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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.

rs72554615

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr8:18400114 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000052 (13/251330, GnomAD_exome)
C=0.000327 (41/125568, TOPMED)
C=0.000033 (4/121316, ExAC) (+ 3 more)
C=0.00010 (3/31396, GnomAD)
C=0.0002 (1/4480, Estonian)
C=0.0000 (0/2188, ALFA Project)
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.18400114T>C
GRCh37.p13 chr 8 NC_000008.10:g.18257624T>C
NAT2 RefSeqGene NG_012246.1:g.13870T>C
Gene: NAT2, N-acetyltransferase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NAT2 transcript NM_000015.3:c.111T>C F [TTT] > F [TTC] Coding Sequence Variant
arylamine N-acetyltransferase 2 NP_000006.2:p.Phe37= F (Phe) > F (Phe) Synonymous Variant
NAT2 transcript variant X1 XM_017012938.1:c.111T>C F [TTT] > F [TTC] Coding Sequence Variant
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Phe37= F (Phe) > F (Phe) 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 2188 T=1.0000 C=0.0000
European Sub 2072 T=1.0000 C=0.0000
African Sub 82 T=1.00 C=0.00
African Others Sub 6 T=1.0 C=0.0
African American Sub 76 T=1.00 C=0.00
Asian Sub 4 T=1.0 C=0.0
East Asian Sub 2 T=1.0 C=0.0
Other Asian Sub 2 T=1.0 C=0.0
Latin American 1 Sub 0 T=0 C=0
Latin American 2 Sub 0 T=0 C=0
South Asian Sub 4 T=1.0 C=0.0
Other Sub 26 T=1.00 C=0.00


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 251330 T=0.999948 C=0.000052
gnomAD - Exomes European Sub 135306 T=0.999904 C=0.000096
gnomAD - Exomes Asian Sub 49008 T=1.00000 C=0.00000
gnomAD - Exomes American Sub 34560 T=1.00000 C=0.00000
gnomAD - Exomes African Sub 16246 T=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6134 T=1.0000 C=0.0000
TopMed Global Study-wide 125568 T=0.999673 C=0.000327
ExAC Global Study-wide 121316 T=0.999967 C=0.000033
ExAC Europe Sub 73294 T=0.99995 C=0.00005
ExAC Asian Sub 25164 T=1.00000 C=0.00000
ExAC American Sub 11546 T=1.00000 C=0.00000
ExAC African Sub 10404 T=1.00000 C=0.00000
ExAC Other Sub 908 T=1.000 C=0.000
gnomAD - Genomes Global Study-wide 31396 T=0.99990 C=0.00010
gnomAD - Genomes European Sub 18900 T=0.99984 C=0.00016
gnomAD - Genomes African Sub 8710 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 1560 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 1088 T=1.0000 C=0.0000
gnomAD - Genomes American Sub 848 T=1.000 C=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=1.000 C=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9998 C=0.0002
ALFA Total Global 2188 T=1.0000 C=0.0000
ALFA European Sub 2072 T=1.0000 C=0.0000
ALFA African Sub 82 T=1.00 C=0.00
ALFA Other Sub 26 T=1.00 C=0.00
ALFA South Asian Sub 4 T=1.0 C=0.0
ALFA Asian Sub 4 T=1.0 C=0.0
ALFA Latin American 1 Sub 0 T=0 C=0
ALFA Latin American 2 Sub 0 T=0 C=0
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= C
GRCh38.p12 chr 8 NC_000008.11:g.18400114= NC_000008.11:g.18400114T>C
GRCh37.p13 chr 8 NC_000008.10:g.18257624= NC_000008.10:g.18257624T>C
NAT2 RefSeqGene NG_012246.1:g.13870= NG_012246.1:g.13870T>C
NAT2 transcript NM_000015.3:c.111= NM_000015.3:c.111T>C
NAT2 transcript NM_000015.2:c.111= NM_000015.2:c.111T>C
NAT2 transcript variant X1 XM_017012938.1:c.111= XM_017012938.1:c.111T>C
arylamine N-acetyltransferase 2 NP_000006.2:p.Phe37= NP_000006.2:p.Phe37=
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Phe37= XP_016868427.1:p.Phe37=
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#.

10 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 AFFY_DM3_1 ss105434763 Feb 13, 2009 (130)
2 EVA_EXAC ss1689107795 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2301164522 Dec 20, 2016 (150)
4 TOPMED ss2470822121 Dec 20, 2016 (150)
5 ILLUMINA ss2711131662 Nov 08, 2017 (151)
6 GNOMAD ss2737016588 Nov 08, 2017 (151)
7 GNOMAD ss2748005904 Nov 08, 2017 (151)
8 GNOMAD ss2863932562 Nov 08, 2017 (151)
9 TOPMED ss3555514674 Nov 08, 2017 (151)
10 EGCUT_WGS ss3670459155 Jul 13, 2019 (153)
11 Genetic variation in the Estonian population NC_000008.10 - 18257624 Oct 12, 2018 (152)
12 ExAC NC_000008.10 - 18257624 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000008.10 - 18257624 Jul 13, 2019 (153)
14 gnomAD - Exomes NC_000008.10 - 18257624 Jul 13, 2019 (153)
15 TopMed NC_000008.11 - 18400114 Oct 12, 2018 (152)
16 dbGaP Population Frequency Project NC_000008.11 - 18400114 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
16197403, 9201148, 111847143, 6184514, ss1689107795, ss2470822121, ss2711131662, ss2737016588, ss2748005904, ss2863932562, ss3670459155 NC_000008.10:18257623:T:C NC_000008.11:18400113:T:C (self)
384382815, 398197056, ss2301164522, ss3555514674 NC_000008.11:18400113:T:C NC_000008.11:18400113:T:C (self)
ss105434763 NT_167187.1:6115769:T:C NC_000008.11:18400113:T:C (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 rs72554615

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