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.
rs2853542
Current Build 157
Released September 3, 2024
- Organism
- Homo sapiens
- Position
-
chr18:657685 (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 / G>T
- Variation Type
- SNV Single Nucleotide Variation
- Frequency
-
T=0.000003 (1/365688, GnomAD_exomes)C=0.43785 (37595/85862, GnomAD_genomes)C=0.39533 (30506/77166, 38KJPN) (+ 8 more)
- Clinical Significance
- Not Reported in ClinVar
- Gene : Consequence
-
TYMSOS : Intron VariantTYMS : 5 Prime UTR Variant
- Publications
- 15 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.
| Population | Group | Sample Size | Ref Allele | Alt Allele | Ref HMOZ | Alt HMOZ | HTRZ | HWEP |
|---|---|---|---|---|---|---|---|---|
| Total | Global | 3088 | G=1.0000 | C=0.0000, T=0.0000 | 1.0 | 0.0 | 0.0 | N/A |
| European | Sub | 1498 | G=1.0000 | C=0.0000, T=0.0000 | 1.0 | 0.0 | 0.0 | N/A |
| African | Sub | 1214 | G=1.0000 | C=0.0000, T=0.0000 | 1.0 | 0.0 | 0.0 | N/A |
| African Others | Sub | 44 | G=1.00 | C=0.00, T=0.00 | 1.0 | 0.0 | 0.0 | N/A |
| African American | Sub | 1170 | G=1.0000 | C=0.0000, T=0.0000 | 1.0 | 0.0 | 0.0 | N/A |
| Asian | Sub | 42 | G=1.00 | C=0.00, T=0.00 | 1.0 | 0.0 | 0.0 | N/A |
| East Asian | Sub | 30 | G=1.00 | C=0.00, T=0.00 | 1.0 | 0.0 | 0.0 | N/A |
| Other Asian | Sub | 12 | G=1.00 | C=0.00, T=0.00 | 1.0 | 0.0 | 0.0 | N/A |
| Latin American 1 | Sub | 28 | G=1.00 | C=0.00, T=0.00 | 1.0 | 0.0 | 0.0 | N/A |
| Latin American 2 | Sub | 132 | G=1.000 | C=0.000, T=0.000 | 1.0 | 0.0 | 0.0 | N/A |
| South Asian | Sub | 26 | G=1.00 | C=0.00, T=0.00 | 1.0 | 0.0 | 0.0 | N/A |
| Other | Sub | 148 | G=1.000 | C=0.000, T=0.000 | 1.0 | 0.0 | 0.0 | N/A |
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 | 365688 | G=0.999997 | T=0.000003 |
| gnomAD v4 - Exomes | European | Sub | 305320 | G=0.999997 | T=0.000003 |
| gnomAD v4 - Exomes | East Asian | Sub | 19058 | G=1.00000 | T=0.00000 |
| gnomAD v4 - Exomes | South Asian | Sub | 17670 | G=1.00000 | T=0.00000 |
| gnomAD v4 - Exomes | African | Sub | 9592 | G=1.0000 | T=0.0000 |
| gnomAD v4 - Exomes | Ashkenazi Jewish | Sub | 7498 | G=1.0000 | T=0.0000 |
| gnomAD v4 - Exomes | American | Sub | 5158 | G=1.0000 | T=0.0000 |
| gnomAD v4 - Exomes | Middle Eastern | sub | 1392 | G=1.0000 | T=0.0000 |
| gnomAD v4 - Genomes | Global | Study-wide | 85862 | G=0.56215 | C=0.43785 |
| gnomAD v4 - Genomes | European | Sub | 45468 | G=0.49039 | C=0.50961 |
| gnomAD v4 - Genomes | African | Sub | 21746 | G=0.73903 | C=0.26097 |
| gnomAD v4 - Genomes | American | Sub | 9634 | G=0.4969 | C=0.5031 |
| gnomAD v4 - Genomes | East Asian | Sub | 3992 | G=0.5749 | C=0.4251 |
