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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.

rs56107638

Current Build 157

Released September 3, 2024

Organism
Homo sapiens
Position
chr15:74753271 (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=0.0001321 (185/1400464, GnomAD_exomes)
A=0.000196 (52/264690, TOPMED)
A=0.000252 (39/154978, ALFA) (+ 9 more)
A=0.000168 (25/149154, GnomAD_genomes)
A=0.000141 (17/120594, ExAC)
A=0.00018 (14/78702, PAGE_STUDY)
A=0.00118 (91/77444, 38KJPN)
A=0.00015 (2/12986, GO-ESP)
A=0.0001 (1/7234, Korea4K)
A=0.0007 (2/2922, KOREAN)
A=0.0005 (1/1832, Korea1K)
A=0.003 (1/358, PharmGKB)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CYP1A2 : Splice Donor Variant
Publications
3 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 HTRZ HWEP
Total Global 154978 G=0.999748 A=0.000252 0.999497 0.0 0.000503 0
European Sub 129448 G=0.999730 A=0.000270 0.999459 0.0 0.000541 0
African Sub 9982 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 368 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 9614 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 3652 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
East Asian Sub 2964 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Other Asian Sub 688 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 1 Sub 822 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 1116 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
South Asian Sub 298 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Sub 9660 G=0.9996 A=0.0004 0.999172 0.0 0.000828 0


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
gnomAD v4 - Exomes Global Study-wide 1400464 G=0.9998679 A=0.0001321
gnomAD v4 - Exomes European Sub 1164534 G=0.9999614 A=0.0000386
gnomAD v4 - Exomes South Asian Sub 86202 G=0.99998 A=0.00002
gnomAD v4 - Exomes American Sub 44716 G=0.99984 A=0.00016
gnomAD v4 - Exomes East Asian Sub 39676 G=0.99942 A=0.00058
gnomAD v4 - Exomes African Sub 33452 G=1.00000 A=0.00000
gnomAD v4 - Exomes Ashkenazi Jewish Sub 26124 G=0.99587 A=0.00413
gnomAD v4 - Exomes Middle Eastern sub 5760 G=1.0000 A=0.0000
TopMed Global Study-wide 264690 G=0.999804 A=0.000196
Allele Frequency Aggregator Total Global 154978 G=0.999748 A=0.000252
Allele Frequency Aggregator European Sub 129448 G=0.999730 A=0.000270
Allele Frequency Aggregator African Sub 9982 G=1.0000 A=0.0000
Allele Frequency Aggregator Other Sub 9660 G=0.9996 A=0.0004
Allele Frequency Aggregator Asian Sub 3652 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 1116 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 1 Sub 822 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 298 G=1.000 A=0.000
gnomAD v4 - Genomes Global Study-wide 149154 G=0.999832 A=0.000168
gnomAD v4 - Genomes European Sub 78644 G=0.99995 A=0.00005
gnomAD v4 - Genomes African Sub 41438 G=1.00000 A=0.00000
gnomAD v4 - Genomes American Sub 15270 G=1.00000 A=0.00000
gnomAD v4 - Genomes East Asian Sub 5190 G=0.9998 A=0.0002
gnomAD v4 - Genomes South Asian Sub 4826 G=1.0000 A=0.0000
gnomAD v4 - Genomes Ashkenazi Jewish Sub 3470 G=0.9942 A=0.0058
gnomAD v4 - Genomes Middle Eastern sub 316 G=1.000 A=0.000
ExAC Global Study-wide 120594 G=0.999859 A=0.000141
ExAC Europe Sub 72892 G=0.99982 A=0.00018
ExAC Asian Sub 25040 G=0.99988 A=0.00012
ExAC American Sub 11460 G=0.99991 A=0.00009
ExAC African Sub 10304 G=1.00000 A=0.00000
ExAC Other Sub 898 G=1.000 A=0.000
The PAGE Study Global Study-wide 78702 G=0.99982 A=0.00018
The PAGE Study AfricanAmerican Sub 32516 G=0.99997 A=0.00003
The PAGE Study Mexican Sub 10810 G=0.99963 A=0.00037
The PAGE Study Asian Sub 8318 G=0.9995 A=0.0005
The PAGE Study PuertoRican Sub 7918 G=0.9997 A=0.0003
The PAGE Study NativeHawaiian Sub 4534 G=0.9998 A=0.0002
The PAGE Study Cuban Sub 4230 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 G=0.9997 A=0.0003
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=0.9992 A=0.0008
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
38KJPN JAPANESE Study-wide 77444 G=0.99882 A=0.00118
GO Exome Sequencing Project Global Study-wide 12986 G=0.99985 A=0.00015
GO Exome Sequencing Project European American Sub 8592 G=0.9998 A=0.0002
GO Exome Sequencing Project African American Sub 4394 G=1.0000 A=0.0000
Korean Genome Project 4K KOREAN Study-wide 7234 G=0.9999 A=0.0001
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9993 A=0.0007
Korean Genome Project KOREAN Study-wide 1832 G=0.9995 A=0.0005
PharmGKB Aggregated Global Study-wide 358 G=0.997 A=0.003
PharmGKB Aggregated PA149529264 Sub 358 G=0.997 A=0.003
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.74753271G>A
GRCh38.p14 chr 15 NC_000015.10:g.74753271G>C
GRCh37.p13 chr 15 NC_000015.9:g.75045612G>A
GRCh37.p13 chr 15 NC_000015.9:g.75045612G>C
CYP1A1-CYP1A2 RefSeqGene NG_008431.2:g.35730G>A
CYP1A1-CYP1A2 RefSeqGene NG_008431.2:g.35730G>C
CYP1A2 RefSeqGene (LRG_1274) NG_061543.1:g.9427G>A
CYP1A2 RefSeqGene (LRG_1274) NG_061543.1:g.9427G>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. N/A Splice Donor 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.74753271= NC_000015.10:g.74753271G>A NC_000015.10:g.74753271G>C
GRCh37.p13 chr 15 NC_000015.9:g.75045612= NC_000015.9:g.75045612G>A NC_000015.9:g.75045612G>C
CYP1A1-CYP1A2 RefSeqGene NG_008431.2:g.35730= NG_008431.2:g.35730G>A NG_008431.2:g.35730G>C
CYP1A2 RefSeqGene (LRG_1274) NG_061543.1:g.9427= NG_061543.1:g.9427G>A NG_061543.1:g.9427G>C
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#.

