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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.

rs56054745

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr8:18400848 (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
A>C / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000032 (4/125568, TOPMED)
G=0.000035 (4/112946, ExAC)
C=0.00003 (2/78698, PAGE_STUDY) (+ 3 more)
C=0.00000 (0/19870, ALFA Project)
G=0.00000 (0/19870, dbGaP Population Frequency Project)
G=0.00008 (1/12938, GO-ESP)
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.18400848A>C
GRCh38.p12 chr 8 NC_000008.11:g.18400848A>G
GRCh37.p13 chr 8 NC_000008.10:g.18258358A>C
GRCh37.p13 chr 8 NC_000008.10:g.18258358A>G
NAT2 RefSeqGene NG_012246.1:g.14604A>C
NAT2 RefSeqGene NG_012246.1:g.14604A>G
Gene: NAT2, N-acetyltransferase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NAT2 transcript NM_000015.3:c.845A>C K [AAA] > T [ACA] Coding Sequence Variant
arylamine N-acetyltransferase 2 NP_000006.2:p.Lys282Thr K (Lys) > T (Thr) Missense Variant
NAT2 transcript NM_000015.3:c.845A>G K [AAA] > R [AGA] Coding Sequence Variant
arylamine N-acetyltransferase 2 NP_000006.2:p.Lys282Arg K (Lys) > R (Arg) Missense Variant
NAT2 transcript variant X1 XM_017012938.1:c.845A>C K [AAA] > T [ACA] Coding Sequence Variant
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Lys282Thr K (Lys) > T (Thr) Missense Variant
NAT2 transcript variant X1 XM_017012938.1:c.845A>G K [AAA] > R [AGA] Coding Sequence Variant
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Lys282Arg K (Lys) > R (Arg) 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 19870 A=1.00000 C=0.00000, G=0.00000
European Sub 19370 A=1.00000 C=0.00000, G=0.00000
African Sub 146 A=1.000 C=0.000, G=0.000
African Others Sub 8 A=1.0 C=0.0, G=0.0
African American Sub 138 A=1.000 C=0.000, G=0.000
Asian Sub 38 A=1.00 C=0.00, G=0.00
East Asian Sub 36 A=1.00 C=0.00, G=0.00
Other Asian Sub 2 A=1.0 C=0.0, G=0.0
Latin American 1 Sub 0 A=0 C=0, G=0
Latin American 2 Sub 0 A=0 C=0, G=0
South Asian Sub 10 A=1.0 C=0.0, G=0.0
Other Sub 306 A=1.000 C=0.000, G=0.000


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 A=0.999968 G=0.000032
ExAC Global Study-wide 112946 A=0.999965 G=0.000035
ExAC Europe Sub 69626 A=0.99994 G=0.00006
ExAC Asian Sub 21872 A=1.00000 G=0.00000
ExAC American Sub 11420 A=1.00000 G=0.00000
ExAC African Sub 9196 A=1.0000 G=0.0000
ExAC Other Sub 832 A=1.000 G=0.000
The PAGE Study Global Study-wide 78698 A=0.99997 C=0.00003
The PAGE Study AfricanAmerican Sub 32512 A=1.00000 C=0.00000
The PAGE Study Mexican Sub 10810 A=1.00000 C=0.00000
The PAGE Study Asian Sub 8318 A=1.0000 C=0.0000
The PAGE Study PuertoRican Sub 7918 A=1.0000 C=0.0000
The PAGE Study NativeHawaiian Sub 4534 A=0.9998 C=0.0002
The PAGE Study Cuban Sub 4230 A=1.0000 C=0.0000
The PAGE Study Dominican Sub 3828 A=1.0000 C=0.0000
The PAGE Study CentralAmerican Sub 2450 A=1.0000 C=0.0000
The PAGE Study SouthAmerican Sub 1982 A=0.9995 C=0.0005
The PAGE Study NativeAmerican Sub 1260 A=1.0000 C=0.0000
The PAGE Study SouthAsian Sub 856 A=1.000 C=0.000
ALFA Total Global 19870 A=1.00000 C=0.00000, G=0.00000
ALFA European Sub 19370 A=1.00000 C=0.00000, G=0.00000
ALFA Other Sub 306 A=1.000 C=0.000, G=0.000
ALFA African Sub 146 A=1.000 C=0.000, G=0.000
ALFA Asian Sub 38 A=1.00 C=0.00, G=0.00
ALFA South Asian Sub 10 A=1.0 C=0.0, G=0.0
ALFA Latin American 1 Sub 0 A=0 C=0, G=0
ALFA Latin American 2 Sub 0 A=0 C=0, G=0
GO Exome Sequencing Project Global Study-wide 12938 A=0.99992 G=0.00008
GO Exome Sequencing Project European American Sub 8560 A=0.9999 G=0.0001
GO Exome Sequencing Project African American Sub 4378 A=1.0000 G=0.0000
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 A= C G
GRCh38.p12 chr 8 NC_000008.11:g.18400848= NC_000008.11:g.18400848A>C NC_000008.11:g.18400848A>G
GRCh37.p13 chr 8 NC_000008.10:g.18258358= NC_000008.10:g.18258358A>C NC_000008.10:g.18258358A>G
NAT2 RefSeqGene NG_012246.1:g.14604= NG_012246.1:g.14604A>C NG_012246.1:g.14604A>G
NAT2 transcript NM_000015.3:c.845= NM_000015.3:c.845A>C NM_000015.3:c.845A>G
NAT2 transcript NM_000015.2:c.845= NM_000015.2:c.845A>C NM_000015.2:c.845A>G
NAT2 transcript variant X1 XM_017012938.1:c.845= XM_017012938.1:c.845A>C XM_017012938.1:c.845A>G
arylamine N-acetyltransferase 2 NP_000006.2:p.Lys282= NP_000006.2:p.Lys282Thr NP_000006.2:p.Lys282Arg
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Lys282= XP_016868427.1:p.Lys282Thr XP_016868427.1:p.Lys282Arg
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#.

