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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.

rs1801268

Current Build 157

Released September 3, 2024

Organism
Homo sapiens
Position
chr1:97079071 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/264690, TOPMED)
A=0.000007 (1/149090, ALFA)
A=0.00001 (1/78702, PAGE_STUDY)
Clinical Significance
Reported in ClinVar
Gene : Consequence
DPYD : 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 HTRZ HWEP
Total Global 149090 C=0.999993 A=0.000007 0.999987 0.0 1.3e-05 0
European Sub 130104 C=0.999992 A=0.000008 0.999985 0.0 0.000015 0
African Sub 6408 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 234 C=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 6174 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 3652 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
East Asian Sub 2992 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Other Asian Sub 660 C=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 1 Sub 1142 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Latin American 2 Sub 1138 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
South Asian Sub 324 C=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Sub 6322 C=1.0000 A=0.0000 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 C=0.999996 A=0.000004
Allele Frequency Aggregator Total Global 149090 C=0.999993 A=0.000007
Allele Frequency Aggregator European Sub 130104 C=0.999992 A=0.000008
Allele Frequency Aggregator African Sub 6408 C=1.0000 A=0.0000
Allele Frequency Aggregator Other Sub 6322 C=1.0000 A=0.0000
Allele Frequency Aggregator Asian Sub 3652 C=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 1 Sub 1142 C=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 1138 C=1.0000 A=0.0000
Allele Frequency Aggregator South Asian Sub 324 C=1.000 A=0.000
The PAGE Study Global Study-wide 78702 C=0.99999 A=0.00001
The PAGE Study AfricanAmerican Sub 32516 C=1.00000 A=0.00000
The PAGE Study Mexican Sub 10810 C=1.00000 A=0.00000
The PAGE Study Asian Sub 8318 C=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 A=0.0000
The PAGE Study Cuban Sub 4230 C=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 C=0.9995 A=0.0005
The PAGE Study NativeAmerican Sub 1260 C=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 A=0.000
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 1 NC_000001.11:g.97079071C>A
GRCh38.p14 chr 1 NC_000001.11:g.97079071C>G
GRCh38.p14 chr 1 NC_000001.11:g.97079071C>T
GRCh37.p13 chr 1 NC_000001.10:g.97544627C>A
GRCh37.p13 chr 1 NC_000001.10:g.97544627C>G
GRCh37.p13 chr 1 NC_000001.10:g.97544627C>T
DPYD RefSeqGene (LRG_722) NG_008807.2:g.846989G>T
DPYD RefSeqGene (LRG_722) NG_008807.2:g.846989G>C
DPYD RefSeqGene (LRG_722) NG_008807.2:g.846989G>A
Gene: DPYD, dihydropyrimidine dehydrogenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
DPYD transcript variant 2 NM_001160301.1:c. N/A Genic Downstream Transcript Variant
DPYD transcript variant 1 NM_000110.4:c.2983G>T V [GTT] > F [TTT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform 1 NP_000101.2:p.Val995Phe V (Val) > F (Phe) Missense Variant
DPYD transcript variant 1 NM_000110.4:c.2983G>C V [GTT] > L [CTT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform 1 NP_000101.2:p.Val995Leu V (Val) > L (Leu) Missense Variant
DPYD transcript variant 1 NM_000110.4:c.2983G>A V [GTT] > I [ATT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform 1 NP_000101.2:p.Val995Ile V (Val) > I (Ile) Missense Variant
DPYD transcript variant X5 XM_006710397.4:c. N/A Genic Downstream Transcript Variant
DPYD transcript variant X2 XM_005270562.3:c.2767G>T V [GTT] > F [TTT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.2:p.Val923Phe V (Val) > F (Phe) Missense Variant
DPYD transcript variant X2 XM_005270562.3:c.2767G>C V [GTT] > L [CTT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.2:p.Val923Leu V (Val) > L (Leu) Missense Variant
DPYD transcript variant X2 XM_005270562.3:c.2767G>A V [GTT] > I [ATT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.2:p.Val923Ile V (Val) > I (Ile) Missense Variant
DPYD transcript variant X1 XM_017000507.2:c.2872G>T V [GTT] > F [TTT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X1 XP_016855996.1:p.Val958Phe V (Val) > F (Phe) Missense Variant
DPYD transcript variant X1 XM_017000507.2:c.2872G>C V [GTT] > L [CTT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X1 XP_016855996.1:p.Val958Leu V (Val) > L (Leu) Missense Variant
DPYD transcript variant X1 XM_017000507.2:c.2872G>A V [GTT] > I [ATT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X1 XP_016855996.1:p.Val958Ile V (Val) > I (Ile) Missense Variant
DPYD transcript variant X3 XM_047448076.1:c.2755G>T V [GTT] > F [TTT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X3 XP_047304032.1:p.Val919Phe V (Val) > F (Phe) Missense Variant
DPYD transcript variant X3 XM_047448076.1:c.2755G>C V [GTT] > L [CTT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X3 XP_047304032.1:p.Val919Leu V (Val) > L (Leu) Missense Variant
DPYD transcript variant X3 XM_047448076.1:c.2755G>A V [GTT] > I [ATT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X3 XP_047304032.1:p.Val919Ile V (Val) > I (Ile) Missense Variant
DPYD transcript variant X4 XM_047448077.1:c.2656G>T V [GTT] > F [TTT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X4 XP_047304033.1:p.Val886Phe V (Val) > F (Phe) Missense Variant
DPYD transcript variant X4 XM_047448077.1:c.2656G>C V [GTT] > L [CTT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X4 XP_047304033.1:p.Val886Leu V (Val) > L (Leu) Missense Variant
DPYD transcript variant X4 XM_047448077.1:c.2656G>A V [GTT] > I [ATT] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X4 XP_047304033.1:p.Val886Ile V (Val) > I (Ile) Missense Variant
DPYD transcript variant X6 XR_001737014.2:n. N/A Genic Downstream Transcript 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.

