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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.

rs138707146

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr8:18400641 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000163 (41/251000, GnomAD_exome)
T=0.000494 (62/125568, TOPMED)
T=0.000198 (24/121080, ExAC) (+ 7 more)
T=0.00001 (1/85998, ALFA Project)
T=0.00079 (62/78700, PAGE_STUDY)
T=0.00045 (14/31408, GnomAD)
T=0.00054 (7/13006, GO-ESP)
T=0.0006 (3/5008, 1000G)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
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.18400641C>T
GRCh37.p13 chr 8 NC_000008.10:g.18258151C>T
NAT2 RefSeqGene NG_012246.1:g.14397C>T
Gene: NAT2, N-acetyltransferase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NAT2 transcript NM_000015.3:c.638C>T P [CCA] > L [CTA] Coding Sequence Variant
arylamine N-acetyltransferase 2 NP_000006.2:p.Pro213Leu P (Pro) > L (Leu) Missense Variant
NAT2 transcript variant X1 XM_017012938.1:c.638C>T P [CCA] > L [CTA] Coding Sequence Variant
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Pro213Leu P (Pro) > 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.

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 85998 C=0.99999 T=0.00001
European Sub 79538 C=0.99999 T=0.00001
African Sub 250 C=1.000 T=0.000
African Others Sub 8 C=1.0 T=0.0
African American Sub 242 C=1.000 T=0.000
Asian Sub 114 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 28 C=1.00 T=0.00
Latin American 1 Sub 6 C=1.0 T=0.0
Latin American 2 Sub 22 C=1.00 T=0.00
South Asian Sub 14 C=1.00 T=0.00
Other Sub 6054 C=1.0000 T=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").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251000 C=0.999837 T=0.000163
gnomAD - Exomes European Sub 135084 C=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 49000 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34554 C=0.99991 T=0.00009
gnomAD - Exomes African Sub 16172 C=0.99765 T=0.00235
gnomAD - Exomes Ashkenazi Jewish Sub 10078 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6112 C=1.0000 T=0.0000
TopMed Global Study-wide 125568 C=0.999506 T=0.000494
ExAC Global Study-wide 121080 C=0.999802 T=0.000198
ExAC Europe Sub 73272 C=1.00000 T=0.00000
ExAC Asian Sub 25148 C=1.00000 T=0.00000
ExAC American Sub 11536 C=0.99983 T=0.00017
ExAC African Sub 10216 C=0.99785 T=0.00215
ExAC Other Sub 908 C=1.000 T=0.000
ALFA Total Global 85998 C=0.99999 T=0.00001
ALFA European Sub 79538 C=0.99999 T=0.00001
ALFA Other Sub 6054 C=1.0000 T=0.0000
ALFA African Sub 250 C=1.000 T=0.000
ALFA Asian Sub 114 C=1.000 T=0.000
ALFA Latin American 2 Sub 22 C=1.00 T=0.00
ALFA South Asian Sub 14 C=1.00 T=0.00
ALFA Latin American 1 Sub 6 C=1.0 T=0.0
The PAGE Study Global Study-wide 78700 C=0.99921 T=0.00079
The PAGE Study AfricanAmerican Sub 32514 C=0.99840 T=0.00160
The PAGE Study Mexican Sub 10810 C=0.99981 T=0.00019
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=0.9997 T=0.0003
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=0.9990 T=0.0010
The PAGE Study CentralAmerican Sub 2450 C=0.9996 T=0.0004
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=0.9992 T=0.0008
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 31408 C=0.99955 T=0.00045
gnomAD - Genomes European Sub 18908 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 8716 C=0.9984 T=0.0016
gnomAD - Genomes East Asian Sub 1558 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1088 C=1.0000 T=0.0000
gnomAD - Genomes American Sub 848 C=1.000 T=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99946 T=0.00054
GO Exome Sequencing Project European American Sub 8600 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9984 T=0.0016
1000Genomes Global Study-wide 5008 C=0.9994 T=0.0006
1000Genomes African Sub 1322 C=0.9977 T=0.0023
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
SGDP_PRJ Global Study-wide 2 C=0.5 T=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 C= T
GRCh38.p12 chr 8 NC_000008.11:g.18400641= NC_000008.11:g.18400641C>T
GRCh37.p13 chr 8 NC_000008.10:g.18258151= NC_000008.10:g.18258151C>T
NAT2 RefSeqGene NG_012246.1:g.14397= NG_012246.1:g.14397C>T
NAT2 transcript NM_000015.3:c.638= NM_000015.3:c.638C>T
NAT2 transcript NM_000015.2:c.638= NM_000015.2:c.638C>T
NAT2 transcript variant X1 XM_017012938.1:c.638= XM_017012938.1:c.638C>T
arylamine N-acetyltransferase 2 NP_000006.2:p.Pro213= NP_000006.2:p.Pro213Leu
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Pro213= XP_016868427.1:p.Pro213Leu
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#.