| gnomAD v4 - Genomes | South Asian | Sub | 2896 | G=0.5853 | C=0.4147 |
| gnomAD v4 - Genomes | Ashkenazi Jewish | Sub | 1984 | G=0.5242 | C=0.4758 |
| gnomAD v4 - Genomes | Middle Eastern | sub | 142 | G=0.577 | C=0.423 |
| 38KJPN | JAPANESE | Study-wide | 77166 | G=0.60467 | C=0.39533 |
| Allele Frequency Aggregator | Total | Global | 3088 | G=1.0000 | C=0.0000, T=0.0000 |
| Allele Frequency Aggregator | European | Sub | 1498 | G=1.0000 | C=0.0000, T=0.0000 |
| Allele Frequency Aggregator | African | Sub | 1214 | G=1.0000 | C=0.0000, T=0.0000 |
| Allele Frequency Aggregator | Other | Sub | 148 | G=1.000 | C=0.000, T=0.000 |
| Allele Frequency Aggregator | Latin American 2 | Sub | 132 | G=1.000 | C=0.000, T=0.000 |
| Allele Frequency Aggregator | Asian | Sub | 42 | G=1.00 | C=0.00, T=0.00 |
| Allele Frequency Aggregator | Latin American 1 | Sub | 28 | G=1.00 | C=0.00, T=0.00 |
| Allele Frequency Aggregator | South Asian | Sub | 26 | G=1.00 | C=0.00, T=0.00 |
| KOREAN population from KRGDB | KOREAN | Study-wide | 2870 | G=0.5474 | A=0.0000, C=0.4526 |
| Northern Sweden | ACPOP | Study-wide | 596 | G=0.700 | C=0.300 |
| SGDP_PRJ | Global | Study-wide | 404 | G=0.391 | C=0.609 |
| Qatari | Global | Study-wide | 216 | G=0.509 | C=0.491 |
| A Vietnamese Genetic Variation Database | Global | Study-wide | 203 | G=0.655 | C=0.345 |
| Siberian | Global | Study-wide | 34 | G=0.41 | C=0.59 |
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.
| Sequence name | Change |
|---|---|
| GRCh38.p14 chr 18 | NC_000018.10:g.657685G>A |
| GRCh38.p14 chr 18 | NC_000018.10:g.657685G>C |
| GRCh38.p14 chr 18 | NC_000018.10:g.657685G>T |
| GRCh37.p13 chr 18 | NC_000018.9:g.657685G>A |
| GRCh37.p13 chr 18 | NC_000018.9:g.657685G>C |
| GRCh37.p13 chr 18 | NC_000018.9:g.657685G>T |
| TYMS RefSeqGene (LRG_783) | NG_028255.1:g.5082G>A |
| TYMS RefSeqGene (LRG_783) | NG_028255.1:g.5082G>C |
| TYMS RefSeqGene (LRG_783) | NG_028255.1:g.5082G>T |
| LOC127888625 genomic region | NG_138210.1:g.409G>A |
| LOC127888625 genomic region | NG_138210.1:g.409G>C |
| LOC127888625 genomic region | NG_138210.1:g.409G>T |
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| TYMS transcript variant 1 | NM_001071.4:c.-58= | N/A | 5 Prime UTR Variant |
| TYMS transcript variant 3 | NM_001354868.2:c.-58= | N/A | 5 Prime UTR Variant |
| TYMS transcript variant 2 | NM_001354867.2:c.-58= | N/A | 5 Prime UTR Variant |
| TYMS transcript variant X1 | XM_024451242.2:c. | N/A | Genic Upstream Transcript Variant |
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| TYMSOS transcript | NR_171001.1:n. | N/A | Intron Variant |
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.
