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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.

rs72549306

Current Build 157

Released September 3, 2024

Organism
Homo sapiens
Position
chr1:97593343 (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=0.0000243 (34/1401464, GnomAD_exomes)
T=0.000011 (3/264690, TOPMED)
T=0.000007 (1/149132, GnomAD_genomes) (+ 7 more)
A=0.000007 (1/146386, ALFA)
T=0.000007 (1/146386, ALFA)
T=0.000016 (2/121364, ExAC)
A=0.00008 (6/78702, PAGE_STUDY)
T=0.0004 (3/7234, Korea4K)
T=0.0007 (2/2930, KOREAN)
T=0.0011 (2/1832, Korea1K)
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 146386 C=0.999986 A=0.000007, T=0.000007 0.999986 0.0 1.4e-05 0
European Sub 127172 C=1.000000 A=0.000000, T=0.000000 1.0 0.0 0.0 N/A
African Sub 9510 C=0.9999 A=0.0000, T=0.0001 1.0 0.0 0.0 N/A
African Others Sub 380 C=1.000 A=0.000, T=0.000 1.0 0.0 0.0 N/A
African American Sub 9130 C=0.9999 A=0.0000, T=0.0001 1.0 0.0 0.0 N/A
Asian Sub 3648 C=0.9997 A=0.0003, T=0.0000 0.999452 0.0 0.000548 0
East Asian Sub 2986 C=0.9997 A=0.0003, T=0.0000 0.99933 0.0 0.00067 0
Other Asian Sub 662 C=1.000 A=0.000, T=0.000 1.0 0.0 0.0 N/A
Latin American 1 Sub 550 C=1.000 A=0.000, T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 1644 C=1.0000 A=0.0000, T=0.0000 1.0 0.0 0.0 N/A
South Asian Sub 320 C=1.000 A=0.000, T=0.000 1.0 0.0 0.0 N/A
Other Sub 3542 C=1.0000 A=0.0000, T=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
gnomAD v4 - Exomes Global Study-wide 1401464 C=0.9999757 T=0.0000243
gnomAD v4 - Exomes European Sub 1165406 C=0.9999957 T=0.0000043
gnomAD v4 - Exomes South Asian Sub 86256 C=0.99997 T=0.00003
gnomAD v4 - Exomes American Sub 44724 C=0.99998 T=0.00002
gnomAD v4 - Exomes East Asian Sub 39694 C=0.99937 T=0.00063
gnomAD v4 - Exomes African Sub 33480 C=1.00000 T=0.00000
gnomAD v4 - Exomes Ashkenazi Jewish Sub 26136 C=1.00000 T=0.00000
gnomAD v4 - Exomes Middle Eastern sub 5768 C=1.0000 T=0.0000
TopMed Global Study-wide 264690 C=0.999989 T=0.000011
gnomAD v4 - Genomes Global Study-wide 149132 C=0.999993 T=0.000007
gnomAD v4 - Genomes European Sub 78638 C=1.00000 T=0.00000
gnomAD v4 - Genomes African Sub 41420 C=0.99998 T=0.00002
gnomAD v4 - Genomes American Sub 15272 C=1.00000 T=0.00000
gnomAD v4 - Genomes East Asian Sub 5186 C=1.0000 T=0.0000
gnomAD v4 - Genomes South Asian Sub 4832 C=1.0000 T=0.0000
gnomAD v4 - Genomes Ashkenazi Jewish Sub 3468 C=1.0000 T=0.0000
gnomAD v4 - Genomes Middle Eastern sub 316 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 146386 C=0.999986 A=0.000007, T=0.000007
Allele Frequency Aggregator European Sub 127172 C=1.000000 A=0.000000, T=0.000000
Allele Frequency Aggregator African Sub 9510 C=0.9999 A=0.0000, T=0.0001
Allele Frequency Aggregator Asian Sub 3648 C=0.9997 A=0.0003, T=0.0000
Allele Frequency Aggregator Other Sub 3542 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 1644 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 1 Sub 550 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 320 C=1.000 A=0.000, T=0.000
ExAC Global Study-wide 121364 C=0.999984 T=0.000016
ExAC Europe Sub 73326 C=1.00000 T=0.00000
ExAC Asian Sub 25148 C=0.99996 T=0.00004
ExAC American Sub 11578 C=1.00000 T=0.00000
ExAC African Sub 10404 C=0.99990 T=0.00010
ExAC Other Sub 908 C=1.000 T=0.000
The PAGE Study Global Study-wide 78702 C=0.99992 A=0.00008
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=0.9993 A=0.0007
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=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 A=0.000
Korean Genome Project 4K KOREAN Study-wide 7234 C=0.9996 T=0.0004
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.9993 T=0.0007
Korean Genome Project KOREAN Study-wide 1832 C=0.9989 T=0.0011
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.97593343C>A
GRCh38.p14 chr 1 NC_000001.11:g.97593343C>T
GRCh37.p13 chr 1 NC_000001.10:g.98058899C>A
GRCh37.p13 chr 1 NC_000001.10:g.98058899C>T
DPYD RefSeqGene (LRG_722) NG_008807.2:g.332717G>T
DPYD RefSeqGene (LRG_722) NG_008807.2:g.332717G>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.1003G>T V [GTG] > L [TTG] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform 1 NP_000101.2:p.Val335Leu V (Val) > L (Leu) Missense Variant
DPYD transcript variant 1 NM_000110.4:c.1003G>A V [GTG] > M [ATG] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform 1 NP_000101.2:p.Val335Met V (Val) > M (Met) Missense Variant
