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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.

rs56393504

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr8:18400841 (GRCh38.p12) 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
A=0.002083 (501/240490, GnomAD_exome)
A=0.007597 (954/125568, TOPMED)
A=0.002531 (288/113808, ExAC) (+ 9 more)
A=0.00034 (33/97586, ALFA Project)
A=0.01173 (923/78696, PAGE_STUDY)
A=0.00672 (211/31396, GnomAD)
A=0.00988 (128/12958, GO-ESP)
A=0.0094 (47/5008, 1000G)
A=0.0000 (0/3854, ALSPAC)
A=0.0003 (1/3708, TWINSUK)
G=0.5 (3/6, SGDP_PRJ)
A=0.5 (3/6, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
NAT2 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 8 NC_000008.11:g.18400841G>A
GRCh38.p12 chr 8 NC_000008.11:g.18400841G>T
GRCh37.p13 chr 8 NC_000008.10:g.18258351G>A
GRCh37.p13 chr 8 NC_000008.10:g.18258351G>T
NAT2 RefSeqGene NG_012246.1:g.14597G>A
NAT2 RefSeqGene NG_012246.1:g.14597G>T
Gene: NAT2, N-acetyltransferase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NAT2 transcript NM_000015.3:c.838G>A V [GTG] > M [ATG] Coding Sequence Variant
arylamine N-acetyltransferase 2 NP_000006.2:p.Val280Met V (Val) > M (Met) Missense Variant
NAT2 transcript NM_000015.3:c.838G>T V [GTG] > L [TTG] Coding Sequence Variant
arylamine N-acetyltransferase 2 NP_000006.2:p.Val280Leu V (Val) > L (Leu) Missense Variant
NAT2 transcript variant X1 XM_017012938.1:c.838G>A V [GTG] > M [ATG] Coding Sequence Variant
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Val280Met V (Val) > M (Met) Missense Variant
NAT2 transcript variant X1 XM_017012938.1:c.838G>T V [GTG] > L [TTG] Coding Sequence Variant
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Val280Leu V (Val) > L (Leu) Missense 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: 722976 )
ClinVar Accession Disease Names Clinical Significance
RCV000892644.1 not provided Benign

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 230654 G=0.999237 A=0.000763
European Sub 197448 G=0.999863 A=0.000137
African Sub 5492 G=0.9789 A=0.0211
African Others Sub 186 G=0.978 A=0.022
African American Sub 5306 G=0.9789 A=0.0211
Asian Sub 6432 G=0.9997 A=0.0003
East Asian Sub 4578 G=0.9996 A=0.0004
Other Asian Sub 1854 G=1.0000 A=0.0000
Latin American 1 Sub 834 G=0.989 A=0.011
Latin American 2 Sub 1092 G=1.0000 A=0.0000
South Asian Sub 312 G=0.997 A=0.003
Other Sub 19044 G=0.99890 A=0.00110