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 | T |
|---|---|---|---|---|
| GRCh38.p14 chr 18 | NC_000018.10:g.657685= | NC_000018.10:g.657685G>A | NC_000018.10:g.657685G>C | NC_000018.10:g.657685G>T |
| GRCh37.p13 chr 18 | NC_000018.9:g.657685= | NC_000018.9:g.657685G>A | NC_000018.9:g.657685G>C | NC_000018.9:g.657685G>T |
| TYMS RefSeqGene (LRG_783) | NG_028255.1:g.5082= | NG_028255.1:g.5082G>A | NG_028255.1:g.5082G>C | NG_028255.1:g.5082G>T |
| TYMS transcript variant 1 | NM_001071.4:c.-58= | NM_001071.4:c.-58G>A | NM_001071.4:c.-58G>C | NM_001071.4:c.-58G>T |
| TYMS transcript variant 1 | NM_001071.3:c.-58= | NM_001071.3:c.-58G>A | NM_001071.3:c.-58G>C | NM_001071.3:c.-58G>T |
| TYMS transcript | NM_001071.2:c.-58= | NM_001071.2:c.-58G>A | NM_001071.2:c.-58G>C | NM_001071.2:c.-58G>T |
| TYMS transcript variant 2 | NM_001354867.2:c.-58= | NM_001354867.2:c.-58G>A | NM_001354867.2:c.-58G>C | NM_001354867.2:c.-58G>T |
| TYMS transcript variant 2 | NM_001354867.1:c.-58= | NM_001354867.1:c.-58G>A | NM_001354867.1:c.-58G>C | NM_001354867.1:c.-58G>T |
| TYMS transcript variant 3 | NM_001354868.2:c.-58= | NM_001354868.2:c.-58G>A | NM_001354868.2:c.-58G>C | NM_001354868.2:c.-58G>T |
| TYMS transcript variant 3 | NM_001354868.1:c.-58= | NM_001354868.1:c.-58G>A | NM_001354868.1:c.-58G>C | NM_001354868.1:c.-58G>T |
| LOC127888625 genomic region | NG_138210.1:g.409= | NG_138210.1:g.409G>A | NG_138210.1:g.409G>C | NG_138210.1:g.409G>T |
| TYMSOS transcript | NM_001012716.2:c.*34+157= | NM_001012716.2:c.*34+157C>T | NM_001012716.2:c.*34+157C>G | NM_001012716.2:c.*34+157C>A |
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#.
| No | Submitter | Submission ID | Date (Build) |
|---|---|---|---|
| 1 | SC_JCM | ss4040147 | Sep 28, 2001 (100) |
| 2 | COMPLETE_GENOMICS | ss167629584 | Jul 04, 2010 (132) |
| 3 | 1000GENOMES | ss339897438 | May 09, 2011 (134) |
| 4 | SSMP | ss661272686 | Apr 25, 2013 (138) |
| 5 | EVA-GONL | ss993409904 | Aug 21, 2014 (142) |
| 6 | HAMMER_LAB | ss1808915370 | Sep 08, 2015 (146) |
| 7 | WEILL_CORNELL_DGM | ss1936879838 | Feb 12, 2016 (147) |
| 8 | ILLUMINA | ss1959780614 | Feb 12, 2016 (147) |
| 9 | USC_VALOUEV | ss2157705199 | Dec 20, 2016 (150) |
| 10 | HUMAN_LONGEVITY | ss2219219836 | Dec 20, 2016 (150) |
| 11 | GRF | ss2702272993 | Nov 08, 2017 (151) |
| 12 | ILLUMINA | ss3021816397 | Nov 08, 2017 (151) |
| 13 | CSHL | ss3351879400 | Nov 08, 2017 (151) |
| 14 | OMUKHERJEE_ADBS | ss3646519507 | Oct 12, 2018 (152) |
| 15 | URBANLAB | ss3650721571 | Oct 12, 2018 (152) |
| 16 | ILLUMINA | ss3652235210 | Oct 12, 2018 (152) |
| 17 | ACPOP | ss3742283313 | Jul 13, 2019 (153) |
| 18 | EVA | ss3755026096 | Jul 13, 2019 (153) |
| 19 | KHV_HUMAN_GENOMES | ss3820288215 | Jul 13, 2019 (153) |
| 20 | EVA | ss3835017230 | Apr 27, 2020 (154) |
| 21 | EVA | ss3841121654 | Apr 27, 2020 (154) |
| 22 | EVA | ss3846620841 | Apr 27, 2020 (154) |
| 23 | SGDP_PRJ | ss3886385730 | Apr 27, 2020 (154) |
| 24 | KRGDB | ss3936187625 | Apr 27, 2020 (154) |
| 25 | FSA-LAB | ss3984128423 | Apr 27, 2021 (155) |
| 26 | TOMMO_GENOMICS | ss6173463651 | Nov 01, 2024 (157) |
