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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.

rs72466456

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr8:18400032 (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 / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000151 (19/125568, TOPMED)
G=0.00006 (1/17564, ALFA Project)
C=0.00031 (4/13006, GO-ESP) (+ 1 more)
C=0.0004 (2/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NAT2 : Missense Variant
Publications
1 citation
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.18400032T>A
GRCh38.p12 chr 8 NC_000008.11:g.18400032T>C
GRCh38.p12 chr 8 NC_000008.11:g.18400032T>G
GRCh37.p13 chr 8 NC_000008.10:g.18257542T>A
GRCh37.p13 chr 8 NC_000008.10:g.18257542T>C
GRCh37.p13 chr 8 NC_000008.10:g.18257542T>G
NAT2 RefSeqGene NG_012246.1:g.13788T>A
NAT2 RefSeqGene NG_012246.1:g.13788T>C
NAT2 RefSeqGene NG_012246.1:g.13788T>G
Gene: NAT2, N-acetyltransferase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NAT2 transcript NM_000015.3:c.29T>A I [ATT] > N [AAT] Coding Sequence Variant
arylamine N-acetyltransferase 2 NP_000006.2:p.Ile10Asn I (Ile) > N (Asn) Missense Variant
NAT2 transcript NM_000015.3:c.29T>C I [ATT] > T [ACT] Coding Sequence Variant
arylamine N-acetyltransferase 2 NP_000006.2:p.Ile10Thr I (Ile) > T (Thr) Missense Variant
NAT2 transcript NM_000015.3:c.29T>G I [ATT] > S [AGT] Coding Sequence Variant
arylamine N-acetyltransferase 2 NP_000006.2:p.Ile10Ser I (Ile) > S (Ser) Missense Variant
NAT2 transcript variant X1 XM_017012938.1:c.29T>A I [ATT] > N [AAT] Coding Sequence Variant
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Ile10Asn I (Ile) > N (Asn) Missense Variant
NAT2 transcript variant X1 XM_017012938.1:c.29T>C I [ATT] > T [ACT] Coding Sequence Variant
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Ile10Thr I (Ile) > T (Thr) Missense Variant
NAT2 transcript variant X1 XM_017012938.1:c.29T>G I [ATT] > S [AGT] Coding Sequence Variant
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Ile10Ser I (Ile) > S (Ser) 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: 20200227123210
Population Group Sample Size Ref Allele Alt Allele
Total Global 17564 T=0.99994 C=0.00000, G=0.00006
European Sub 14272 T=1.00000 C=0.00000, G=0.00000
African Sub 676 T=1.000 C=0.000, G=0.000
African Others Sub 14 T=1.00 C=0.00, G=0.00
African American Sub 662 T=1.000 C=0.000, G=0.000
Asian Sub 60 T=1.00 C=0.00, G=0.00
East Asian Sub 28 T=1.00 C=0.00, G=0.00
Other Asian Sub 32 T=1.00 C=0.00, G=0.00
Latin American 1 Sub 0 T=0 C=0, G=0
Latin American 2 Sub 0 T=0 C=0, G=0
South Asian Sub 4 T=1.0 C=0.0, G=0.0
Other Sub 2552 T=0.9996 C=0.0000, G=0.0004