Allele: A (allele ID: 623098 )
ClinVar Accession Disease Names Clinical Significance
RCV000786704.3 fluorouracil response - Other Drug-Response
RCV003479218.1 Dihydropyrimidine dehydrogenase deficiency Likely-Pathogenic
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 C= A G T
GRCh38.p14 chr 1 NC_000001.11:g.97079071= NC_000001.11:g.97079071C>A NC_000001.11:g.97079071C>G NC_000001.11:g.97079071C>T
GRCh37.p13 chr 1 NC_000001.10:g.97544627= NC_000001.10:g.97544627C>A NC_000001.10:g.97544627C>G NC_000001.10:g.97544627C>T
DPYD RefSeqGene (LRG_722) NG_008807.2:g.846989= NG_008807.2:g.846989G>T NG_008807.2:g.846989G>C NG_008807.2:g.846989G>A
DPYD transcript variant 1 NM_000110.4:c.2983= NM_000110.4:c.2983G>T NM_000110.4:c.2983G>C NM_000110.4:c.2983G>A
DPYD transcript variant 1 NM_000110.3:c.2983= NM_000110.3:c.2983G>T NM_000110.3:c.2983G>C NM_000110.3:c.2983G>A
DPYD transcript variant X2 XM_005270562.3:c.2767= XM_005270562.3:c.2767G>T XM_005270562.3:c.2767G>C XM_005270562.3:c.2767G>A
DPYD transcript variant X2 XM_005270562.2:c.2767= XM_005270562.2:c.2767G>T XM_005270562.2:c.2767G>C XM_005270562.2:c.2767G>A
DPYD transcript variant X2 XM_005270562.1:c.2767= XM_005270562.1:c.2767G>T XM_005270562.1:c.2767G>C XM_005270562.1:c.2767G>A
DPYD transcript variant X1 XM_017000507.2:c.2872= XM_017000507.2:c.2872G>T XM_017000507.2:c.2872G>C XM_017000507.2:c.2872G>A
DPYD transcript variant X1 XM_017000507.1:c.2872= XM_017000507.1:c.2872G>T XM_017000507.1:c.2872G>C XM_017000507.1:c.2872G>A
DPYD transcript variant X3 XM_047448076.1:c.2755= XM_047448076.1:c.2755G>T XM_047448076.1:c.2755G>C XM_047448076.1:c.2755G>A
DPYD transcript variant X4 XM_047448077.1:c.2656= XM_047448077.1:c.2656G>T XM_047448077.1:c.2656G>C XM_047448077.1:c.2656G>A
dihydropyrimidine dehydrogenase [NADP(+)] isoform 1 NP_000101.2:p.Val995= NP_000101.2:p.Val995Phe NP_000101.2:p.Val995Leu NP_000101.2:p.Val995Ile
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.2:p.Val923= XP_005270619.2:p.Val923Phe XP_005270619.2:p.Val923Leu XP_005270619.2:p.Val923Ile
dihydropyrimidine dehydrogenase [NADP(+)] isoform X1 XP_016855996.1:p.Val958= XP_016855996.1:p.Val958Phe XP_016855996.1:p.Val958Leu XP_016855996.1:p.Val958Ile
dihydropyrimidine dehydrogenase [NADP(+)] isoform X3 XP_047304032.1:p.Val919= XP_047304032.1:p.Val919Phe XP_047304032.1:p.Val919Leu XP_047304032.1:p.Val919Ile
dihydropyrimidine dehydrogenase [NADP(+)] isoform X4 XP_047304033.1:p.Val886= XP_047304033.1:p.Val886Phe XP_047304033.1:p.Val886Leu XP_047304033.1:p.Val886Ile
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.1:p.Val923= XP_005270619.1:p.Val923Phe XP_005270619.1:p.Val923Leu XP_005270619.1:p.Val923Ile
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#.