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 - Exomes Global Study-wide 240490 G=0.997917 A=0.002083
gnomAD - Exomes European Sub 130226 G=0.999770 A=0.000230
gnomAD - Exomes Asian Sub 46600 G=0.99966 A=0.00034
gnomAD - Exomes American Sub 33160 G=0.99897 A=0.00103
gnomAD - Exomes African Sub 15360 G=0.97305 A=0.02695
gnomAD - Exomes Ashkenazi Jewish Sub 9330 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 5814 G=0.9988 A=0.0012
TopMed Global Study-wide 125568 G=0.992403 A=0.007597
ExAC Global Study-wide 113808 G=0.997469 A=0.002531
ExAC Europe Sub 69936 G=0.99971 A=0.00029
ExAC Asian Sub 22344 G=0.99973 A=0.00027
ExAC American Sub 11440 G=0.99921 A=0.00079
ExAC African Sub 9242 G=0.9728 A=0.0272
ExAC Other Sub 846 G=0.998 A=0.002
ALFA Total Global 97586 G=0.99966 A=0.00034
ALFA European Sub 87956 G=0.99985 A=0.00015
ALFA Other Sub 8474 G=0.9992 A=0.0008
ALFA African Sub 922 G=0.986 A=0.014
ALFA Asian Sub 178 G=1.000 A=0.000
ALFA Latin American 2 Sub 34 G=1.00 A=0.00
ALFA South Asian Sub 14 G=1.00 A=0.00
ALFA Latin American 1 Sub 8 G=1.0 A=0.0
The PAGE Study Global Study-wide 78696 G=0.98827 A=0.01173
The PAGE Study AfricanAmerican Sub 32512 G=0.97542 A=0.02458
The PAGE Study Mexican Sub 10810 G=0.99806 A=0.00194
The PAGE Study Asian Sub 8318 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 G=0.9958 A=0.0042
The PAGE Study NativeHawaiian Sub 4534 G=0.9996 A=0.0004
The PAGE Study Cuban Sub 4230 G=0.9957 A=0.0043
The PAGE Study Dominican Sub 3828 G=0.9911 A=0.0089
The PAGE Study CentralAmerican Sub 2450 G=0.9963 A=0.0037
The PAGE Study SouthAmerican Sub 1982 G=0.9980 A=0.0020
The PAGE Study NativeAmerican Sub 1258 G=0.9976 A=0.0024
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
gnomAD - Genomes Global Study-wide 31396 G=0.99328 A=0.00672
gnomAD - Genomes European Sub 18900 G=0.99989 A=0.00011
gnomAD - Genomes African Sub 8712 G=0.9764 A=0.0236
gnomAD - Genomes East Asian Sub 1560 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1088 G=0.9972 A=0.0028
gnomAD - Genomes American Sub 846 G=1.000 A=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 12958 G=0.99012 A=0.00988
GO Exome Sequencing Project European American Sub 8572 G=0.9995 A=0.0005
GO Exome Sequencing Project African American Sub 4386 G=0.9717 A=0.0283
1000Genomes Global Study-wide 5008 G=0.9906 A=0.0094
1000Genomes African Sub 1322 G=0.9660 A=0.0340
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9990 A=0.0010
1000Genomes South Asian Sub 978 G=0.999 A=0.001
1000Genomes American Sub 694 G=1.000 A=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=1.0000 A=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9997 A=0.0003
SGDP_PRJ Global Study-wide 6 G=0.5 A=0.5
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.p12 chr 8 NC_000008.11:g.18400841= NC_000008.11:g.18400841G>A NC_000008.11:g.18400841G>T
GRCh37.p13 chr 8 NC_000008.10:g.18258351= NC_000008.10:g.18258351G>A NC_000008.10:g.18258351G>T
NAT2 RefSeqGene NG_012246.1:g.14597= NG_012246.1:g.14597G>A NG_012246.1:g.14597G>T
NAT2 transcript NM_000015.3:c.838= NM_000015.3:c.838G>A NM_000015.3:c.838G>T
NAT2 transcript NM_000015.2:c.838= NM_000015.2:c.838G>A NM_000015.2:c.838G>T
NAT2 transcript variant X1 XM_017012938.1:c.838= XM_017012938.1:c.838G>A XM_017012938.1:c.838G>T
arylamine N-acetyltransferase 2 NP_000006.2:p.Val280= NP_000006.2:p.Val280Met NP_000006.2:p.Val280Leu
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Val280= XP_016868427.1:p.Val280Met XP_016868427.1:p.Val280Leu
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#.

