Name: rs55934565
Published: September 21, 2022
License: Open Access

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.

rs55934565

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:54859613 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.012316 (3260/264690, TOPMED)
C=0.014012 (1965/140238, GnomAD)
C=0.01972 (374/18964, ALFA) (+ 15 more)
C=0.0206 (132/6404, 1000G_30x)
C=0.0210 (105/5008, 1000G)
C=0.0114 (52/4566, GO-ESP)
C=0.0371 (166/4480, Estonian)
C=0.0145 (56/3854, ALSPAC)
C=0.0143 (53/3708, TWINSUK)
C=0.0003 (1/2922, KOREAN)
C=0.009 (9/998, GoNL)
C=0.038 (23/600, NorthernSweden)
C=0.022 (12/534, MGP)
C=0.009 (2/216, Qatari)
T=0.50 (10/20, SGDP_PRJ)
C=0.50 (10/20, SGDP_PRJ)
T=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GCH1 : Intron Variant
Publications: 0 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18964	T=0.98028	C=0.01972
European	Sub	14336	T=0.97740	C=0.02260
African	Sub	2960	T=0.9970	C=0.0030
African Others	Sub	114	T=0.991	C=0.009
African American	Sub	2846	T=0.9972	C=0.0028
Asian	Sub	112	T=1.000	C=0.000
East Asian	Sub	86	T=1.00	C=0.00
Other Asian	Sub	26	T=1.00	C=0.00
Latin American 1	Sub	146	T=0.986	C=0.014
Latin American 2	Sub	610	T=0.966	C=0.034
South Asian	Sub	98	T=0.95	C=0.05
Other	Sub	702	T=0.981	C=0.019

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.987684	C=0.012316
gnomAD - Genomes	Global	Study-wide	140238	T=0.985988	C=0.014012
gnomAD - Genomes	European	Sub	75932	T=0.97936	C=0.02064
gnomAD - Genomes	African	Sub	42042	T=0.99710	C=0.00290
gnomAD - Genomes	American	Sub	13658	T=0.98521	C=0.01479
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.9910	C=0.0090
gnomAD - Genomes	East Asian	Sub	3130	T=0.9974	C=0.0026
gnomAD - Genomes	Other	Sub	2154	T=0.9833	C=0.0167
Allele Frequency Aggregator	Total	Global	18964	T=0.98028	C=0.01972
Allele Frequency Aggregator	European	Sub	14336	T=0.97740	C=0.02260
Allele Frequency Aggregator	African	Sub	2960	T=0.9970	C=0.0030
Allele Frequency Aggregator	Other	Sub	702	T=0.981	C=0.019
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.966	C=0.034
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.986	C=0.014
Allele Frequency Aggregator	Asian	Sub	112	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=0.95	C=0.05
1000Genomes_30x	Global	Study-wide	6404	T=0.9794	C=0.0206
1000Genomes_30x	African	Sub	1786	T=1.0000	C=0.0000
1000Genomes_30x	Europe	Sub	1266	T=0.9700	C=0.0300
1000Genomes_30x	South Asian	Sub	1202	T=0.9451	C=0.0549
1000Genomes_30x	East Asian	Sub	1170	T=0.9966	C=0.0034
1000Genomes_30x	American	Sub	980	T=0.976	C=0.024
1000Genomes	Global	Study-wide	5008	T=0.9790	C=0.0210
1000Genomes	African	Sub	1322	T=1.0000	C=0.0000
1000Genomes	East Asian	Sub	1008	T=0.9960	C=0.0040
1000Genomes	Europe	Sub	1006	T=0.9692	C=0.0308
1000Genomes	South Asian	Sub	978	T=0.945	C=0.055
1000Genomes	American	Sub	694	T=0.977	C=0.023
GO Exome Sequencing Project	Global	Study-wide	4566	T=0.9886	C=0.0114
GO Exome Sequencing Project	European American	Sub	3182	T=0.9846	C=0.0154
GO Exome Sequencing Project	African American	Sub	1384	T=0.9978	C=0.0022
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9629	C=0.0371
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9855	C=0.0145
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9857	C=0.0143
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9997	C=0.0003
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.991	C=0.009
Northern Sweden	ACPOP	Study-wide	600	T=0.962	C=0.038
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	T=0.978	C=0.022
Qatari	Global	Study-wide	216	T=0.991	C=0.009
SGDP_PRJ	Global	Study-wide	20	T=0.50	C=0.50
Siberian	Global	Study-wide	4	T=0.5	C=0.5

