Name: rs72547513
Published: September 3, 2024
License: Open Access

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.

rs72547513

Current Build 157

Released September 3, 2024

Organism: Homo sapiens
Position: chr15:74750296 (GRCh38.p14) 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>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000038 (10/264690, TOPMED)
T=0.000020 (3/149202, GnomAD_genomes)
T=0.000016 (2/121398, ExAC) (+ 3 more)
A=0.00018 (14/77444, 38KJPN)
A=0.21203 (16354/77132, ALFA)
T=0.00008 (1/12986, GO-ESP)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CYP1A2 : Missense Variant
Publications: 2 citations
Genomic View: See rs on genome

ALFA Allele Frequency
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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HWEP
Total	Global	77132	C=0.78790	A=0.21203, T=0.00008	0.787941	0.212059	32
European	Sub	58818	C=0.72653	A=0.27342, T=0.00005	0.726552	0.273448	32
African	Sub	8350	C=0.9996	A=0.0000, T=0.0004	1.0	0.0	N/A
African Others	Sub	306	C=1.000	A=0.000, T=0.000	1.0	0.0	N/A
African American	Sub	8044	C=0.9996	A=0.0000, T=0.0004	1.0	0.0	N/A
Asian	Sub	212	C=0.792	A=0.208, T=0.000	0.792453	0.207547	32
East Asian	Sub	156	C=0.718	A=0.282, T=0.000	0.717949	0.282051	32
Other Asian	Sub	56	C=1.00	A=0.00, T=0.00	1.0	0.0	N/A
Latin American 1	Sub	500	C=1.000	A=0.000, T=0.000	1.0	0.0	N/A
Latin American 2	Sub	628	C=1.000	A=0.000, T=0.000	1.0	0.0	N/A
South Asian	Sub	98	C=1.00	A=0.00, T=0.00	1.0	0.0	N/A
Other	Sub	8526	C=0.9733	A=0.0267, T=0.0000	0.973258	0.026742	32

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
TopMed	Global	Study-wide	264690	C=0.999962	T=0.000038
gnomAD v4 - Genomes	Global	Study-wide	149202	C=0.999980	T=0.000020
gnomAD v4 - Genomes	European	Sub	78662	C=0.99999	T=0.00001
gnomAD v4 - Genomes	African	Sub	41428	C=0.99995	T=0.00005
gnomAD v4 - Genomes	American	Sub	15286	C=1.00000	T=0.00000
gnomAD v4 - Genomes	East Asian	Sub	5202	C=1.0000	T=0.0000
gnomAD v4 - Genomes	South Asian	Sub	4836	C=1.0000	T=0.0000
gnomAD v4 - Genomes	Ashkenazi Jewish	Sub	3472	C=1.0000	T=0.0000
gnomAD v4 - Genomes	Middle Eastern	sub	316	C=1.000	T=0.000
ExAC	Global	Study-wide	121398	C=0.999984	T=0.000016
ExAC	Europe	Sub	73342	C=1.00000	T=0.00000
ExAC	Asian	Sub	25164	C=0.99996	T=0.00004
ExAC	American	Sub	11578	C=0.99991	T=0.00009
ExAC	African	Sub	10406	C=1.00000	T=0.00000
ExAC	Other	Sub	908	C=1.000	T=0.000
38KJPN	JAPANESE	Study-wide	77444	C=0.99982	A=0.00018
Allele Frequency Aggregator	Total	Global	77132	C=0.78790	A=0.21203, T=0.00008
Allele Frequency Aggregator	European	Sub	58818	C=0.72653	A=0.27342, T=0.00005
Allele Frequency Aggregator	Other	Sub	8526	C=0.9733	A=0.0267, T=0.0000
Allele Frequency Aggregator	African	Sub	8350	C=0.9996	A=0.0000, T=0.0004
Allele Frequency Aggregator	Latin American 2	Sub	628	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	500	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	212	C=0.792	A=0.208, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	A=0.00, T=0.00
GO Exome Sequencing Project	Global	Study-wide	12986	C=0.99992	T=0.00008
GO Exome Sequencing Project	European American	Sub	8592	C=1.0000	T=0.0000
GO Exome Sequencing Project	African American	Sub	4394	C=0.9998	T=0.0002

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.p14 chr 15	NC_000015.10:g.74750296C>A
GRCh38.p14 chr 15	NC_000015.10:g.74750296C>T
GRCh37.p13 chr 15	NC_000015.9:g.75042637C>A
GRCh37.p13 chr 15	NC_000015.9:g.75042637C>T
CYP1A1-CYP1A2 RefSeqGene	NG_008431.2:g.32755C>A
CYP1A1-CYP1A2 RefSeqGene	NG_008431.2:g.32755C>T
CYP1A2 RefSeqGene (LRG_1274)	NG_061543.1:g.6452C>A
CYP1A2 RefSeqGene (LRG_1274)	NG_061543.1:g.6452C>T

