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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.

rs45477599

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr8:18400073 (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
T>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000152 (38/250816, GnomAD_exome)
A=0.000422 (53/125568, TOPMED)
A=0.000174 (21/120930, ExAC) (+ 5 more)
A=0.00038 (12/31386, GnomAD)
A=0.00046 (6/13006, GO-ESP)
A=0.0006 (3/5008, 1000G)
A=0.0000 (0/2188, ALFA Project)
A=0.005 (1/216, Qatari)
Clinical Significance
Not 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.18400073T>A
GRCh37.p13 chr 8 NC_000008.10:g.18257583T>A
NAT2 RefSeqGene NG_012246.1:g.13829T>A
Gene: NAT2, N-acetyltransferase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NAT2 transcript NM_000015.3:c.70T>A L [TTA] > I [ATA] Coding Sequence Variant
arylamine N-acetyltransferase 2 NP_000006.2:p.Leu24Ile L (Leu) > I (Ile) Missense Variant
NAT2 transcript variant X1 XM_017012938.1:c.70T>A L [TTA] > I [ATA] Coding Sequence Variant
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Leu24Ile L (Leu) > I (Ile) 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.

Not Reported in ClinVar

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 79402 T=0.99995 A=0.00005, C=0.00000
European Sub 69320 T=1.00000 A=0.00000, C=0.00000
African Sub 3692 T=0.9989 A=0.0011, C=0.0000
African Others Sub 164 T=0.994 A=0.006, C=0.000
African American Sub 3528 T=0.9991 A=0.0009, C=0.0000
Asian Sub 3274 T=1.0000 A=0.0000, C=0.0000
East Asian Sub 2648 T=1.0000 A=0.0000, C=0.0000
Other Asian Sub 626 T=1.000 A=0.000, C=0.000
Latin American 1 Sub 434 T=1.000 A=0.000, C=0.000
Latin American 2 Sub 928 T=1.000 A=0.000, C=0.000
South Asian Sub 274 T=1.000 A=0.000, C=0.000
Other Sub 1480 T=1.0000 A=0.0000, C=0.0000


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 250816 T=0.999848 A=0.000152
gnomAD - Exomes European Sub 135056 T=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 48880 T=1.00000 A=0.00000
gnomAD - Exomes American Sub 34494 T=0.99988 A=0.00012
gnomAD - Exomes African Sub 16242 T=0.99797 A=0.00203
gnomAD - Exomes Ashkenazi Jewish Sub 10034 T=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6110 T=0.9998 A=0.0002
TopMed Global Study-wide 125568 T=0.999578 A=0.000422
ExAC Global Study-wide 120930 T=0.999826 A=0.000174
ExAC Europe Sub 73148 T=1.00000 A=0.00000
ExAC Asian Sub 24940 T=1.00000 A=0.00000
ExAC American Sub 11542 T=0.99991 A=0.00009
ExAC African Sub 10396 T=0.99817 A=0.00183
ExAC Other Sub 904 T=0.999 A=0.001
gnomAD - Genomes Global Study-wide 31386 T=0.99962 A=0.00038
gnomAD - Genomes European Sub 18902 T=1.00000 A=0.00000
gnomAD - Genomes African Sub 8704 T=0.9986 A=0.0014
gnomAD - Genomes East Asian Sub 1560 T=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1084 T=1.0000 A=0.0000
gnomAD - Genomes American Sub 846 T=1.000 A=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 T=0.99954 A=0.00046
GO Exome Sequencing Project European American Sub 8600 T=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4406 T=0.9986 A=0.0014
1000Genomes Global Study-wide 5008 T=0.9994 A=0.0006
1000Genomes African Sub 1322 T=0.9977 A=0.0023
1000Genomes East Asian Sub 1008 T=1.0000 A=0.0000
1000Genomes Europe Sub 1006 T=1.0000 A=0.0000
1000Genomes South Asian Sub 978 T=1.000 A=0.000
1000Genomes American Sub 694 T=1.000 A=0.000
ALFA Total Global 2188 T=1.0000 A=0.0000
ALFA European Sub 2072 T=1.0000 A=0.0000
ALFA African Sub 82 T=1.00 A=0.00
ALFA Other Sub 26 T=1.00 A=0.00
ALFA South Asian Sub 4 T=1.0 A=0.0
ALFA Asian Sub 4 T=1.0 A=0.0
ALFA Latin American 1 Sub 0 T=0 A=0
ALFA Latin American 2 Sub 0 T=0 A=0
Qatari Global Study-wide 216 T=0.995 A=0.005
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 T= A
GRCh38.p12 chr 8 NC_000008.11:g.18400073= NC_000008.11:g.18400073T>A
GRCh37.p13 chr 8 NC_000008.10:g.18257583= NC_000008.10:g.18257583T>A
NAT2 RefSeqGene NG_012246.1:g.13829= NG_012246.1:g.13829T>A
NAT2 transcript NM_000015.3:c.70= NM_000015.3:c.70T>A
NAT2 transcript NM_000015.2:c.70= NM_000015.2:c.70T>A
NAT2 transcript variant X1 XM_017012938.1:c.70= XM_017012938.1:c.70T>A
arylamine N-acetyltransferase 2 NP_000006.2:p.Leu24= NP_000006.2:p.Leu24Ile
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Leu24= XP_016868427.1:p.Leu24Ile
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#.