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 125568 T=0.999849 C=0.000151
ALFA Total Global 17564 T=0.99994 C=0.00000, G=0.00006
ALFA European Sub 14272 T=1.00000 C=0.00000, G=0.00000
ALFA Other Sub 2552 T=0.9996 C=0.0000, G=0.0004
ALFA African Sub 676 T=1.000 C=0.000, G=0.000
ALFA Asian Sub 60 T=1.00 C=0.00, G=0.00
ALFA South Asian Sub 4 T=1.0 C=0.0, G=0.0
ALFA Latin American 1 Sub 0 T=0 C=0, G=0
ALFA Latin American 2 Sub 0 T=0 C=0, G=0
GO Exome Sequencing Project Global Study-wide 13006 T=0.99969 C=0.00031
GO Exome Sequencing Project European American Sub 8600 T=1.0000 C=0.0000
GO Exome Sequencing Project African American Sub 4406 T=0.9991 C=0.0009
1000Genomes Global Study-wide 5008 T=0.9996 C=0.0004
1000Genomes African Sub 1322 T=0.9992 C=0.0008
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=0.999 C=0.001
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 C G
GRCh38.p12 chr 8 NC_000008.11:g.18400032= NC_000008.11:g.18400032T>A NC_000008.11:g.18400032T>C NC_000008.11:g.18400032T>G
GRCh37.p13 chr 8 NC_000008.10:g.18257542= NC_000008.10:g.18257542T>A NC_000008.10:g.18257542T>C NC_000008.10:g.18257542T>G
NAT2 RefSeqGene NG_012246.1:g.13788= NG_012246.1:g.13788T>A NG_012246.1:g.13788T>C NG_012246.1:g.13788T>G
NAT2 transcript NM_000015.3:c.29= NM_000015.3:c.29T>A NM_000015.3:c.29T>C NM_000015.3:c.29T>G
NAT2 transcript NM_000015.2:c.29= NM_000015.2:c.29T>A NM_000015.2:c.29T>C NM_000015.2:c.29T>G
NAT2 transcript variant X1 XM_017012938.1:c.29= XM_017012938.1:c.29T>A XM_017012938.1:c.29T>C XM_017012938.1:c.29T>G
arylamine N-acetyltransferase 2 NP_000006.2:p.Ile10= NP_000006.2:p.Ile10Asn NP_000006.2:p.Ile10Thr NP_000006.2:p.Ile10Ser
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Ile10= XP_016868427.1:p.Ile10Asn XP_016868427.1:p.Ile10Thr XP_016868427.1:p.Ile10Ser
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#.

21 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 LGH ss102664284 Feb 13, 2009 (130)
2 NHLBI-ESP ss342253594 May 09, 2011 (134)
3 1000GENOMES ss460256624 Sep 17, 2011 (135)
4 1000GENOMES ss490960715 May 04, 2012 (137)
5 EXOME_CHIP ss491410749 May 04, 2012 (137)
6 1000GENOMES ss1328853886 Aug 21, 2014 (142)
7 EVA_EXAC ss1689107771 Apr 01, 2015 (144)
8 EVA_EXAC ss1689107772 Apr 01, 2015 (144)
9 EVA_EXAC ss1689107773 Apr 01, 2015 (144)
10 HUMAN_LONGEVITY ss2301164516 Dec 20, 2016 (150)
11 TOPMED ss2470822112 Dec 20, 2016 (150)
12 ILLUMINA ss2711131660 Nov 08, 2017 (151)
13 GNOMAD ss2737016560 Nov 08, 2017 (151)
14 GNOMAD ss2748005893 Nov 08, 2017 (151)
15 GNOMAD ss2863932551 Nov 08, 2017 (151)
16 AFFY ss2985432603 Nov 08, 2017 (151)
17 TOPMED ss3555514655 Nov 08, 2017 (151)
18 TOPMED ss3555514656 Nov 08, 2017 (151)
19 ILLUMINA ss3654194393 Oct 12, 2018 (152)
20 KHV_HUMAN_GENOMES ss3810861609 Jul 13, 2019 (153)
21 EVA ss3824350605 Apr 26, 2020 (154)
22 1000Genomes NC_000008.10 - 18257542 Oct 12, 2018 (152)
23 ExAC

Submission ignored due to conflicting rows:
Row 9201124 (NC_000008.10:18257541:T:T 116404/116410, NC_000008.10:18257541:T:C 6/116410)
Row 9201125 (NC_000008.10:18257541:T:T 116406/116410, NC_000008.10:18257541:T:G 4/116410)
Row 9201126 (NC_000008.10:18257541:T:T 116408/116410, NC_000008.10:18257541:T:A 2/116410)

- Oct 12, 2018 (152)
24 ExAC

Submission ignored due to conflicting rows:
Row 9201124 (NC_000008.10:18257541:T:T 116404/116410, NC_000008.10:18257541:T:C 6/116410)
Row 9201125 (NC_000008.10:18257541:T:T 116406/116410, NC_000008.10:18257541:T:G 4/116410)
Row 9201126 (NC_000008.10:18257541:T:T 116408/116410, NC_000008.10:18257541:T:A 2/116410)

- Oct 12, 2018 (152)
25 ExAC

Submission ignored due to conflicting rows:
Row 9201124 (NC_000008.10:18257541:T:T 116404/116410, NC_000008.10:18257541:T:C 6/116410)
Row 9201125 (NC_000008.10:18257541:T:T 116406/116410, NC_000008.10:18257541:T:G 4/116410)
Row 9201126 (NC_000008.10:18257541:T:T 116408/116410, NC_000008.10:18257541:T:A 2/116410)

