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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs72547517

Current Build 157

Released September 3, 2024

Organism
Homo sapiens
Position
chr15:74754904 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000049 (13/264690, TOPMED)
A=0.000047 (7/149220, GnomAD_genomes)
A=0.000033 (4/121394, ExAC) (+ 5 more)
A=0.00056 (44/78702, PAGE_STUDY)
A=0.00647 (501/77444, 38KJPN)
A=0.00000 (0/31068, ALFA)
A=0.0001 (1/7234, Korea4K)
A=0.0003 (1/2922, KOREAN)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CYP1A2 : Missense Variant
Publications
1 citation
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 HTRZ HWEP
Total Global 31068 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 25854 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
African Sub 3332 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 3218 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 190 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 164 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 26 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 104 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Sub 832 G=1.000 A=0.000 1.0 0.0 0.0 N/A


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 264690 G=0.999951 A=0.000049
gnomAD v4 - Genomes Global Study-wide 149220 G=0.999953 A=0.000047
gnomAD v4 - Genomes European Sub 78670 G=1.00000 A=0.00000
gnomAD v4 - Genomes African Sub 41456 G=0.99993 A=0.00007
gnomAD v4 - Genomes American Sub 15286 G=1.00000 A=0.00000
gnomAD v4 - Genomes East Asian Sub 5186 G=0.9994 A=0.0006
gnomAD v4 - Genomes South Asian Sub 4836 G=0.9998 A=0.0002
gnomAD v4 - Genomes Ashkenazi Jewish Sub 3470 G=1.0000 A=0.0000
gnomAD v4 - Genomes Middle Eastern sub 316 G=1.000 A=0.000
ExAC Global Study-wide 121394 G=0.999967 A=0.000033
ExAC Europe Sub 73338 G=0.99999 A=0.00001
ExAC Asian Sub 25166 G=0.99996 A=0.00004
ExAC American Sub 11578 G=1.00000 A=0.00000
ExAC African Sub 10404 G=0.99981 A=0.00019
ExAC Other Sub 908 G=1.000 A=0.000
The PAGE Study Global Study-wide 78702 G=0.99944 A=0.00056
The PAGE Study AfricanAmerican Sub 32516 G=0.99978 A=0.00022
The PAGE Study Mexican Sub 10810 G=1.00000 A=0.00000
The PAGE Study Asian Sub 8318 G=0.9957 A=0.0043
The PAGE Study PuertoRican Sub 7918 G=0.9999 A=0.0001
The PAGE Study NativeHawaiian Sub 4534 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4230 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 G=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
38KJPN JAPANESE Study-wide 77444 G=0.99353 A=0.00647
Allele Frequency Aggregator Total Global 31068 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 25854 G=1.00000 A=0.00000
Allele Frequency Aggregator African Sub 3332 G=1.0000 A=0.0000
Allele Frequency Aggregator Other Sub 832 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 190 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 104 G=1.000 A=0.000
Korean Genome Project 4K KOREAN Study-wide 7234 G=0.9999 A=0.0001
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9997 A=0.0003
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.p14 chr 15 NC_000015.10:g.74754904G>A
GRCh38.p14 chr 15 NC_000015.10:g.74754904G>C
GRCh37.p13 chr 15 NC_000015.9:g.75047245G>A
GRCh37.p13 chr 15 NC_000015.9:g.75047245G>C
CYP1A1-CYP1A2 RefSeqGene NG_008431.2:g.37363G>A
CYP1A1-CYP1A2 RefSeqGene NG_008431.2:g.37363G>C
CYP1A2 RefSeqGene (LRG_1274) NG_061543.1:g.11060G>A
CYP1A2 RefSeqGene (LRG_1274) NG_061543.1:g.11060G>C
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.1367G>A R [CGC] > H [CAC] Coding Sequence Variant
cytochrome P450 1A2 NP_000752.2:p.Arg456His R (Arg) > H (His) Missense Variant
CYP1A2 transcript NM_000761.5:c.1367G>C R [CGC] > P [CCC] Coding Sequence Variant
cytochrome P450 1A2 NP_000752.2:p.Arg456Pro R (Arg) > P (Pro) 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
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 G= A C
GRCh38.p14 chr 15 NC_000015.10:g.74754904= NC_000015.10:g.74754904G>A NC_000015.10:g.74754904G>C
GRCh37.p13 chr 15 NC_000015.9:g.75047245= NC_000015.9:g.75047245G>A NC_000015.9:g.75047245G>C
CYP1A1-CYP1A2 RefSeqGene NG_008431.2:g.37363= NG_008431.2:g.37363G>A NG_008431.2:g.37363G>C
CYP1A2 transcript NM_000761.5:c.1367= NM_000761.5:c.1367G>A NM_000761.5:c.1367G>C
CYP1A2 transcript NM_000761.4:c.1367= NM_000761.4:c.1367G>A NM_000761.4:c.1367G>C
CYP1A2 transcript NM_000761.3:c.1367= NM_000761.3:c.1367G>A NM_000761.3:c.1367G>C
CYP1A2 RefSeqGene (LRG_1274) NG_061543.1:g.11060= NG_061543.1:g.11060G>A NG_061543.1:g.11060G>C
cytochrome P450 1A2 NP_000752.2:p.Arg456= NP_000752.2:p.Arg456His NP_000752.2:p.Arg456Pro
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#.

