (142)
7 EVA_EXAC ss1691286294 Apr 01, 2015 (144)
8 ILLUMINA ss1752106535 Sep 08, 2015 (146)
9 ILLUMINA ss1917883410 Feb 12, 2016 (147)
10 ILLUMINA ss1946360844 Feb 12, 2016 (147)
11 ILLUMINA ss1959500723 Feb 12, 2016 (147)
12 AMU ss1966651959 Feb 12, 2016 (147)
13 HUMAN_LONGEVITY ss2196204960 Dec 20, 2016 (150)
14 GRF ss2700377258 Nov 08, 2017 (151)
15 GNOMAD ss2740407659 Nov 08, 2017 (151)
16 GNOMAD ss2749045157 Nov 08, 2017 (151)
17 GNOMAD ss2919474549 Nov 08, 2017 (151)
18 ILLUMINA ss3021507475 Nov 08, 2017 (151)
19 ILLUMINA ss3627062965 Oct 12, 2018 (152)
20 ILLUMINA ss3634544525 Oct 12, 2018 (152)
21 ILLUMINA ss3640251855 Oct 12, 2018 (152)
22 ILLUMINA ss3644613879 Oct 12, 2018 (152)
23 ILLUMINA ss3651895067 Oct 12, 2018 (152)
24 ILLUMINA ss3744405947 Jul 13, 2019 (153)
25 ILLUMINA ss3744845218 Jul 13, 2019 (153)
26 EVA ss3751446750 Jul 13, 2019 (153)
27 PAGE_CC ss3771745936 Jul 13, 2019 (153)
28 ILLUMINA ss3772344286 Jul 13, 2019 (153)
29 KHV_HUMAN_GENOMES ss3816776905 Jul 13, 2019 (153)
30 SGDP_PRJ ss3879945349 Apr 27, 2020 (154)
31 KRGDB ss3928796378 Apr 27, 2020 (154)
32 KOGIC ss3973534016 Apr 27, 2020 (154)
33 EVA ss3984680230 Apr 26, 2021 (155)
34 EVA ss3986601548 Apr 26, 2021 (155)
35 TOPMED ss4945746781 Apr 26, 2021 (155)
36 TOMMO_GENOMICS ss6141980591 Nov 03, 2024 (157)
37 EVA ss6263383776 Nov 03, 2024 (157)
38 EVA ss6312201376 Nov 03, 2024 (157)
39 EVA ss6349855885 Nov 03, 2024 (157)
40 KOGIC ss6388480792 Nov 03, 2024 (157)
41 GNOMAD ss6449874102 Nov 03, 2024 (157)
42 GNOMAD ss6934455725 Nov 03, 2024 (157)
43 TOMMO_GENOMICS ss8209927424 Nov 03, 2024 (157)
44 EVA ss8236912907 Nov 03, 2024 (157)
45 1000G_HIGH_COVERAGE ss8293681542 Nov 03, 2024 (157)
46 EVA ss8315683108 Nov 03, 2024 (157)
47 EVA ss8410672973 Nov 03, 2024 (157)
48 1000G_HIGH_COVERAGE ss8592604079 Nov 03, 2024 (157)
49 TOMMO_GENOMICS ss8761782728 Nov 03, 2024 (157)
50 EVA ss8799403951 Nov 03, 2024 (157)
51 YY_MCH ss8814099642 Nov 03, 2024 (157)
52 EVA ss8847698398 Nov 03, 2024 (157)
53 EVA ss8925048279 Nov 03, 2024 (157)
54 EVA ss8946159995 Nov 03, 2024 (157)
55 EVA ss8981769092 Nov 03, 2024 (157)
56 1000Genomes NC_000013.10 - 48611934 Oct 12, 2018 (152)
57 1000Genomes_30X NC_000013.11 - 48037798 Nov 03, 2024 (157)
58 ExAC NC_000013.10 - 48611934 Oct 12, 2018 (152)
59 gnomAD v4 - Exomes NC_000013.11 - 48037798 Nov 03, 2024 (157)
60 gnomAD v4 - Genomes NC_000013.11 - 48037798 Nov 03, 2024 (157)
61 KOREAN population from KRGDB NC_000013.10 - 48611934 Apr 27, 2020 (154)
62 Korean Genome Project NC_000013.11 - 48037798 Apr 27, 2020 (154)
63 Korean Genome Project 4K NC_000013.11 - 48037798 Nov 03, 2024 (157)
64 The PAGE Study NC_000013.11 - 48037798 Jul 13, 2019 (153)
65 CNV burdens in cranial meningiomas NC_000013.10 - 48611934 Apr 26, 2021 (155)
66 SGDP_PRJ NC_000013.10 - 48611934 Apr 27, 2020 (154)
67 38KJPN NC_000013.11 - 48037798 Nov 03, 2024 (157)
68 TopMed NC_000013.11 - 48037798 Apr 26, 2021 (155)
69 ALFA NC_000013.11 - 48037798 Nov 03, 2024 (157)
70 ClinVar RCV000210850.2 Oct 16, 2022 (156)
71 ClinVar RCV003937795.1 Nov 03, 2024 (157)
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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
61032022, 1615028, 35973772, 229735, 31962329, ss463351466, ss491059964, ss491478994, ss780773477, ss783453266, ss1348162918, ss1691286294, ss1752106535, ss1917883410, ss1946360844, ss1959500723, ss1966651959, ss2700377258, ss2740407659, ss2749045157, ss2919474549, ss3021507475, ss3627062965, ss3634544525, ss3640251855, ss3644613879, ss3651895067, ss3744405947, ss3744845218, ss3751446750, ss3772344286, ss3879945349, ss3928796378, ss3984680230, ss3986601548, ss6263383776, ss6312201376, ss6349855885, ss8209927424, ss8315683108, ss8410672973, ss8799403951, ss8847698398, ss8946159995, ss8981769092 NC_000013.10:48611933:G:A NC_000013.11:48037797:G:A (self)
RCV000210850.2, RCV003937795.1, 80130014, 45203067, 461774294, 29912017, 38332690, 967405, 159356411, 161292439, 3164343140, ss2196204960, ss3771745936, ss3816776905, ss3973534016, ss4945746781, ss6141980591, ss6388480792, ss6449874102, ss6934455725, ss8236912907, ss8293681542, ss8592604079, ss8761782728, ss8814099642, ss8925048279 NC_000013.11:48037797:G:A NC_000013.11:48037797:G:A (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 rs186364861
PMID Title Author Year Journal
26878724 NUDT15 polymorphisms alter thiopurine metabolism and hematopoietic toxicity. Moriyama T et al. 2016 Nature genetics
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.post825+45319f0