31 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342253615 May 09, 2011 (134)
2 EXOME_CHIP ss491410767 May 04, 2012 (137)
3 ILLUMINA ss780867831 Sep 08, 2015 (146)
4 ILLUMINA ss783552762 Sep 08, 2015 (146)
5 1000GENOMES ss1328853918 Aug 21, 2014 (142)
6 EVA_EXAC ss1689107906 Apr 01, 2015 (144)
7 ILLUMINA ss1752722193 Sep 08, 2015 (146)
8 ILLUMINA ss1917826211 Feb 12, 2016 (147)
9 ILLUMINA ss1946231118 Feb 12, 2016 (147)
10 ILLUMINA ss1959092413 Feb 12, 2016 (147)
11 HUMAN_LONGEVITY ss2301164566 Dec 20, 2016 (150)
12 TOPMED ss2470822164 Dec 20, 2016 (150)
13 GNOMAD ss2737016747 Nov 08, 2017 (151)
14 GNOMAD ss2748005959 Nov 08, 2017 (151)
15 GNOMAD ss2863932617 Nov 08, 2017 (151)
16 AFFY ss2985432620 Nov 08, 2017 (151)
17 ILLUMINA ss3022824460 Nov 08, 2017 (151)
18 TOPMED ss3555514779 Nov 08, 2017 (151)
19 ILLUMINA ss3630009732 Oct 12, 2018 (152)
20 ILLUMINA ss3635161291 Oct 12, 2018 (152)
21 ILLUMINA ss3640868581 Oct 12, 2018 (152)
22 ILLUMINA ss3644964292 Oct 12, 2018 (152)
23 ILLUMINA ss3653365290 Oct 12, 2018 (152)
24 ILLUMINA ss3654194411 Oct 12, 2018 (152)
25 ILLUMINA ss3726518841 Jul 13, 2019 (153)
26 ILLUMINA ss3744577639 Jul 13, 2019 (153)
27 ILLUMINA ss3745461081 Jul 13, 2019 (153)
28 PAGE_CC ss3771427494 Jul 13, 2019 (153)
29 ILLUMINA ss3772953679 Jul 13, 2019 (153)
30 EVA ss3824350634 Apr 26, 2020 (154)
31 SGDP_PRJ ss3869405016 Apr 26, 2020 (154)
32 1000Genomes NC_000008.10 - 18258151 Oct 12, 2018 (152)
33 ExAC NC_000008.10 - 18258151 Oct 12, 2018 (152)
34 gnomAD - Genomes NC_000008.10 - 18258151 Jul 13, 2019 (153)
35 gnomAD - Exomes NC_000008.10 - 18258151 Jul 13, 2019 (153)
36 GO Exome Sequencing Project NC_000008.10 - 18258151 Oct 12, 2018 (152)
37 The PAGE Study NC_000008.11 - 18400641 Jul 13, 2019 (153)
38 SGDP_PRJ NC_000008.10 - 18258151 Apr 26, 2020 (154)
39 TopMed NC_000008.11 - 18400641 Oct 12, 2018 (152)
40 dbGaP Population Frequency Project NC_000008.11 - 18400641 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
40947100, 9201265, 111847195, 6184693, 808492, 21421996, ss342253615, ss491410767, ss780867831, ss783552762, ss1328853918, ss1689107906, ss1752722193, ss1917826211, ss1946231118, ss1959092413, ss2470822164, ss2737016747, ss2748005959, ss2863932617, ss2985432620, ss3022824460, ss3630009732, ss3635161291, ss3640868581, ss3644964292, ss3653365290, ss3654194411, ss3744577639, ss3745461081, ss3772953679, ss3824350634, ss3869405016 NC_000008.10:18258150:C:T NC_000008.11:18400640:C:T (self)
648963, 384382904, 828865468, ss2301164566, ss3555514779, ss3726518841, ss3771427494 NC_000008.11:18400640:C:T NC_000008.11:18400640:C: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 rs138707146

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