DPYD transcript variant X2 XM_005270562.3:c.1003G>T V [GTG] > L [TTG] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.2:p.Val335Leu V (Val) > L (Leu) Missense Variant
DPYD transcript variant X2 XM_005270562.3:c.1003G>A V [GTG] > M [ATG] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.2:p.Val335Met V (Val) > M (Met) Missense Variant
DPYD transcript variant X1 XM_017000507.2:c.892G>T V [GTG] > L [TTG] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X1 XP_016855996.1:p.Val298Leu V (Val) > L (Leu) Missense Variant
DPYD transcript variant X1 XM_017000507.2:c.892G>A V [GTG] > M [ATG] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X1 XP_016855996.1:p.Val298Met V (Val) > M (Met) Missense Variant
DPYD transcript variant X3 XM_047448076.1:c.775G>T V [GTG] > L [TTG] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X3 XP_047304032.1:p.Val259Leu V (Val) > L (Leu) Missense Variant
DPYD transcript variant X3 XM_047448076.1:c.775G>A V [GTG] > M [ATG] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X3 XP_047304032.1:p.Val259Met V (Val) > M (Met) Missense Variant
DPYD transcript variant X4 XM_047448077.1:c.892G>T V [GTG] > L [TTG] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X4 XP_047304033.1:p.Val298Leu V (Val) > L (Leu) Missense Variant
DPYD transcript variant X4 XM_047448077.1:c.892G>A V [GTG] > M [ATG] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X4 XP_047304033.1:p.Val298Met V (Val) > M (Met) Missense Variant
DPYD transcript variant X5 XM_006710397.4:c.1003G>T V [GTG] > L [TTG] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X5 XP_006710460.1:p.Val335Leu V (Val) > L (Leu) Missense Variant
DPYD transcript variant X5 XM_006710397.4:c.1003G>A V [GTG] > M [ATG] Coding Sequence Variant
dihydropyrimidine dehydrogenase [NADP(+)] isoform X5 XP_006710460.1:p.Val335Met V (Val) > M (Met) 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: 1317929 )
ClinVar Accession Disease Names Clinical Significance
RCV001787696.1 fluorouracil response - Other 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 T
GRCh38.p14 chr 1 NC_000001.11:g.97593343= NC_000001.11:g.97593343C>A NC_000001.11:g.97593343C>T
GRCh37.p13 chr 1 NC_000001.10:g.98058899= NC_000001.10:g.98058899C>A NC_000001.10:g.98058899C>T
DPYD RefSeqGene (LRG_722) NG_008807.2:g.332717= NG_008807.2:g.332717G>T NG_008807.2:g.332717G>A
DPYD transcript variant 1 NM_000110.4:c.1003= NM_000110.4:c.1003G>T NM_000110.4:c.1003G>A
DPYD transcript variant 1 NM_000110.3:c.1003= NM_000110.3:c.1003G>T NM_000110.3:c.1003G>A
DPYD transcript variant X5 XM_006710397.4:c.1003= XM_006710397.4:c.1003G>T XM_006710397.4:c.1003G>A
DPYD transcript variant X3 XM_006710397.3:c.1003= XM_006710397.3:c.1003G>T XM_006710397.3:c.1003G>A
DPYD transcript variant X2 XM_006710397.2:c.1003= XM_006710397.2:c.1003G>T XM_006710397.2:c.1003G>A
DPYD transcript variant X3 XM_006710397.1:c.1003= XM_006710397.1:c.1003G>T XM_006710397.1:c.1003G>A
DPYD transcript variant X2 XM_005270562.3:c.1003= XM_005270562.3:c.1003G>T XM_005270562.3:c.1003G>A
DPYD transcript variant X2 XM_005270562.2:c.1003= XM_005270562.2:c.1003G>T XM_005270562.2:c.1003G>A
DPYD transcript variant X2 XM_005270562.1:c.1003= XM_005270562.1:c.1003G>T XM_005270562.1:c.1003G>A
DPYD transcript variant X1 XM_017000507.2:c.892= XM_017000507.2:c.892G>T XM_017000507.2:c.892G>A
DPYD transcript variant X1 XM_017000507.1:c.892= XM_017000507.1:c.892G>T XM_017000507.1:c.892G>A
DPYD transcript variant X3 XM_047448076.1:c.775= XM_047448076.1:c.775G>T XM_047448076.1:c.775G>A
DPYD transcript variant X4 XM_047448077.1:c.892= XM_047448077.1:c.892G>T XM_047448077.1:c.892G>A
dihydropyrimidine dehydrogenase [NADP(+)] isoform 1 NP_000101.2:p.Val335= NP_000101.2:p.Val335Leu NP_000101.2:p.Val335Met
dihydropyrimidine dehydrogenase [NADP(+)] isoform X5 XP_006710460.1:p.Val335= XP_006710460.1:p.Val335Leu XP_006710460.1:p.Val335Met
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.2:p.Val335= XP_005270619.2:p.Val335Leu XP_005270619.2:p.Val335Met
dihydropyrimidine dehydrogenase [NADP(+)] isoform X1 XP_016855996.1:p.Val298= XP_016855996.1:p.Val298Leu XP_016855996.1:p.Val298Met
dihydropyrimidine dehydrogenase [NADP(+)] isoform X3 XP_047304032.1:p.Val259= XP_047304032.1:p.Val259Leu XP_047304032.1:p.Val259Met
dihydropyrimidine dehydrogenase [NADP(+)] isoform X4 XP_047304033.1:p.Val298= XP_047304033.1:p.Val298Leu XP_047304033.1:p.Val298Met
dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 XP_005270619.1:p.Val335= XP_005270619.1:p.Val335Leu XP_005270619.1:p.Val335Met
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#.