Gene: CYP1A2, cytochrome P450 family 1 subfamily A member 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CYP1A2 transcript	NM_000761.5:c.558C>A	F [TTC] > L [TTA]	Coding Sequence Variant
cytochrome P450 1A2	NP_000752.2:p.Phe186Leu	F (Phe) > L (Leu)	Missense Variant
CYP1A2 transcript	NM_000761.5:c.558C>T	F [TTC] > F [TTT]	Coding Sequence Variant
cytochrome P450 1A2	NP_000752.2:p.Phe186=	F (Phe) > F (Phe)	Synonymous Variant

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

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=	A	T
GRCh38.p14 chr 15	NC_000015.10:g.74750296=	NC_000015.10:g.74750296C>A	NC_000015.10:g.74750296C>T
GRCh37.p13 chr 15	NC_000015.9:g.75042637=	NC_000015.9:g.75042637C>A	NC_000015.9:g.75042637C>T
CYP1A1-CYP1A2 RefSeqGene	NG_008431.2:g.32755=	NG_008431.2:g.32755C>A	NG_008431.2:g.32755C>T
CYP1A2 transcript	NM_000761.5:c.558=	NM_000761.5:c.558C>A	NM_000761.5:c.558C>T
CYP1A2 transcript	NM_000761.4:c.558=	NM_000761.4:c.558C>A	NM_000761.4:c.558C>T
CYP1A2 transcript	NM_000761.3:c.558=	NM_000761.3:c.558C>A	NM_000761.3:c.558C>T
CYP1A2 RefSeqGene (LRG_1274)	NG_061543.1:g.6452=	NG_061543.1:g.6452C>A	NG_061543.1:g.6452C>T
cytochrome P450 1A2	NP_000752.2:p.Phe186=	NP_000752.2:p.Phe186Leu	NP_000752.2:p.Phe186=

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#.

16 SubSNP, 8 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	AFFY_DM3_1	ss105434102	Feb 13, 2009 (130)
2	NHLBI-ESP	ss713249459	Apr 25, 2013 (138)
3	EVA_EXAC	ss1691925767	Apr 01, 2015 (144)
4	ILLUMINA	ss2710820368	Nov 08, 2017 (151)
5	GNOMAD	ss2741398691	Nov 08, 2017 (151)
6	EVA	ss3824939573	Apr 27, 2020 (154)
7	TOPMED	ss4997226406	Apr 27, 2021 (155)
8	TOMMO_GENOMICS	ss6157347053	Nov 01, 2024 (157)
9	GNOMAD	ss6454534893	Nov 01, 2024 (157)
10	GNOMAD	ss6454534894	Nov 01, 2024 (157)
11	GNOMAD	ss6981064441	Nov 01, 2024 (157)
12	TOMMO_GENOMICS	ss8216965618	Nov 01, 2024 (157)
13	EVA	ss8237553875	Nov 01, 2024 (157)
14	EVA	ss8237553876	Nov 01, 2024 (157)
15	EVA	ss8237664505	Nov 01, 2024 (157)
16	TOMMO_GENOMICS	ss8771002593	Nov 01, 2024 (157)
17	ExAC	NC_000015.9 - 75042637	Oct 12, 2018 (152)
18	gnomAD v4 - Exomes Submission ignored due to conflicting rows: Row 49866995 (NC_000015.10:74750295:C:A 1/1401496) Row 49866996 (NC_000015.10:74750295:C:T 25/1401496)	-	Nov 01, 2024 (157)
19	gnomAD v4 - Exomes Submission ignored due to conflicting rows: Row 49866995 (NC_000015.10:74750295:C:A 1/1401496) Row 49866996 (NC_000015.10:74750295:C:T 25/1401496)	-	Nov 01, 2024 (157)
20	gnomAD v4 - Genomes	NC_000015.10 - 74750296	Nov 01, 2024 (157)
21	GO Exome Sequencing Project	NC_000015.9 - 75042637	Oct 12, 2018 (152)
22	38KJPN	NC_000015.10 - 74750296	Nov 01, 2024 (157)
23	TopMed	NC_000015.10 - 74750296	Apr 27, 2021 (155)
24	ALFA	NC_000015.10 - 74750296	Nov 01, 2024 (157)

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
ss2710820368, ss8216965618, ss8237553875	NC_000015.9:75042636:C:A	NC_000015.10:74750295:C:A	(self)
174722873, 3113162425, ss6157347053, ss6454534893, ss8771002593	NC_000015.10:74750295:C:A	NC_000015.10:74750295:C:A	(self)
ss105434102	NT_010194.17:45833193:C:A	NC_000015.10:74750295:C:A	(self)
2306906, 1396825, ss713249459, ss1691925767, ss2741398691, ss3824939573, ss8237553876	NC_000015.9:75042636:C:T	NC_000015.10:74750295:C:T	(self)
508488563, 212772066, 3113162425, ss4997226406, ss6454534894, ss6981064441, ss8237664505	NC_000015.10:74750295:C:T	NC_000015.10:74750295:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs72547513

PMID	Title	Author	Year	Journal
21918647	Pathway-Targeted Pharmacogenomics of CYP1A2 in Human Liver.	Klein K et al.	2010	Frontiers in pharmacology
24944790	Screening for 392 polymorphisms in 141 pharmacogenes.	Kim JY et al.	2014	Biomedical reports

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs72547513