63 SubSNP, 11 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CGM_KYOTO ss76869176 Dec 07, 2007 (129)
2 1000GENOMES ss115075149 Jan 25, 2009 (130)
3 SEATTLESEQ ss159716518 Dec 01, 2009 (131)
4 ILLUMINA ss161103334 Dec 01, 2009 (131)
5 COMPLETE_GENOMICS ss164094726 Jul 04, 2010 (132)
6 1000GENOMES ss223576395 Jul 14, 2010 (132)
7 NHLBI-ESP ss342253626 May 09, 2011 (134)
8 ILLUMINA ss410878058 Sep 17, 2011 (135)
9 ILLUMINA ss479271948 Sep 08, 2015 (146)
10 ILLUMINA ss482124281 May 04, 2012 (137)
11 ILLUMINA ss485580726 May 04, 2012 (137)
12 1000GENOMES ss490960731 May 04, 2012 (137)
13 EXOME_CHIP ss491410772 May 04, 2012 (137)
14 CLINSEQ_SNP ss491921844 May 04, 2012 (137)
15 ILLUMINA ss534509885 Sep 08, 2015 (146)
16 TISHKOFF ss560588646 Apr 25, 2013 (138)
17 ILLUMINA ss779464537 Sep 08, 2015 (146)
18 ILLUMINA ss780867836 Sep 08, 2015 (146)
19 ILLUMINA ss781657053 Sep 08, 2015 (146)
20 ILLUMINA ss783552767 Sep 08, 2015 (146)
21 ILLUMINA ss834934340 Sep 08, 2015 (146)
22 1000GENOMES ss1328853926 Aug 21, 2014 (142)
23 EVA_UK10K_ALSPAC ss1620100549 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1663094582 Apr 01, 2015 (144)
25 EVA_EXAC ss1689107947 Apr 01, 2015 (144)
26 ILLUMINA ss1752722196 Sep 08, 2015 (146)
27 ILLUMINA ss1917826214 Feb 12, 2016 (147)
28 ILLUMINA ss1946231123 Feb 12, 2016 (147)
29 ILLUMINA ss1959092421 Feb 12, 2016 (147)
30 ILLUMINA ss1959092422 Feb 12, 2016 (147)
31 HUMAN_LONGEVITY ss2301164583 Dec 20, 2016 (150)
32 TOPMED ss2470822181 Dec 20, 2016 (150)
33 ILLUMINA ss2634717918 Nov 08, 2017 (151)
34 ILLUMINA ss2634717919 Nov 08, 2017 (151)
35 ILLUMINA ss2711131682 Nov 08, 2017 (151)
36 GNOMAD ss2737016808 Nov 08, 2017 (151)
37 GNOMAD ss2748005977 Nov 08, 2017 (151)
38 GNOMAD ss2863932635 Nov 08, 2017 (151)
39 AFFY ss2985432624 Nov 08, 2017 (151)
40 ILLUMINA ss3022824466 Nov 08, 2017 (151)
41 ILLUMINA ss3022824467 Nov 08, 2017 (151)
42 TOPMED ss3555514811 Nov 08, 2017 (151)
43 ILLUMINA ss3625946945 Oct 12, 2018 (152)
44 ILLUMINA ss3630009740 Oct 12, 2018 (152)
45 ILLUMINA ss3630009741 Oct 12, 2018 (152)
46 ILLUMINA ss3632618573 Oct 12, 2018 (152)
47 ILLUMINA ss3635161295 Oct 12, 2018 (152)
48 ILLUMINA ss3636898285 Oct 12, 2018 (152)
49 ILLUMINA ss3640868585 Oct 12, 2018 (152)
50 ILLUMINA ss3644964297 Oct 12, 2018 (152)
51 ILLUMINA ss3653365296 Oct 12, 2018 (152)
52 ILLUMINA ss3653365297 Oct 12, 2018 (152)
53 ILLUMINA ss3654194415 Oct 12, 2018 (152)
54 ILLUMINA ss3726518847 Jul 13, 2019 (153)
55 ILLUMINA ss3744302591 Jul 13, 2019 (153)
56 ILLUMINA ss3744577642 Jul 13, 2019 (153)
57 ILLUMINA ss3745461085 Jul 13, 2019 (153)
58 PAGE_CC ss3771427500 Jul 13, 2019 (153)
59 ILLUMINA ss3772953682 Jul 13, 2019 (153)
60 KHV_HUMAN_GENOMES ss3810861621 Jul 13, 2019 (153)
61 EVA ss3824350647 Apr 26, 2020 (154)
62 EVA ss3825736892 Apr 26, 2020 (154)
63 SGDP_PRJ ss3869405020 Apr 26, 2020 (154)
64 1000Genomes NC_000008.10 - 18258351 Oct 12, 2018 (152)
65 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 18258351 Oct 12, 2018 (152)
66 ExAC NC_000008.10 - 18258351 Oct 12, 2018 (152)
67 gnomAD - Genomes NC_000008.10 - 18258351 Jul 13, 2019 (153)
68 gnomAD - Exomes NC_000008.10 - 18258351 Jul 13, 2019 (153)
69 GO Exome Sequencing Project NC_000008.10 - 18258351 Oct 12, 2018 (152)
70 The PAGE Study NC_000008.11 - 18400841 Jul 13, 2019 (153)
71 SGDP_PRJ NC_000008.10 - 18258351 Apr 26, 2020 (154)
72 TopMed NC_000008.11 - 18400841 Oct 12, 2018 (152)
73 UK 10K study - Twins NC_000008.10 - 18258351 Oct 12, 2018 (152)
74 dbGaP Population Frequency Project NC_000008.11 - 18400841 Apr 26, 2020 (154)
75 ClinVar RCV000892644.1 Apr 26, 2020 (154)
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
ss115075149, ss164094726, ss485580726, ss491921844 NC_000008.9:18302630:G:A NC_000008.11:18400840:G:A (self)
40947108, 22761479, 9201307, 111847213, 6184758, 808504, 21422000, 22761479, ss223576395, ss342253626, ss479271948, ss482124281, ss490960731, ss491410772, ss534509885, ss560588646, ss779464537, ss780867836, ss781657053, ss783552767, ss834934340, ss1328853926, ss1620100549, ss1663094582, ss1689107947, ss1752722196, ss1917826214, ss1946231123, ss1959092421, ss1959092422, ss2470822181, ss2634717918, ss2634717919, ss2711131682, ss2737016808, ss2748005977, ss2863932635, ss2985432624, ss3022824466, ss3022824467, ss3625946945, ss3630009740, ss3630009741, ss3632618573, ss3635161295, ss3636898285, ss3640868585, ss3644964297, ss3653365296, ss3653365297, ss3654194415, ss3744302591, ss3744577642, ss3745461085, ss3772953682, ss3824350647, ss3825736892, ss3869405020 NC_000008.10:18258350:G:A NC_000008.11:18400840:G:A (self)
RCV000892644.1, 648969, 384382934, 893765322, ss2301164583, ss3555514811, ss3726518847, ss3771427500, ss3810861621 NC_000008.11:18400840:G:A NC_000008.11:18400840:G:A (self)
ss76869176, ss159716518, ss161103334, ss410878058 NT_167187.1:6116496:G:A NC_000008.11:18400840:G:A (self)
ss2737016808 NC_000008.10:18258350:G:T NC_000008.11:18400840: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 rs56393504

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.post557+f76c771