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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.

rs78060119

Current Build 157

Released September 3, 2024

Organism
Homo sapiens
Position
chr1:97573943 (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=0.000008 (2/264690, TOPMED)
A=0.000007 (1/149148, GnomAD_genomes)
A=0.00000 (0/82764, ALFA) (+ 1 more)
A=0.00006 (5/77156, 38KJPN)
Clinical Significance
Reported in ClinVar
Gene : Consequence
DPYD : Stop Gained
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 82764 C=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 72464 C=1.00000 A=0.00000 1.0 0.0 0.0 N/A
African Sub 3236 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 156 C=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 3080 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 3278 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
East Asian Sub 2650 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Other Asian Sub 628 C=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 1 Sub 518 C=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 1474 C=1.0000 A=0.0000 1.0 0.0 0.0 N/A
South Asian Sub 292 C=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Sub 1502 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=0.999992 A=0.000008
gnomAD v4 - Genomes Global Study-wide 149148 C=0.999993 A=0.000007
gnomAD v4 - Genomes European Sub 78646 C=1.00000 A=0.00000
gnomAD v4 - Genomes African Sub 41448 C=1.00000 A=0.00000
gnomAD v4 - Genomes American Sub 15248 C=0.99993 A=0.00007
gnomAD v4 - Genomes East Asian Sub 5186 C=1.0000 A=0.0000
gnomAD v4 - Genomes South Asian Sub 4834 C=1.0000 A=0.0000
gnomAD v4 - Genomes Ashkenazi Jewish Sub 3470 C=1.0000 A=0.0000
gnomAD v4 - Genomes Middle Eastern sub 316 C=1.000 A=0.000
Allele Frequency Aggregator Total Global 82764 C=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 72464 C=1.00000 A=0.00000
Allele Frequency Aggregator Asian Sub 3278 C=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 3236 C=1.0000 A=0.0000
Allele Frequency Aggregator Other Sub 1502 C=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 1474 C=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 1 Sub 518 C=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 292 C=1.000 A=0.000
38KJPN JAPANESE Study-wide 77156 C=0.99994 A=0.00006
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.97573943C>A
GRCh38.p14 chr 1 NC_000001.11:g.97573943C>G
GRCh38.p14 chr 1 NC_000001.11:g.97573943C>T
GRCh37.p13 chr 1 NC_000001.10:g.98039499C>A
GRCh37.p13 chr 1 NC_000001.10:g.98039499C>G
GRCh37.p13 chr 1 NC_000001.10:g.98039499C>T
DPYD RefSeqGene (LRG_722) NG_008807.2:g.352117G>T
DPYD RefSeqGene (LRG_722) NG_008807.2:g.352117G>C
DPYD RefSeqGene (LRG_722) NG_008807.2:g.352117G>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.1156G>T E [GAA] > * [TAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform 1 NP_000101.2:p.Glu386Ter E (Glu) > * (Ter) Stop Gained
DPYD transcript variant 1 NM_000110.4:c.1156G>C E [GAA] > Q [CAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform 1 NP_000101.2:p.Glu386Gln E (Glu) > Q (Gln) Missense Variant
DPYD transcript variant 1 NM_000110.4:c.1156G>A E [GAA] > K [AAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform 1 NP_000101.2:p.Glu386Lys E (Glu) > K (Lys) Missense Variant
DPYD transcript variant X2 XM_005270562.3:c.1156G>T E [GAA] > * [TAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.2:p.Glu386Ter E (Glu) > * (Ter) Stop Gained
DPYD transcript variant X2 XM_005270562.3:c.1156G>C E [GAA] > Q [CAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.2:p.Glu386Gln E (Glu) > Q (Gln) Missense Variant
DPYD transcript variant X2 XM_005270562.3:c.1156G>A E [GAA] > K [AAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.2:p.Glu386Lys E (Glu) > K (Lys) Missense Variant
DPYD transcript variant X1 XM_017000507.2:c.1045G>T E [GAA] > * [TAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X1 XP_016855996.1:p.Glu349Ter E (Glu) > * (Ter) Stop Gained
DPYD transcript variant X1 XM_017000507.2:c.1045G>C E [GAA] > Q [CAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X1 XP_016855996.1:p.Glu349Gln E (Glu) > Q (Gln) Missense Variant
DPYD transcript variant X1 XM_017000507.2:c.1045G>A E [GAA] > K [AAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X1 XP_016855996.1:p.Glu349Lys E (Glu) > K (Lys) Missense Variant
DPYD transcript variant X3 XM_047448076.1:c.928G>T E [GAA] > * [TAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X3 XP_047304032.1:p.Glu310Ter E (Glu) > * (Ter) Stop Gained
DPYD transcript variant X3 XM_047448076.1:c.928G>C E [GAA] > Q [CAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X3 XP_047304032.1:p.Glu310Gln E (Glu) > Q (Gln) Missense Variant