30 SubSNP, 5 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 HGBASE ss2421507 Nov 14, 2000 (89)
2 ILLUMINA ss75245731 Dec 07, 2007 (129)
3 KRIBB_YJKIM ss119404012 Dec 01, 2009 (131)
4 ILLUMINA ss160463019 Dec 01, 2009 (131)
5 ILLUMINA ss172925466 Jul 04, 2010 (132)
6 ILLUMINA ss481067871 Sep 08, 2015 (146)
7 ILLUMINA ss536992451 Sep 08, 2015 (146)
8 ILLUMINA ss1946002529 Feb 12, 2016 (147)
9 ILLUMINA ss1958295823 Feb 12, 2016 (147)
10 ILLUMINA ss2632551287 Nov 08, 2017 (151)
11 ILLUMINA ss2710677975 Nov 08, 2017 (151)
12 ILLUMINA ss3021112682 Nov 08, 2017 (151)
13 ILLUMINA ss3625545858 Oct 11, 2018 (152)
14 ILLUMINA ss3626161324 Oct 11, 2018 (152)
15 ILLUMINA ss3636015512 Oct 11, 2018 (152)
16 ILLUMINA ss3637774030 Oct 11, 2018 (152)
17 ILLUMINA ss3642784302 Oct 11, 2018 (152)
18 ILLUMINA ss3644498490 Oct 11, 2018 (152)
19 ILLUMINA ss3651443299 Oct 11, 2018 (152)
20 ILLUMINA ss3725047092 Jul 12, 2019 (153)
21 ILLUMINA ss3744050764 Jul 12, 2019 (153)
22 PAGE_CC ss3770827217 Jul 12, 2019 (153)
23 EVA ss4016926451 Apr 25, 2021 (155)
24 TOPMED ss4460056342 Apr 25, 2021 (155)
25 EVA ss6349480995 Nov 02, 2024 (157)
26 GNOMAD ss6407777117 Nov 02, 2024 (157)
27 GNOMAD ss6407777118 Nov 02, 2024 (157)
28 EVA ss8847548044 Nov 02, 2024 (157)
29 EVA ss8937957370 Nov 02, 2024 (157)
30 EVA ss8979282989 Nov 02, 2024 (157)
31 gnomAD v4 - Exomes

Submission ignored due to conflicting rows:
Row 3075449 (NC_000001.11:97079070:C:A 3/1401156)
Row 3075450 (NC_000001.11:97079070:C:T 1/1401156)

- Nov 02, 2024 (157)
32 gnomAD v4 - Exomes

Submission ignored due to conflicting rows:
Row 3075449 (NC_000001.11:97079070:C:A 3/1401156)
Row 3075450 (NC_000001.11:97079070:C:T 1/1401156)

- Nov 02, 2024 (157)
33 The PAGE Study NC_000001.11 - 97079071 Jul 12, 2019 (153)
34 TopMed NC_000001.11 - 97079071 Apr 25, 2021 (155)
35 ALFA NC_000001.11 - 97079071 Nov 02, 2024 (157)
36 ClinVar RCV000786704.3 Oct 12, 2022 (156)
37 ClinVar RCV003479218.1 Nov 02, 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)
rs386545629 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3642784302 NC_000001.9:97317214:C:A NC_000001.11:97079070:C:A (self)
ss481067871, ss536992451, ss1946002529, ss1958295823, ss2632551287, ss2710677975, ss3021112682, ss3625545858, ss3626161324, ss3636015512, ss3637774030, ss3644498490, ss3651443299, ss3744050764, ss4016926451, ss8847548044, ss8937957370, ss8979282989 NC_000001.10:97544626:C:A NC_000001.11:97079070:C:A (self)
RCV000786704.3, RCV003479218.1, 48686, 23662677, 1966707497, ss3725047092, ss3770827217, ss4460056342, ss6407777117 NC_000001.11:97079070:C:A NC_000001.11:97079070:C:A (self)
ss2421507, ss75245731, ss119404012, ss160463019, ss172925466 NT_032977.9:67516544:C:A NC_000001.11:97079070:C:A (self)
ss6349480995 NC_000001.10:97544626:C:G NC_000001.11:97079070:C:G
ss6407777118 NC_000001.11:97079070:C:T NC_000001.11:97079070:C:T
Help

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

2 citations for rs1801268
PMID Title Author Year Journal
24944790 Screening for 392 polymorphisms in 141 pharmacogenes. Kim JY et al. 2014 Biomedical reports
34621706 Comprehensive analysis of important pharmacogenes in Koreans using the DMET™ platform. Kim B et al. 2021 Translational and clinical pharmacology
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