37 SubSNP, 11 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 AFFY_DM3_1 ss105434297 Feb 13, 2009 (130)
2 ILLUMINA ss152536535 Dec 01, 2009 (131)
3 ILLUMINA ss159102657 Dec 01, 2009 (131)
4 ILLUMINA ss159849680 Dec 01, 2009 (131)
5 ILLUMINA ss169483362 Jul 04, 2010 (132)
6 ILLUMINA ss479158813 Sep 08, 2015 (146)
7 ILLUMINA ss532749669 Sep 08, 2015 (146)
8 ILLUMINA ss832615453 Jul 12, 2019 (153)
9 EVA_EXAC ss1685650191 Apr 01, 2015 (144)
10 ILLUMINA ss1946002623 Feb 12, 2016 (147)
11 ILLUMINA ss1958296069 Feb 12, 2016 (147)
12 ILLUMINA ss2632552000 Nov 08, 2017 (151)
13 ILLUMINA ss2710678055 Nov 08, 2017 (151)
14 GNOMAD ss2731657330 Nov 08, 2017 (151)
15 ILLUMINA ss3021112950 Nov 08, 2017 (151)
16 ILLUMINA ss3625545931 Oct 11, 2018 (152)
17 ILLUMINA ss3626162407 Oct 11, 2018 (152)
18 ILLUMINA ss3636016072 Oct 11, 2018 (152)
19 ILLUMINA ss3637774631 Oct 11, 2018 (152)
20 ILLUMINA ss3644498583 Oct 11, 2018 (152)
21 ILLUMINA ss3651443599 Oct 11, 2018 (152)
22 ILLUMINA ss3725047340 Jul 12, 2019 (153)
23 ILLUMINA ss3744050828 Jul 12, 2019 (153)
24 PAGE_CC ss3770827408 Jul 12, 2019 (153)
25 KRGDB ss3894525456 Apr 25, 2020 (154)
26 KOGIC ss3945067457 Apr 25, 2020 (154)
27 TOPMED ss4460188134 Apr 25, 2021 (155)
28 KOGIC ss6352004235 Nov 02, 2024 (157)
29 EVA ss6403965887 Nov 02, 2024 (157)
30 GNOMAD ss6407781830 Nov 02, 2024 (157)
31 GNOMAD ss6494964310 Nov 02, 2024 (157)
32 TOMMO_GENOMICS ss8145252998 Nov 02, 2024 (157)
33 TOMMO_GENOMICS ss8670395743 Nov 02, 2024 (157)
34 EVA ss8847548199 Nov 02, 2024 (157)
35 EVA ss8937964650 Nov 02, 2024 (157)
36 TOMMO_GENOMICS ss8989737523 Nov 02, 2024 (157)
37 TOMMO_GENOMICS ss8989737524 Nov 02, 2024 (157)
38 ExAC NC_000001.10 - 98058899 Oct 11, 2018 (152)
39 gnomAD v4 - Exomes NC_000001.11 - 97593343 Nov 02, 2024 (157)
40 gnomAD v4 - Genomes NC_000001.11 - 97593343 Nov 02, 2024 (157)
41 KOREAN population from KRGDB NC_000001.10 - 98058899 Apr 25, 2020 (154)
42 Korean Genome Project NC_000001.11 - 97593343 Apr 25, 2020 (154)
43 Korean Genome Project 4K NC_000001.11 - 97593343 Nov 02, 2024 (157)
44 The PAGE Study NC_000001.11 - 97593343 Jul 12, 2019 (153)
45 38KJPN