| 27 | EVA | ss6322598537 | Nov 01, 2024 (157) |
| 28 | EVA | ss6328053223 | Nov 01, 2024 (157) |
| 29 | YEGNASUBRAMANIAN_LAB | ss6347303174 | Nov 01, 2024 (157) |
| 30 | GNOMAD | ss6462578563 | Nov 01, 2024 (157) |
| 31 | TOMMO_GENOMICS | ss8223834618 | Nov 01, 2024 (157) |
| 32 | EVA | ss8237241983 | Nov 01, 2024 (157) |
| 33 | 1000G_HIGH_COVERAGE | ss8304204924 | Nov 01, 2024 (157) |
| 34 | HUGCELL_USP | ss8497136242 | Nov 01, 2024 (157) |
| 35 | EVA | ss8624078277 | Nov 01, 2024 (157) |
| 36 | TOMMO_GENOMICS | ss8780509894 | Nov 01, 2024 (157) |
| 37 | EVA | ss8800071811 | Nov 01, 2024 (157) |
| 38 | EVA | ss8800213374 | Nov 01, 2024 (157) |
| 39 | EVA | ss8827134175 | Nov 01, 2024 (157) |
| 40 | EVA | ss8848463835 | Nov 01, 2024 (157) |
| 41 | EVA | ss8872897594 | Nov 01, 2024 (157) |
| 42 | EVA | ss8952090057 | Nov 01, 2024 (157) |
| 43 | EVA | ss8980990872 | Nov 01, 2024 (157) |
| 44 | EVA | ss8981824412 | Nov 01, 2024 (157) |
| 45 | EVA | ss8981824413 | Nov 01, 2024 (157) |
| 46 | GNOMAD | ss10025559630 | Nov 01, 2024 (157) |
| 47 | gnomAD v4 - Exomes | NC_000018.10 - 657685 | Nov 01, 2024 (157) |
| 48 | gnomAD v4 - Genomes | NC_000018.10 - 657685 | Nov 01, 2024 (157) |
| 49 | KOREAN population from KRGDB | NC_000018.9 - 657685 | Apr 27, 2020 (154) |
| 50 | Northern Sweden | NC_000018.9 - 657685 | Jul 13, 2019 (153) |
| 51 | Qatari | NC_000018.9 - 657685 | Apr 27, 2020 (154) |
| 52 | SGDP_PRJ | NC_000018.9 - 657685 | Apr 27, 2020 (154) |
| 53 | Siberian | NC_000018.9 - 657685 | Apr 27, 2020 (154) |
| 54 | 38KJPN | NC_000018.10 - 657685 | Nov 01, 2024 (157) |
| 55 | A Vietnamese Genetic Variation Database | NC_000018.9 - 657685 | Jul 13, 2019 (153) |
| 56 | ALFA | NC_000018.10 - 657685 | Nov 01, 2024 (157) |
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) |
|---|---|
| rs11540151 | May 13, 2013 (138) |
| Submission IDs | Observation SPDI | Canonical SPDI | Source RSIDs |
|---|---|---|---|
| 43365019, ss3936187625 | NC_000018.9:657684:G:A | NC_000018.10:657684:G:A | (self) |
| ss167629584 | NC_000018.8:647684:G:C | NC_000018.10:657684:G:C | (self) |
| 43365019, 15568178, 18921760, 38402710, 10221553, 8953148, ss339897438, ss661272686, ss993409904, ss1808915370, ss1936879838, ss1959780614, ss2157705199, ss2702272993, ss3021816397, ss3351879400, ss3646519507, ss3652235210, ss3742283313, ss3755026096, ss3835017230, ss3841121654, ss3886385730, ss3936187625, ss3984128423, ss6322598537, ss6328053223, ss6347303174, ss8223834618, ss8624078277, ss8800071811, ss8800213374, ss8827134175, ss8848463835, ss8952090057, ss8980990872, ss8981824412, ss8981824413 | NC_000018.9:657684:G:C | NC_000018.10:657684:G:C | (self) |
| 553102553, 190839471, 12193690784, ss2219219836, ss3650721571, ss3820288215, ss3846620841, ss6173463651, ss8237241983, ss8304204924, ss8497136242, ss8780509894, ss8872897594, ss10025559630 | NC_000018.10:657684:G:C | NC_000018.10:657684:G:C | (self) |
| ss4040147 | NT_010859.14:647684:G:C | NC_000018.10:657684:G:C | (self) |
| 57918763, 12193690784, ss6462578563 | NC_000018.10:657684:G:T | NC_000018.10:657684:G:T | (self) |
Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.