29 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA ss75244832 Dec 07, 2007 (129)
2 AFFY_DM3_1 ss105434767 Feb 06, 2009 (130)
3 ILLUMINA ss161065267 Dec 01, 2009 (131)
4 ILLUMINA ss169136132 Jul 04, 2010 (132)
5 NHLBI-ESP ss342253627 May 09, 2011 (134)
6 ILLUMINA ss483025660 Sep 08, 2015 (146)
7 ILLUMINA ss537652766 Sep 08, 2015 (146)
8 EVA_EXAC ss1689107949 Apr 01, 2015 (144)
9 ILLUMINA ss1946231124 Feb 12, 2016 (147)
10 ILLUMINA ss1959092424 Feb 12, 2016 (147)
11 HUMAN_LONGEVITY ss2301164584 Dec 20, 2016 (150)
12 TOPMED ss2470822183 Dec 20, 2016 (150)
13 ILLUMINA ss2634717920 Nov 08, 2017 (151)
14 ILLUMINA ss2711131683 Nov 08, 2017 (151)
15 GNOMAD ss2737016811 Nov 08, 2017 (151)
16 ILLUMINA ss3022824468 Nov 08, 2017 (151)
17 TOPMED ss3555514815 Nov 08, 2017 (151)
18 TOPMED ss3555514816 Nov 08, 2017 (151)
19 ILLUMINA ss3625946946 Oct 12, 2018 (152)
20 ILLUMINA ss3630009742 Oct 12, 2018 (152)
21 ILLUMINA ss3636898286 Oct 12, 2018 (152)
22 ILLUMINA ss3638747292 Oct 12, 2018 (152)
23 ILLUMINA ss3643679171 Oct 12, 2018 (152)
24 ILLUMINA ss3644964298 Oct 12, 2018 (152)
25 ILLUMINA ss3653365298 Oct 12, 2018 (152)
26 ILLUMINA ss3726518848 Jul 13, 2019 (153)
27 ILLUMINA ss3744302592 Jul 13, 2019 (153)
28 PAGE_CC ss3771427501 Jul 13, 2019 (153)
29 EVA ss3824350648 Apr 26, 2020 (154)
30 ExAC NC_000008.10 - 18258358 Oct 12, 2018 (152)
31 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 6184761 (NC_000008.10:18258357:A:A 237551/237554, NC_000008.10:18258357:A:C 3/237554)
Row 6184762 (NC_000008.10:18258357:A:A 237550/237554, NC_000008.10:18258357:A:G 4/237554)

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

Submission ignored due to conflicting rows:
Row 6184761 (NC_000008.10:18258357:A:A 237551/237554, NC_000008.10:18258357:A:C 3/237554)
Row 6184762 (NC_000008.10:18258357:A:A 237550/237554, NC_000008.10:18258357:A:G 4/237554)

- Jul 13, 2019 (153)
33 GO Exome Sequencing Project NC_000008.10 - 18258358 Oct 12, 2018 (152)
34 The PAGE Study NC_000008.11 - 18400848 Jul 13, 2019 (153)
35 TopMed NC_000008.11 - 18400848 Oct 12, 2018 (152)
36 dbGaP Population Frequency Project NC_000008.11 - 18400848 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
ss161065267, ss3643679171 NC_000008.9:18302637:A:C NC_000008.11:18400847:A:C (self)
ss483025660, ss537652766, ss1946231124, ss1959092424, ss2634717920, ss2711131683, ss2737016811, ss3022824468, ss3625946946, ss3630009742, ss3636898286, ss3638747292, ss3644964298, ss3653365298, ss3744302592 NC_000008.10:18258357:A:C NC_000008.11:18400847:A:C (self)
648970, 850436035, ss2301164584, ss3555514815, ss3726518848, ss3771427501 NC_000008.11:18400847:A:C NC_000008.11:18400847:A:C (self)
ss75244832, ss105434767, ss169136132 NT_167187.1:6116503:A:C NC_000008.11:18400847:A:C (self)
9201309, 808505, ss342253627, ss1689107949, ss2470822183, ss2737016811, ss3824350648 NC_000008.10:18258357:A:G NC_000008.11:18400847:A:G (self)
384382938, 850436035, ss3555514816 NC_000008.11:18400847:A:G NC_000008.11:18400847:A:G (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 rs56054745

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.post502+8584b1c