41 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA ss75239645 Dec 07, 2007 (129)
2 CGM_KYOTO ss76860124 Dec 07, 2007 (129)
3 PHARMGKB_AB_DME ss84158689 Dec 14, 2007 (130)
4 AFFY_DM3_1 ss105434108 Feb 04, 2009 (130)
5 ILLUMINA ss161034237 Dec 01, 2009 (131)
6 ILLUMINA ss169135727 Jul 04, 2010 (132)
7 BUSHMAN ss201038403 Jul 04, 2010 (132)
8 NHLBI-ESP ss342408583 May 09, 2011 (134)
9 ILLUMINA ss483025585 Sep 08, 2015 (146)
10 CLINSEQ_SNP ss491704193 May 04, 2012 (137)
11 ILLUMINA ss537652740 Sep 08, 2015 (146)
12 EVA_EXAC ss1691925992 Apr 01, 2015 (144)
13 ILLUMINA ss1946398606 Feb 12, 2016 (147)
14 ILLUMINA ss1959626425 Feb 12, 2016 (147)
15 HUMAN_LONGEVITY ss2208165079 Dec 20, 2016 (150)
16 GNOMAD ss2741399010 Nov 08, 2017 (151)
17 GNOMAD ss2749350765 Nov 08, 2017 (151)
18 GNOMAD ss2936802282 Nov 08, 2017 (151)
19 ILLUMINA ss3021649439 Nov 08, 2017 (151)
20 ILLUMINA ss3625678488 Oct 12, 2018 (152)
21 ILLUMINA ss3627401458 Oct 12, 2018 (152)
22 ILLUMINA ss3636304934 Oct 12, 2018 (152)
23 ILLUMINA ss3638095683 Oct 12, 2018 (152)
24 ILLUMINA ss3643079201 Oct 12, 2018 (152)
25 ILLUMINA ss3644651718 Oct 12, 2018 (152)
26 ILLUMINA ss3652051128 Oct 12, 2018 (152)
27 ILLUMINA ss3725514508 Jul 13, 2019 (153)
28 ILLUMINA ss3744133531 Jul 13, 2019 (153)
29 PAGE_CC ss3771841927 Jul 13, 2019 (153)
30 EVA ss3824939617 Apr 27, 2020 (154)
31 KRGDB ss3932477567 Apr 27, 2020 (154)
32 KOGIC ss3976481044 Apr 27, 2020 (154)
33 TOPMED ss4997227158 Apr 27, 2021 (155)
34 TOMMO_GENOMICS ss6157347246 Nov 01, 2024 (157)
35 KOGIC ss6392444849 Nov 01, 2024 (157)
36 GNOMAD ss6454536137 Nov 01, 2024 (157)
37 GNOMAD ss6981065116 Nov 01, 2024 (157)
38 TOMMO_GENOMICS ss8216965710 Nov 01, 2024 (157)
39 TOMMO_GENOMICS ss8771002709 Nov 01, 2024 (157)
40 EVA ss8847749791 Nov 01, 2024 (157)
41 EVA ss8949253659 Nov 01, 2024 (157)
42 ExAC NC_000015.9 - 75045612 Oct 12, 2018 (152)
43 gnomAD v4 - Exomes NC_000015.10 - 74753271 Nov 01, 2024 (157)
44 gnomAD v4 - Genomes NC_000015.10 - 74753271 Nov 01, 2024 (157)
45 GO Exome Sequencing Project NC_000015.9 - 75045612 Oct 12, 2018 (152)
46 KOREAN population from KRGDB NC_000015.9 - 75045612 Apr 27, 2020 (154)
47 Korean Genome Project NC_000015.10 - 74753271 Apr 27, 2020 (154)
48 Korean Genome Project 4K NC_000015.10 - 74753271 Nov 01, 2024 (157)
49 The PAGE Study NC_000015.10 - 74753271 Jul 13, 2019 (153)
50 PharmGKB Aggregated NC_000015.10 - 74753271 Apr 27, 2020 (154)
51 38KJPN NC_000015.10 - 74753271 Nov 01, 2024 (157)
52 TopMed NC_000015.10 - 74753271 Apr 27, 2021 (155)
53 ALFA NC_000015.10 - 74753271 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).