DPYD transcript variant X3 XM_047448076.1:c.928G>A E [GAA] > K [AAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X3 XP_047304032.1:p.Glu310Lys E (Glu) > K (Lys) Missense Variant
DPYD transcript variant X4 XM_047448077.1:c.1045G>T E [GAA] > * [TAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X4 XP_047304033.1:p.Glu349Ter E (Glu) > * (Ter) Stop Gained
DPYD transcript variant X4 XM_047448077.1:c.1045G>C E [GAA] > Q [CAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X4 XP_047304033.1:p.Glu349Gln E (Glu) > Q (Gln) Missense Variant
DPYD transcript variant X4 XM_047448077.1:c.1045G>A E [GAA] > K [AAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X4 XP_047304033.1:p.Glu349Lys E (Glu) > K (Lys) Missense Variant
DPYD transcript variant X5 XM_006710397.4:c.1156G>T E [GAA] > * [TAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X5 XP_006710460.1:p.Glu386Ter E (Glu) > * (Ter) Stop Gained
DPYD transcript variant X5 XM_006710397.4:c.1156G>C E [GAA] > Q [CAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X5 XP_006710460.1:p.Glu386Gln E (Glu) > Q (Gln) Missense Variant
DPYD transcript variant X5 XM_006710397.4:c.1156G>A E [GAA] > K [AAA] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X5 XP_006710460.1:p.Glu386Lys E (Glu) > K (Lys) 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: 1019440 )
ClinVar Accession Disease Names Clinical Significance
RCV001335114.5 Dihydropyrimidine dehydrogenase deficiency Pathogenic
RCV001788460.1 fluorouracil response - Other Drug-Response
RCV001788461.2 fluorouracil response - Toxicity Drug-Response
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.97573943= NC_000001.11:g.97573943C>A NC_000001.11:g.97573943C>G NC_000001.11:g.97573943C>T
GRCh37.p13 chr 1 NC_000001.10:g.98039499= NC_000001.10:g.98039499C>A NC_000001.10:g.98039499C>G NC_000001.10:g.98039499C>T
DPYD RefSeqGene (LRG_722) NG_008807.2:g.352117= NG_008807.2:g.352117G>T NG_008807.2:g.352117G>C NG_008807.2:g.352117G>A
DPYD transcript variant 1 NM_000110.4:c.1156= NM_000110.4:c.1156G>T NM_000110.4:c.1156G>C NM_000110.4:c.1156G>A
DPYD transcript variant 1 NM_000110.3:c.1156= NM_000110.3:c.1156G>T NM_000110.3:c.1156G>C NM_000110.3:c.1156G>A
DPYD transcript variant X5 XM_006710397.4:c.1156= XM_006710397.4:c.1156G>T XM_006710397.4:c.1156G>C XM_006710397.4:c.1156G>A
DPYD transcript variant X3 XM_006710397.3:c.1156= XM_006710397.3:c.1156G>T XM_006710397.3:c.1156G>C XM_006710397.3:c.1156G>A
DPYD transcript variant X2 XM_006710397.2:c.1156= XM_006710397.2:c.1156G>T XM_006710397.2:c.1156G>C XM_006710397.2:c.1156G>A
DPYD transcript variant X3 XM_006710397.1:c.1156= XM_006710397.1:c.1156G>T XM_006710397.1:c.1156G>C XM_006710397.1:c.1156G>A
DPYD transcript variant X2 XM_005270562.3:c.1156= XM_005270562.3:c.1156G>T XM_005270562.3:c.1156G>C XM_005270562.3:c.1156G>A
DPYD transcript variant X2 XM_005270562.2:c.1156= XM_005270562.2:c.1156G>T XM_005270562.2:c.1156G>C XM_005270562.2:c.1156G>A
DPYD transcript variant X2 XM_005270562.1:c.1156= XM_005270562.1:c.1156G>T XM_005270562.1:c.1156G>C XM_005270562.1:c.1156G>A
DPYD transcript variant X1 XM_017000507.2:c.1045= XM_017000507.2:c.1045G>T XM_017000507.2:c.1045G>C XM_017000507.2:c.1045G>A
DPYD transcript variant X1 XM_017000507.1:c.1045= XM_017000507.1:c.1045G>T XM_017000507.1:c.1045G>C XM_017000507.1:c.1045G>A
DPYD transcript variant X3 XM_047448076.1:c.928= XM_047448076.1:c.928G>T XM_047448076.1:c.928G>C XM_047448076.1:c.928G>A
DPYD transcript variant X4 XM_047448077.1:c.1045= XM_047448077.1:c.1045G>T XM_047448077.1:c.1045G>C XM_047448077.1:c.1045G>A
dihydropyrimidine dehydrogenase [NADP(+)] isoform 1 NP_000101.2:p.Glu386= NP_000101.2:p.Glu386Ter NP_000101.2:p.Glu386Gln NP_000101.2:p.Glu386Lys
dihydropyrimidine dehydrogenase [NADP(+)] isoform X5 XP_006710460.1:p.Glu386= XP_006710460.1:p.Glu386Ter XP_006710460.1:p.Glu386Gln XP_006710460.1:p.Glu386Lys
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.2:p.Glu386= XP_005270619.2:p.Glu386Ter XP_005270619.2:p.Glu386Gln XP_005270619.2:p.Glu386Lys
dihydropyrimidine dehydrogenase [NADP(+)] isoform X1 XP_016855996.1:p.Glu349= XP_016855996.1:p.Glu349Ter XP_016855996.1:p.Glu349Gln XP_016855996.1:p.Glu349Lys
dihydropyrimidine dehydrogenase [NADP(+)] isoform X3 XP_047304032.1:p.Glu310= XP_047304032.1:p.Glu310Ter XP_047304032.1:p.Glu310Gln XP_047304032.1:p.Glu310Lys
dihydropyrimidine dehydrogenase [NADP(+)] isoform X4 XP_047304033.1:p.Glu349= XP_047304033.1:p.Glu349Ter XP_047304033.1:p.Glu349Gln XP_047304033.1:p.Glu349Lys
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.1:p.Glu386= XP_005270619.1:p.Glu386Ter XP_005270619.1:p.Glu386Gln XP_005270619.1:p.Glu386Lys
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#.

