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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs998259

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr14:54888313 (GRCh38.p7) 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=0.15214 (19104/125568, TOPMED)
T=0.1479 (4568/30892, GnomAD)
T=0.078 (390/5008, 1000G) (+ 2 more)
T=0.229 (884/3854, ALSPAC)
T=0.228 (847/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GCH1 : Intron Variant
Publications
3 citations
Genomic View
See rs on genome
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.p7 chr 14 NC_000014.9:g.54888313C>A
GRCh38.p7 chr 14 NC_000014.9:g.54888313C>T
GRCh37.p13 chr 14 NC_000014.8:g.55355031C>A
GRCh37.p13 chr 14 NC_000014.8:g.55355031C>T
GCH1 RefSeqGene NG_008647.1:g.19512G>T
GCH1 RefSeqGene NG_008647.1:g.19512G>A
Gene: GCH1, GTP cyclohydrolase 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GCH1 transcript variant 1 NM_000161.2:c. N/A Intron Variant
GCH1 transcript variant 2 NM_001024024.1:c. N/A Intron Variant
GCH1 transcript variant 3 NM_001024070.1:c. N/A Intron Variant
GCH1 transcript variant 4 NM_001024071.1:c. N/A Intron Variant
GCH1 transcript variant X1 XM_017021218.1:c. N/A Genic Upstream 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.

Not Reported in ClinVar
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
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.84786 T=0.15214
The Genome Aggregation Database Global Study-wide 30892 C=0.8521 T=0.1479
The Genome Aggregation Database European Sub 18442 C=0.7949 T=0.2051
The Genome Aggregation Database African Sub 8712 C=0.958 T=0.042
The Genome Aggregation Database East Asian Sub 1618 C=1.000 T=0.000
The Genome Aggregation Database Other Sub 980 C=0.80 T=0.20
The Genome Aggregation Database American Sub 838 C=0.84 T=0.16
The Genome Aggregation Database Ashkenazi Jewish Sub 302 C=0.70 T=0.30
1000Genomes Global Study-wide 5008 C=0.922 T=0.078
1000Genomes African Sub 1322 C=0.991 T=0.009
1000Genomes East Asian Sub 1008 C=0.998 T=0.002
1000Genomes Europe Sub 1006 C=0.788 T=0.212
1000Genomes South Asian Sub 978 C=0.96 T=0.04
1000Genomes American Sub 694 C=0.82 T=0.18
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.771 T=0.229
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.772 T=0.228
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 Note
GRCh38.p7 chr 14 NC_000014.9:g.548...

NC_000014.9:g.54888313C=

NC_000014.9:g.548...

NC_000014.9:g.54888313C>A

NC_000014.9:g.548...

NC_000014.9:g.54888313C>T

GRCh37.p13 chr 14 NC_000014.8:g.553...

NC_000014.8:g.55355031C=

NC_000014.8:g.553...

NC_000014.8:g.55355031C>A

NC_000014.8:g.553...

NC_000014.8:g.55355031C>T

GCH1 RefSeqGene NG_008647.1:g.195...

NG_008647.1:g.19512G=

NG_008647.1:g.195...

NG_008647.1:g.19512G>T

NG_008647.1:g.195...

NG_008647.1:g.19512G>A

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#.