30 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss70456611 May 16, 2007 (127)
2 NHLBI-ESP ss342253597 May 09, 2011 (134)
3 1000GENOMES ss488883395 May 04, 2012 (137)
4 EXOME_CHIP ss491410750 May 04, 2012 (137)
5 ILLUMINA ss780867817 Sep 08, 2015 (146)
6 ILLUMINA ss783552748 Sep 08, 2015 (146)
7 1000GENOMES ss1328853889 Aug 21, 2014 (142)
8 EVA_DECODE ss1594845133 Apr 01, 2015 (144)
9 EVA_EXAC ss1689107786 Apr 01, 2015 (144)
10 WEILL_CORNELL_DGM ss1928545812 Feb 12, 2016 (147)
11 HUMAN_LONGEVITY ss2301164520 Dec 20, 2016 (150)
12 TOPMED ss2470822116 Dec 20, 2016 (150)
13 ILLUMINA ss2634717892 Nov 08, 2017 (151)
14 ILLUMINA ss2711131661 Nov 08, 2017 (151)
15 GNOMAD ss2737016575 Nov 08, 2017 (151)
16 GNOMAD ss2748005898 Nov 08, 2017 (151)
17 GNOMAD ss2863932556 Nov 08, 2017 (151)
18 AFFY ss2985432605 Nov 08, 2017 (151)
19 ILLUMINA ss3022824440 Nov 08, 2017 (151)
20 TOPMED ss3555514665 Nov 08, 2017 (151)
21 ILLUMINA ss3625946935 Oct 12, 2018 (152)
22 ILLUMINA ss3630009707 Oct 12, 2018 (152)
23 ILLUMINA ss3635161270 Oct 12, 2018 (152)
24 ILLUMINA ss3640868560 Oct 12, 2018 (152)
25 ILLUMINA ss3653365270 Oct 12, 2018 (152)
26 ILLUMINA ss3654194395 Oct 12, 2018 (152)
27 EVA_DECODE ss3721526498 Jul 13, 2019 (153)
28 ILLUMINA ss3726518823 Jul 13, 2019 (153)
29 ILLUMINA ss3745461060 Jul 13, 2019 (153)
30 EVA ss3824350606 Apr 26, 2020 (154)
31 1000Genomes NC_000008.10 - 18257583 Oct 12, 2018 (152)
32 ExAC NC_000008.10 - 18257583 Oct 12, 2018 (152)
33 gnomAD - Genomes NC_000008.10 - 18257583 Jul 13, 2019 (153)
34 gnomAD - Exomes NC_000008.10 - 18257583 Jul 13, 2019 (153)
35 GO Exome Sequencing Project NC_000008.10 - 18257583 Oct 12, 2018 (152)
36 Qatari NC_000008.10 - 18257583 Apr 26, 2020 (154)
37 TopMed NC_000008.11 - 18400073 Oct 12, 2018 (152)
38 dbGaP Population Frequency Project NC_000008.11 - 18400073 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
ss1594845133 NC_000008.9:18301862:T:A NC_000008.11:18400072:T:A (self)
40947071, 9201139, 111847138, 6184500, 808466, 10587742, ss342253597, ss488883395, ss491410750, ss780867817, ss783552748, ss1328853889, ss1689107786, ss1928545812, ss2470822116, ss2634717892, ss2711131661, ss2737016575, ss2748005898, ss2863932556, ss2985432605, ss3022824440, ss3625946935, ss3630009707, ss3635161270, ss3640868560, ss3653365270, ss3654194395, ss3745461060, ss3824350606 NC_000008.10:18257582:T:A NC_000008.11:18400072:T:A (self)
384382807, 550762678, ss2301164520, ss3555514665, ss3721526498, ss3726518823 NC_000008.11:18400072:T:A NC_000008.11:18400072:T:A (self)
ss70456611 NT_167187.1:6115728:T:A NC_000008.11:18400072:T:A (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 rs45477599

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