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 14	NC_000014.9:g.54859613T>C
GRCh37.p13 chr 14	NC_000014.8:g.55326331T>C
GCH1 RefSeqGene	NG_008647.1:g.48212A>G

Gene: GCH1, GTP cyclohydrolase 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GCH1 transcript variant 1	NM_000161.3:c.509+68A>G	N/A	Intron Variant
GCH1 transcript variant 2	NM_001024024.2:c.509+68A>G	N/A	Intron Variant
GCH1 transcript variant 3	NM_001024070.2:c.509+68A>G	N/A	Intron Variant
GCH1 transcript variant 4	NM_001024071.2:c.509+68A>G	N/A	Intron Variant
GCH1 transcript variant X2	XM_017021218.2:c.215+68A>G	N/A	Intron Variant
GCH1 transcript variant X1	XM_047431261.1:c.509+68A>G	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.

Not Reported in ClinVar

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	T=	C
GRCh38.p14 chr 14	NC_000014.9:g.54859613=	NC_000014.9:g.54859613T>C
GRCh37.p13 chr 14	NC_000014.8:g.55326331=	NC_000014.8:g.55326331T>C
GCH1 RefSeqGene	NG_008647.1:g.48212=	NG_008647.1:g.48212A>G
GCH1 transcript variant 1	NM_000161.2:c.509+68=	NM_000161.2:c.509+68A>G
GCH1 transcript variant 1	NM_000161.3:c.509+68=	NM_000161.3:c.509+68A>G
GCH1 transcript variant 2	NM_001024024.1:c.509+68=	NM_001024024.1:c.509+68A>G
GCH1 transcript variant 2	NM_001024024.2:c.509+68=	NM_001024024.2:c.509+68A>G
GCH1 transcript variant 3	NM_001024070.1:c.509+68=	NM_001024070.1:c.509+68A>G
GCH1 transcript variant 3	NM_001024070.2:c.509+68=	NM_001024070.2:c.509+68A>G
GCH1 transcript variant 4	NM_001024071.1:c.509+68=	NM_001024071.1:c.509+68A>G
GCH1 transcript variant 4	NM_001024071.2:c.509+68=	NM_001024071.2:c.509+68A>G
GCH1 transcript variant X2	XM_005267530.1:c.509+68=	XM_005267530.1:c.509+68A>G
GCH1 transcript variant X2	XM_017021218.2:c.215+68=	XM_017021218.2:c.215+68A>G
GCH1 transcript variant X1	XM_047431261.1:c.509+68=	XM_047431261.1:c.509+68A>G

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#.