5 Frequency, 45 SubSNP submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1457064 Oct 05, 2000 (86)
2 PERLEGEN ss24615954 Sep 20, 2004 (123)
3 AFFY ss65994934 Nov 29, 2006 (127)
4 AFFY ss66263588 Nov 29, 2006 (127)
5 ILLUMINA ss66761647 Nov 29, 2006 (127)
6 ILLUMINA ss67966849 Nov 29, 2006 (127)
7 ILLUMINA ss68073072 Nov 29, 2006 (127)
8 PERLEGEN ss69157924 May 16, 2007 (127)
9 AFFY ss76408591 Dec 08, 2007 (130)
10 KRIBB_YJKIM ss83649096 Dec 15, 2007 (130)
11 BCMHGSC_JDW ss89955057 Mar 24, 2008 (129)
12 ENSEMBL ss133985645 Dec 01, 2009 (131)
13 AFFY ss173497297 Jul 04, 2010 (132)
14 ILLUMINA ss174941671 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss207040730 Jul 04, 2010 (132)
16 1000GENOMES ss236550002 Jul 15, 2010 (132)
17 ILLUMINA ss244316288 Jul 04, 2010 (132)
18 ILLUMINA ss537650830 Sep 08, 2015 (146)
19 TISHKOFF ss564105283 Apr 25, 2013 (138)
20 EVA-GONL ss991168378 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1079671490 Aug 21, 2014 (142)
22 1000GENOMES ss1351091918 Aug 21, 2014 (142)
23 HAMMER_LAB ss1397681053 Sep 08, 2015 (146)
24 DDI ss1427430823 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1577268339 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1631778980 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1674773013 Apr 01, 2015 (144)
28 EVA_DECODE ss1695167728 Apr 01, 2015 (144)
29 EVA_SVP ss1713445946 Apr 01, 2015 (144)
30 WEILL_CORNELL_DGM ss1934544627 Feb 12, 2016 (147)
31 JJLAB ss2028049836 Sep 14, 2016 (149)
32 USC_VALOUEV ss2156424121 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2202158681 Dec 20, 2016 (150)
34 TOPMED ss2366511671 Dec 20, 2016 (150)
35 GNOMAD ss2927944196 Nov 08, 2017 (151)
36 AFFY ss2985655543 Nov 08, 2017 (151)
37 SWEGEN ss3012236861 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3027850266 Nov 08, 2017 (151)
39 TOPMED ss3211762999 Nov 08, 2017 (151)
40 TOPMED ss3211763000 Nov 08, 2017 (151)
41 CSHL ss3350816687 Nov 08, 2017 (151)
42 ILLUMINA ss3627222987 Jul 20, 2018 (151)
43 ILLUMINA ss3638051570 Jul 20, 2018 (151)
44 ILLUMINA ss3639039291 Jul 20, 2018 (151)
45 ILLUMINA ss3639524351 Jul 20, 2018 (151)
46 1000Genomes NC_000014.8 - 55355031 Jul 20, 2018 (151)
47 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 55355031 Jul 20, 2018 (151)
48 The Genome Aggregation Database NC_000014.8 - 55355031 Jul 20, 2018 (151)
49 Trans-Omics for Precision Medicine NC_000014.9 - 54888313 Jul 20, 2018 (151)
50 UK 10K study - Twins NC_000014.8 - 55355031 Jul 20, 2018 (151)
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)
rs17832257 Oct 08, 2004 (123)
rs56540413 May 25, 2008 (130)
rs59836095 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss89955057, ss207040730, ss1397681053, ss1695167728, ss1713445946, ss3639039291, ss3639524351 NC_000014.7:54424780:C= NC_000014.9:54888312:C= (self)
64075866, 35592043, 61645721, 35592043, ss236550002, ss537650830, ss564105283, ss991168378, ss1079671490, ss1351091918, ss1427430823, ss1577268339, ss1631778980, ss1674773013, ss1934544627, ss2028049836, ss2156424121, ss2366511671, ss2927944196, ss2985655543, ss3012236861, ss3350816687, ss3627222987, ss3638051570 NC_000014.8:55355030:C= NC_000014.9:54888312:C= (self)
116980051, ss2202158681, ss3027850266, ss3211762999, ss3211763000 NC_000014.9:54888312:C= NC_000014.9:54888312:C= (self)
ss1457064, ss24615954, ss65994934, ss66263588, ss66761647, ss67966849, ss68073072, ss69157924, ss76408591, ss83649096, ss133985645, ss173497297, ss174941671, ss244316288 NT_026437.12:36355030:C= NC_000014.9:54888312:C= (self)
ss3211762999 NC_000014.9:54888312:C>A NC_000014.9:54888312:C>A (self)
ss89955057, ss207040730, ss1397681053, ss1695167728, ss1713445946, ss3639039291, ss3639524351 NC_000014.7:54424780:C>T NC_000014.9:54888312:C>T (self)
64075866, 35592043, 61645721, 35592043, ss236550002, ss537650830, ss564105283, ss991168378, ss1079671490, ss1351091918, ss1427430823, ss1577268339, ss1631778980, ss1674773013, ss1934544627, ss2028049836, ss2156424121, ss2366511671, ss2927944196, ss2985655543, ss3012236861, ss3350816687, ss3627222987, ss3638051570 NC_000014.8:55355030:C>T NC_000014.9:54888312:C>T (self)
116980051, ss2202158681, ss3027850266, ss3211763000 NC_000014.9:54888312:C>T NC_000014.9:54888312:C>T (self)
ss1457064, ss24615954, ss65994934, ss66263588, ss66761647, ss67966849, ss68073072, ss69157924, ss76408591, ss83649096, ss133985645, ss173497297, ss174941671, ss244316288 NT_026437.12:36355030:C>T NC_000014.9:54888312: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.

3 citations for rs998259
PMID Title Author Year Journal
17343757 Lack of influence of GTP cyclohydrolase gene (GCH1) variations on pain sensitivity in humans. Kim H et al. 2007 Molecular pain
20838263 Polymorphic variation of the guanosine triphosphate cyclohydrolase 1 gene predicts outcome in patients undergoing surgical treatment for lumbar degenerative disc disease. Kim DH et al. 2010 Spine
26835600 GWAS of 89,283 individuals identifies genetic variants associated with self-reporting of being a morning person. Hu Y et al. 2016 Nature communications

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: 0.1.4.post833+d3ba21e