| PMID | Title | Author | Year | Journal |
|---|---|---|---|---|
| 21615938 | Genetic polymorphisms in folate pathway enzymes, DRD4 and GSTM1 are related to temporomandibular disorder. | Aneiros-Guerrero A et al. | 2011 | BMC medical genetics |
| 22045187 | Methylenetetrahydrofolate reductase genetic polymorphisms and toxicity to 5-FU-based chemoradiation in rectal cancer. | Thomas F et al. | 2011 | British journal of cancer |
| 22486600 | Multifactorial pharmacogenetic analysis in colorectal cancer patients receiving 5-fluorouracil-based therapy together with cetuximab-irinotecan. | Etienne-Grimaldi MC et al. | 2012 | British journal of clinical pharmacology |
| 25177243 | The influence of folate pathway polymorphisms on high-dose methotrexate-related toxicity and survival in children with non-Hodgkin malignant lymphoma. | Erculj N et al. | 2014 | Radiology and oncology |
| 25279663 | Role of key TYMS polymorphisms on methotrexate therapeutic outcome in portuguese rheumatoid arthritis patients. | Lima A et al. | 2014 | PloS one |
| 25372392 | Potentially functional SNPs (pfSNPs) as novel genomic predictors of 5-FU response in metastatic colorectal cancer patients. | Wang J et al. | 2014 | PloS one |
| 25521664 | Novel SNP improves differential survivability and mortality in non-small cell lung cancer patients. | Mah TL et al. | 2014 | BMC genomics |
| 26166093 | Delimiting Allelic Imbalance of TYMS by Allele-Specific Analysis. | Balboa-Beltrán E et al. | 2015 | Medicine |
| 27009482 | Thymidylate synthase enhancer region: Novel allele in Indians. | Dhawan D et al. | 2017 | Annals of human biology |
| 29257755 | Thymidylate synthase gene variants as predictors of clinical response and toxicity to fluoropyrimidine-based chemotherapy for colorectal cancer. | Castro-Rojas CA et al. | 2017 | Drug metabolism and personalized therapy |
| 30222710 | The role of genetic polymorphisms in the thymidylate synthase (TYMS) gene in methotrexate-induced oral mucositis in children with acute lymphoblastic leukemia. | Oosterom N et al. | 2018 | Pharmacogenetics and genomics |
| 31395900 | Sex-Related Differences in Impact on Safety of Pharmacogenetic Profile for Colon Cancer Patients Treated with FOLFOX-4 or XELOX Adjuvant Chemotherapy. | Ruzzo A et al. | 2019 | Scientific reports |
| 32625092 | Germline and Somatic Pharmacogenomics to Refine Rectal Cancer Patients Selection for Neo-Adjuvant Chemoradiotherapy. | De Mattia E et al. | 2020 | Frontiers in pharmacology |
| 35582139 | The use of pharmacogenetics to increase the safety of colorectal cancer patients treated with fluoropyrimidines. | De Mattia E et al. | 2019 | Cancer drug resistance (Alhambra, Calif.) |
| 37256234 | Pharmacogenomic-guided dosing of fluoropyrimidines beyond DPYD: time for a polygenic algorithm? | Maslarinou A et al. | 2023 | Frontiers in pharmacology |
The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.
Genomic regions, transcripts, and products
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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.
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.