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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.

rs45532639

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr8:18400348 (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=0.000504 (126/249908, GnomAD_exome)
T=0.000780 (98/125568, TOPMED)
T=0.000530 (64/120756, ExAC) (+ 7 more)
T=0.00045 (14/31364, GnomAD)
T=0.00077 (10/13006, GO-ESP)
T=0.00027 (3/11174, ALFA Project)
T=0.0008 (4/5008, 1000G)
T=0.0000 (0/3854, ALSPAC)
T=0.0003 (1/3708, TWINSUK)
T=0.004 (2/534, MGP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NAT2 : Synonymous 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.18400348C>T
GRCh37.p13 chr 8 NC_000008.10:g.18257858C>T
NAT2 RefSeqGene NG_012246.1:g.14104C>T
Gene: NAT2, N-acetyltransferase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NAT2 transcript NM_000015.3:c.345C>T D [GAC] > D [GAT] Coding Sequence Variant
arylamine N-acetyltransferase 2 NP_000006.2:p.Asp115= D (Asp) > D (Asp) Synonymous Variant
NAT2 transcript variant X1 XM_017012938.1:c.345C>T D [GAC] > D [GAT] Coding Sequence Variant
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Asp115= D (Asp) > D (Asp) Synonymous 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 11174 C=0.99973 T=0.00027
European Sub 8134 C=0.9998 T=0.0002
African Sub 676 C=0.999 T=0.001
African Others Sub 14 C=1.00 T=0.00
African American Sub 662 C=0.998 T=0.002
Asian Sub 60 C=1.00 T=0.00
East Asian Sub 28 C=1.00 T=0.00
Other Asian Sub 32 C=1.00 T=0.00
Latin American 1 Sub 0 C=0 T=0
Latin American 2 Sub 0 C=0 T=0
South Asian Sub 4 C=1.0 T=0.0
Other Sub 2300 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 249908 C=0.999496 T=0.000504
gnomAD - Exomes European Sub 134636 C=0.999636 T=0.000364
gnomAD - Exomes Asian Sub 48752 C=0.99992 T=0.00008
gnomAD - Exomes American Sub 34352 C=0.99916 T=0.00084
gnomAD - Exomes African Sub 16224 C=0.99747 T=0.00253
gnomAD - Exomes Ashkenazi Jewish Sub 9870 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 6074 C=0.9995 T=0.0005
TopMed Global Study-wide 125568 C=0.999220 T=0.000780
ExAC Global Study-wide 120756 C=0.999470 T=0.000530
ExAC Europe Sub 73104 C=0.99962 T=0.00038
ExAC Asian Sub 24834 C=0.99980 T=0.00020
ExAC American Sub 11532 C=0.99948 T=0.00052
ExAC African Sub 10384 C=0.99769 T=0.00231
ExAC Other Sub 902 C=0.999 T=0.001
gnomAD - Genomes Global Study-wide 31364 C=0.99955 T=0.00045
gnomAD - Genomes European Sub 18896 C=0.99979 T=0.00021
gnomAD - Genomes African Sub 8702 C=0.9989 T=0.0011
gnomAD - Genomes East Asian Sub 1552 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 1082 C=1.0000 T=0.0000
gnomAD - Genomes American Sub 842 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=0.99923 T=0.00077
GO Exome Sequencing Project European American Sub 8600 C=0.9998 T=0.0002
GO Exome Sequencing Project African American Sub 4406 C=0.9982 T=0.0018
ALFA Total Global 11174 C=0.99973 T=0.00027
ALFA European Sub 8134 C=0.9998 T=0.0002
ALFA Other Sub 2300 C=1.0000 T=0.0000
ALFA African Sub 676 C=0.999 T=0.001
ALFA Asian Sub 60 C=1.00 T=0.00
ALFA South Asian Sub 4 C=1.0 T=0.0
ALFA Latin American 1 Sub 0 C=0 T=0
ALFA Latin American 2 Sub 0 C=0 T=0
1000Genomes Global Study-wide 5008 C=0.9992 T=0.0008
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=0.9990 T=0.0010
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=1.0000 T=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9997 T=0.0003
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.996 T=0.004
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.18400348= NC_000008.11:g.18400348C>T
GRCh37.p13 chr 8 NC_000008.10:g.18257858= NC_000008.10:g.18257858C>T
NAT2 RefSeqGene NG_012246.1:g.14104= NG_012246.1:g.14104C>T
NAT2 transcript NM_000015.3:c.345= NM_000015.3:c.345C>T
NAT2 transcript NM_000015.2:c.345= NM_000015.2:c.345C>T
NAT2 transcript variant X1 XM_017012938.1:c.345= XM_017012938.1:c.345C>T
arylamine N-acetyltransferase 2 NP_000006.2:p.Asp115= NP_000006.2:p.Asp115=
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Asp115= XP_016868427.1:p.Asp115=
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#.

15 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss70456615 May 17, 2007 (127)
2 NHLBI-ESP ss342253603 May 09, 2011 (134)
3 1000GENOMES ss1328853897 Aug 21, 2014 (142)
4 EVA_UK10K_ALSPAC ss1620100537 Apr 01, 2015 (144)
5 EVA_UK10K_TWINSUK ss1663094570 Apr 01, 2015 (144)
6 EVA_EXAC ss1689107838 Apr 01, 2015 (144)
7 EVA_MGP ss1711194413 Apr 01, 2015 (144)
8 HUMAN_LONGEVITY ss2301164542 Dec 20, 2016 (150)
9 TOPMED ss2470822137 Dec 20, 2016 (150)
10 GNOMAD ss2737016661 Nov 08, 2017 (151)
11 GNOMAD ss2748005927 Nov 08, 2017 (151)
12 GNOMAD ss2863932585 Nov 08, 2017 (151)
13 TOPMED ss3555514717 Nov 08, 2017 (151)
14 EVA_DECODE ss3721526502 Jul 13, 2019 (153)
15 EVA ss3824350616 Apr 26, 2020 (154)
16 1000Genomes NC_000008.10 - 18257858 Oct 12, 2018 (152)
17 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 18257858 Oct 12, 2018 (152)
18 ExAC NC_000008.10 - 18257858 Oct 12, 2018 (152)
19 gnomAD - Genomes NC_000008.10 - 18257858 Jul 13, 2019 (153)
20 gnomAD - Exomes NC_000008.10 - 18257858 Jul 13, 2019 (153)
21 GO Exome Sequencing Project NC_000008.10 - 18257858 Oct 12, 2018 (152)
22 Medical Genome Project healthy controls from Spanish population NC_000008.10 - 18257858 Apr 26, 2020 (154)
23 TopMed NC_000008.11 - 18400348 Oct 12, 2018 (152)
24 UK 10K study - Twins NC_000008.10 - 18257858 Oct 12, 2018 (152)
25 dbGaP Population Frequency Project NC_000008.11 - 18400348 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
40947079, 22761467, 9201195, 111847164, 6184597, 808475, 310173, 22761467, ss342253603, ss1328853897, ss1620100537, ss1663094570, ss1689107838, ss1711194413, ss2470822137, ss2737016661, ss2748005927, ss2863932585, ss3824350616 NC_000008.10:18257857:C:T NC_000008.11:18400347:C:T (self)
384382854, 210429587, ss2301164542, ss3555514717, ss3721526502 NC_000008.11:18400347:C:T NC_000008.11:18400347:C:T (self)
ss70456615 NT_167187.1:6116003:C:T NC_000008.11:18400347: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 rs45532639

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