42 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CGM_KYOTO	ss76876509	Dec 06, 2007 (129)
2	1000GENOMES	ss236549934	Jul 15, 2010 (132)
3	GMI	ss282012344	May 04, 2012 (137)
4	SSMP	ss659784588	Apr 25, 2013 (138)
5	NHLBI-ESP	ss713179350	Apr 25, 2013 (138)
6	EVA-GONL	ss991168141	Aug 21, 2014 (142)
7	JMKIDD_LAB	ss1079671358	Aug 21, 2014 (142)
8	1000GENOMES	ss1351091041	Aug 21, 2014 (142)
9	EVA_UK10K_ALSPAC	ss1631778588	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1674772621	Apr 01, 2015 (144)
11	EVA_DECODE	ss1695167539	Apr 01, 2015 (144)
12	EVA_MGP	ss1711372853	Apr 01, 2015 (144)
13	WEILL_CORNELL_DGM	ss1934544378	Feb 12, 2016 (147)
14	USC_VALOUEV	ss2156423988	Dec 20, 2016 (150)
15	HUMAN_LONGEVITY	ss2202157107	Dec 20, 2016 (150)
16	GRF	ss2700848964	Nov 08, 2017 (151)
17	GNOMAD	ss2927941625	Nov 08, 2017 (151)
18	SWEGEN	ss3012236464	Nov 08, 2017 (151)
19	OMUKHERJEE_ADBS	ss3646460553	Oct 12, 2018 (152)
20	EGCUT_WGS	ss3679484351	Jul 13, 2019 (153)
21	EVA_DECODE	ss3696720690	Jul 13, 2019 (153)
22	ACPOP	ss3740400408	Jul 13, 2019 (153)
23	EVA	ss3752347727	Jul 13, 2019 (153)
24	KHV_HUMAN_GENOMES	ss3817680964	Jul 13, 2019 (153)
25	EVA	ss3824851305	Apr 27, 2020 (154)
26	EVA	ss3825846089	Apr 27, 2020 (154)
27	EVA	ss3833930521	Apr 27, 2020 (154)
28	SGDP_PRJ	ss3881551701	Apr 27, 2020 (154)
29	KRGDB	ss3930569010	Apr 27, 2020 (154)
30	FSA-LAB	ss3984056511	Apr 27, 2021 (155)
31	EVA	ss3986619083	Apr 27, 2021 (155)
32	TOPMED	ss4971396822	Apr 27, 2021 (155)
33	1000G_HIGH_COVERAGE	ss5296299478	Oct 16, 2022 (156)
34	EVA	ss5415401826	Oct 16, 2022 (156)
35	HUGCELL_USP	ss5490334642	Oct 16, 2022 (156)
36	EVA	ss5511248491	Oct 16, 2022 (156)
37	1000G_HIGH_COVERAGE	ss5596623281	Oct 16, 2022 (156)
38	SANFORD_IMAGENETICS	ss5656265742	Oct 16, 2022 (156)
39	EVA	ss5841137173	Oct 16, 2022 (156)
40	EVA	ss5848384329	Oct 16, 2022 (156)
41	EVA	ss5901426782	Oct 16, 2022 (156)
42	EVA	ss5947696002	Oct 16, 2022 (156)
43	1000Genomes	NC_000014.8 - 55326331	Oct 12, 2018 (152)
44	1000Genomes_30x	NC_000014.9 - 54859613	Oct 16, 2022 (156)
45	The Avon Longitudinal Study of Parents and Children	NC_000014.8 - 55326331	Oct 12, 2018 (152)
46	Genetic variation in the Estonian population	NC_000014.8 - 55326331	Oct 12, 2018 (152)
47	gnomAD - Genomes	NC_000014.9 - 54859613	Apr 27, 2021 (155)
48	GO Exome Sequencing Project	NC_000014.8 - 55326331	Oct 12, 2018 (152)
49	Genome of the Netherlands Release 5	NC_000014.8 - 55326331	Apr 27, 2020 (154)
50	KOREAN population from KRGDB	NC_000014.8 - 55326331	Apr 27, 2020 (154)
51	Medical Genome Project healthy controls from Spanish population	NC_000014.8 - 55326331	Apr 27, 2020 (154)
52	Northern Sweden	NC_000014.8 - 55326331	Jul 13, 2019 (153)
53	Qatari	NC_000014.8 - 55326331	Apr 27, 2020 (154)
54	SGDP_PRJ	NC_000014.8 - 55326331	Apr 27, 2020 (154)
55	Siberian	NC_000014.8 - 55326331	Apr 27, 2020 (154)
56	TopMed	NC_000014.9 - 54859613	Apr 27, 2021 (155)
57	UK 10K study - Twins	NC_000014.8 - 55326331	Oct 12, 2018 (152)
58	ALFA	NC_000014.9 - 54859613	Apr 27, 2021 (155)

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
ss282012344, ss1695167539	NC_000014.7:54396080:T:C	NC_000014.9:54859612:T:C	(self)
64074962, 35591612, 25222599, 1308637, 15898566, 37746404, 488613, 13685273, 16586308, 33568681, 8940342, 35591612, ss236549934, ss659784588, ss713179350, ss991168141, ss1079671358, ss1351091041, ss1631778588, ss1674772621, ss1711372853, ss1934544378, ss2156423988, ss2700848964, ss2927941625, ss3012236464, ss3646460553, ss3679484351, ss3740400408, ss3752347727, ss3824851305, ss3825846089, ss3833930521, ss3881551701, ss3930569010, ss3984056511, ss3986619083, ss5415401826, ss5511248491, ss5656265742, ss5841137173, ss5848384329, ss5947696002	NC_000014.8:55326330:T:C	NC_000014.9:54859612:T:C	(self)
84149216, 451803028, 186942481, 13401038825, ss2202157107, ss3696720690, ss3817680964, ss4971396822, ss5296299478, ss5490334642, ss5596623281, ss5901426782	NC_000014.9:54859612:T:C	NC_000014.9:54859612:T:C	(self)
ss76876509	NT_026437.12:36326330:T:C	NC_000014.9:54859612:T:C	(self)

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

No publications for rs55934565

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs55934565