Associated ID History Updated (Build)
rs57702151 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss491704193, ss3643079201 NC_000015.8:72832664:G:A NC_000015.10:74753270:G:A (self)
2307143, 1396869, 39654961, ss342408583, ss483025585, ss537652740, ss1691925992, ss1946398606, ss1959626425, ss2741399010, ss2749350765, ss2936802282, ss3021649439, ss3625678488, ss3627401458, ss3636304934, ss3638095683, ss3644651718, ss3652051128, ss3744133531, ss3824939617, ss3932477567, ss8216965710, ss8847749791, ss8949253659 NC_000015.9:75045611:G:A NC_000015.10:74753270:G:A (self)
49868239, 508489238, 32859045, 42296747, 1063396, 3610, 174723066, 212772818, 9748735358, ss2208165079, ss3725514508, ss3771841927, ss3976481044, ss4997227158, ss6157347246, ss6392444849, ss6454536137, ss6981065116, ss8771002709 NC_000015.10:74753270:G:A NC_000015.10:74753270:G:A (self)
ss75239645, ss76860124, ss84158689, ss105434108, ss161034237, ss169135727 NT_010194.17:45836168:G:A NC_000015.10:74753270:G:A (self)
ss201038403 NC_000015.8:72832664:G:C NC_000015.10:74753270:G:C (self)
Help

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

3 citations for rs56107638
PMID Title Author Year Journal
21918647 Pathway-Targeted Pharmacogenomics of CYP1A2 in Human Liver. Klein K et al. 2010 Frontiers in pharmacology
22448283 Genotyping performance between saliva and blood-derived genomic DNAs on the DMET array: a comparison. Hu Y et al. 2012 PloS one
30214584 Influence of SLCO1B1 in gastric cancer patients treated with EOF chemotherapy. Feng W et al. 2018 Oncology letters
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