- Oct 12, 2018 (152)
26 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 111847131 (NC_000008.10:18257541:T:T 31397/31398, NC_000008.10:18257541:T:A 1/31398)
Row 111847132 (NC_000008.10:18257541:T:T 31391/31398, NC_000008.10:18257541:T:C 7/31398)
Row 111847133 (NC_000008.10:18257541:T:T 31397/31398, NC_000008.10:18257541:T:G 1/31398)

- Jul 13, 2019 (153)
27 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 111847131 (NC_000008.10:18257541:T:T 31397/31398, NC_000008.10:18257541:T:A 1/31398)
Row 111847132 (NC_000008.10:18257541:T:T 31391/31398, NC_000008.10:18257541:T:C 7/31398)
Row 111847133 (NC_000008.10:18257541:T:T 31397/31398, NC_000008.10:18257541:T:G 1/31398)

- Jul 13, 2019 (153)
28 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 111847131 (NC_000008.10:18257541:T:T 31397/31398, NC_000008.10:18257541:T:A 1/31398)
Row 111847132 (NC_000008.10:18257541:T:T 31391/31398, NC_000008.10:18257541:T:C 7/31398)
Row 111847133 (NC_000008.10:18257541:T:T 31397/31398, NC_000008.10:18257541:T:G 1/31398)

- Jul 13, 2019 (153)
29 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 6184484 (NC_000008.10:18257541:T:T 242388/242396, NC_000008.10:18257541:T:A 8/242396)
Row 6184485 (NC_000008.10:18257541:T:T 242380/242396, NC_000008.10:18257541:T:C 16/242396)
Row 6184486 (NC_000008.10:18257541:T:T 242387/242396, NC_000008.10:18257541:T:G 9/242396)

- Jul 13, 2019 (153)
30 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 6184484 (NC_000008.10:18257541:T:T 242388/242396, NC_000008.10:18257541:T:A 8/242396)
Row 6184485 (NC_000008.10:18257541:T:T 242380/242396, NC_000008.10:18257541:T:C 16/242396)
Row 6184486 (NC_000008.10:18257541:T:T 242387/242396, NC_000008.10:18257541:T:G 9/242396)

- Jul 13, 2019 (153)
31 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 6184484 (NC_000008.10:18257541:T:T 242388/242396, NC_000008.10:18257541:T:A 8/242396)
Row 6184485 (NC_000008.10:18257541:T:T 242380/242396, NC_000008.10:18257541:T:C 16/242396)
Row 6184486 (NC_000008.10:18257541:T:T 242387/242396, NC_000008.10:18257541:T:G 9/242396)

- Jul 13, 2019 (153)
32 GO Exome Sequencing Project NC_000008.10 - 18257542 Oct 12, 2018 (152)
33 TopMed NC_000008.11 - 18400032 Oct 12, 2018 (152)
34 dbGaP Population Frequency Project NC_000008.11 - 18400032 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
ss1689107773, ss2737016560, ss2748005893, ss2863932551 NC_000008.10:18257541:T:A NC_000008.11:18400031:T:A (self)
ss2301164516 NC_000008.11:18400031:T:A NC_000008.11:18400031:T:A (self)
40947068, 808465, ss342253594, ss460256624, ss490960715, ss491410749, ss1328853886, ss1689107771, ss2470822112, ss2711131660, ss2737016560, ss2748005893, ss2863932551, ss2985432603, ss3654194393, ss3824350605 NC_000008.10:18257541:T:C NC_000008.11:18400031:T:C (self)
384382798, 696274428, ss2301164516, ss3555514655 NC_000008.11:18400031:T:C NC_000008.11:18400031:T:C (self)
ss102664284 NT_167187.1:6115687:T:C NC_000008.11:18400031:T:C (self)
ss1689107772, ss2737016560, ss2748005893, ss2863932551 NC_000008.10:18257541:T:G NC_000008.11:18400031:T:G (self)
696274428, ss3555514656, ss3810861609 NC_000008.11:18400031:T:G NC_000008.11:18400031:T: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 rs72466456
PMID Title Author Year Journal
28771511 Exploring public genomics data for population pharmacogenomics. Lakiotaki K et al. 2017 PloS one
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.post536+f5d31d6