22 SubSNP, 6 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA ss152537266 Dec 01, 2009 (131)
2 ILLUMINA ss159102796 Dec 01, 2009 (131)
3 ILLUMINA ss159849718 Dec 01, 2009 (131)
4 ILLUMINA ss169483417 Jul 04, 2010 (132)
5 ILLUMINA ss479465539 Sep 08, 2015 (146)
6 ILLUMINA ss536563706 Sep 08, 2015 (146)
7 ILLUMINA ss832615592 Aug 21, 2014 (142)
8 ILLUMINA ss833206281 Aug 21, 2014 (142)
9 ILLUMINA ss2632551980 Nov 08, 2017 (151)
10 GNOMAD ss2731657257 Nov 08, 2017 (151)
11 ILLUMINA ss3626162371 Oct 11, 2018 (152)
12 ILLUMINA ss3636016059 Oct 11, 2018 (152)
13 ILLUMINA ss3637774616 Oct 11, 2018 (152)
14 TOPMED ss4460183057 Apr 25, 2021 (155)
15 GNOMAD ss6407781507 Nov 02, 2024 (157)
16 GNOMAD ss6407781508 Nov 02, 2024 (157)
17 GNOMAD ss6494959783 Nov 02, 2024 (157)
18 TOMMO_GENOMICS ss8145252335 Nov 02, 2024 (157)
19 EVA ss8512473820 Nov 02, 2024 (157)
20 TOMMO_GENOMICS ss8670394907 Nov 02, 2024 (157)
21 EVA ss8935519488 Nov 02, 2024 (157)
22 TOMMO_GENOMICS ss8989736180 Nov 02, 2024 (157)
23 gnomAD v4 - Exomes

Submission ignored due to conflicting rows:
Row 3079840 (NC_000001.11:97573942:C:A 7/1400914)
Row 3079841 (NC_000001.11:97573942:C:G 1/1400914)

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

Submission ignored due to conflicting rows:
Row 3079840 (NC_000001.11:97573942:C:A 7/1400914)
Row 3079841 (NC_000001.11:97573942:C:G 1/1400914)

- Nov 02, 2024 (157)
25 gnomAD v4 - Genomes NC_000001.11 - 97573943 Nov 02, 2024 (157)
26 38KJPN NC_000001.11 - 97573943 Nov 02, 2024 (157)
27 TopMed NC_000001.11 - 97573943 Apr 25, 2021 (155)
28 ALFA NC_000001.11 - 97573943 Nov 02, 2024 (157)
29 ClinVar RCV001335114.5 Nov 02, 2024 (157)
30 ClinVar RCV001788460.1 Oct 12, 2022 (156)
31 ClinVar RCV001788461.2 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)
rs386508634 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss479465539, ss536563706, ss832615592, ss833206281, ss2632551980, ss2731657257, ss3626162371, ss3636016059, ss3637774616, ss8145252335, ss8512473820 NC_000001.10:98039498:C:A NC_000001.11:97573942:C:A (self)
RCV001335114.5, RCV001788460.1, RCV001788461.2, 21274563, 7112000, 23789392, 7173518170, ss4460183057, ss6407781507, ss6494959783, ss8670394907, ss8989736180 NC_000001.11:97573942:C:A NC_000001.11:97573942:C:A (self)
ss152537266, ss159102796, ss159849718, ss169483417 NT_032977.9:68011416:C:A NC_000001.11:97573942:C:A (self)
ss8935519488 NC_000001.10:98039498:C:G NC_000001.11:97573942:C:G (self)
ss6407781508 NC_000001.11:97573942:C:G NC_000001.11:97573942:C:G
ss8935519488 NC_000001.10:98039498:C:T NC_000001.11:97573942:C:T (self)
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 rs78060119
PMID Title Author Year Journal
32619063 Impact of DPYD, DPYS, and UPB1 gene variations on severe drug-related toxicity in patients with cancer. Yokoi K et al. 2020 Cancer science
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