Submission ignored due to conflicting rows:
Row 7113343 (NC_000001.11:97593342:C:T 78/77442)
Row 7113344 (NC_000001.11:97593342:C:A 7/77442)

- Nov 02, 2024 (157)
46 38KJPN

Submission ignored due to conflicting rows:
Row 7113343 (NC_000001.11:97593342:C:T 78/77442)
Row 7113344 (NC_000001.11:97593342:C:A 7/77442)

- Nov 02, 2024 (157)
47 TopMed NC_000001.11 - 97593343 Apr 25, 2021 (155)
48 ALFA NC_000001.11 - 97593343 Nov 02, 2024 (157)
49 ClinVar RCV001787696.1 Oct 12, 2022 (156)
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
ss479158813, ss532749669, ss832615453, ss1946002623, ss1958296069, ss2632552000, ss2710678055, ss3021112950, ss3625545931, ss3626162407, ss3636016072, ss3637774631, ss3644498583, ss3651443599, ss3744050828, ss8847548199, ss8937964650 NC_000001.10:98058898:C:A NC_000001.11:97593342:C:A (self)
RCV001787696.1, 48877, 4078017611, ss3725047340, ss3770827408, ss8989737524 NC_000001.11:97593342:C:A NC_000001.11:97593342:C:A (self)
ss105434297, ss152536535, ss159102657, ss159849680, ss169483362 NT_032977.9:68030816:C:A NC_000001.11:97593342:C:A (self)
4856113, 1702850, ss1685650191, ss2731657330, ss3894525456, ss6403965887, ss8145252998 NC_000001.10:98058898:C:T NC_000001.11:97593342:C:T (self)
3080163, 21279092, 1445458, 1856133, 23794469, 4078017611, ss3945067457, ss4460188134, ss6352004235, ss6407781830, ss6494964310, ss8670395743, ss8989737523 NC_000001.11:97593342:C:T NC_000001.11:97593342: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.

2 citations for rs72549306
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
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