23 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 AFFY_DM3_1 ss105434109 Feb 13, 2009 (130)
2 EVA_EXAC ss1691926032 Apr 01, 2015 (144)
3 ILLUMINA ss1959626431 Feb 12, 2016 (147)
4 HUMAN_LONGEVITY ss2208165167 Dec 20, 2016 (150)
5 ILLUMINA ss2710820380 Nov 08, 2017 (151)
6 GNOMAD ss2741399069 Nov 08, 2017 (151)
7 GNOMAD ss2749350784 Nov 08, 2017 (151)
8 GNOMAD ss2936802404 Nov 08, 2017 (151)
9 ILLUMINA ss3021649444 Nov 08, 2017 (151)
10 ILLUMINA ss3652051133 Oct 12, 2018 (152)
11 ILLUMINA ss3725514513 Jul 13, 2019 (153)
12 PAGE_CC ss3771841932 Jul 13, 2019 (153)
13 KRGDB ss3932477599 Apr 27, 2020 (154)
14 TOPMED ss4997227530 Apr 27, 2021 (155)
15 TOMMO_GENOMICS ss6157347372 Nov 01, 2024 (157)
16 KOGIC ss6392444883 Nov 01, 2024 (157)
17 GNOMAD ss6454536395 Nov 01, 2024 (157)
18 GNOMAD ss6454536396 Nov 01, 2024 (157)
19 GNOMAD ss6981065485 Nov 01, 2024 (157)
20 TOMMO_GENOMICS ss8216965775 Nov 01, 2024 (157)
21 TOMMO_GENOMICS ss8771002780 Nov 01, 2024 (157)
22 EVA ss8847749796 Nov 01, 2024 (157)
23 EVA ss8979467003 Nov 01, 2024 (157)
24 ExAC NC_000015.9 - 75047245 Oct 12, 2018 (152)
25 gnomAD v4 - Exomes

Submission ignored due to conflicting rows:
Row 49868497 (NC_000015.10:74754903:G:A 151/1401498)
Row 49868498 (NC_000015.10:74754903:G:C 2/1401498)

- Nov 01, 2024 (157)
26 gnomAD v4 - Exomes

Submission ignored due to conflicting rows:
Row 49868497 (NC_000015.10:74754903:G:A 151/1401498)
Row 49868498 (NC_000015.10:74754903:G:C 2/1401498)

- Nov 01, 2024 (157)
27 gnomAD v4 - Genomes NC_000015.10 - 74754904 Nov 01, 2024 (157)
28 KOREAN population from KRGDB NC_000015.9 - 75047245 Apr 27, 2020 (154)
29 Korean Genome Project 4K NC_000015.10 - 74754904 Nov 01, 2024 (157)
30 The PAGE Study NC_000015.10 - 74754904 Jul 13, 2019 (153)
31 38KJPN NC_000015.10 - 74754904 Nov 01, 2024 (157)
32 TopMed NC_000015.10 - 74754904 Apr 27, 2021 (155)
33 ALFA NC_000015.10 - 74754904 Nov 01, 2024 (157)
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
2307186, 39654993, ss1691926032, ss1959626431, ss2710820380, ss2741399069, ss2749350784, ss2936802404, ss3021649444, ss3652051133, ss3932477599, ss8216965775, ss8847749796, ss8979467003 NC_000015.9:75047244:G:A NC_000015.10:74754903:G:A (self)
508489607, 42296781, 1063401, 174723192, 212773190, 13786976929, ss2208165167, ss3725514513, ss3771841932, ss4997227530, ss6157347372, ss6392444883, ss6454536395, ss6981065485, ss8771002780 NC_000015.10:74754903:G:A NC_000015.10:74754903:G:A (self)
ss105434109 NT_010194.17:45837801:G:A NC_000015.10:74754903:G:A (self)
ss6454536396 NC_000015.10:74754903:G:C NC_000015.10:74754903:G:C
Help

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

1 citation for rs72547517
PMID Title Author Year Journal
24944790 Screening for 392 polymorphisms in 141 pharmacogenes. Kim JY et al. 2014 Biomedical reports
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.post825+45319f0