Name: rs28417208
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.

rs28417208

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:54887070 (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>A / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.413159 (109359/264690, TOPMED)
A=0.408708 (57233/140034, GnomAD)
A=0.46033 (13008/28258, 14KJPN) (+ 15 more)
A=0.35680 (6740/18890, ALFA)
A=0.45758 (7669/16760, 8.3KJPN)
A=0.4613 (2954/6404, 1000G_30x)
A=0.4553 (2280/5008, 1000G)
A=0.2951 (1322/4480, Estonian)
A=0.3363 (1296/3854, ALSPAC)
A=0.3287 (1219/3708, TWINSUK)
A=0.4884 (1431/2930, KOREAN)
A=0.4864 (891/1832, Korea1K)
A=0.330 (329/998, GoNL)
A=0.313 (188/600, NorthernSweden)
T=0.358 (123/344, SGDP_PRJ)
A=0.292 (63/216, Qatari)
A=0.33 (13/40, GENOME_DK)
T=0.36 (10/28, 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	18890	T=0.64320	A=0.35680
European	Sub	14286	T=0.69117	A=0.30883
African	Sub	2946	T=0.4284	A=0.5716
African Others	Sub	114	T=0.307	A=0.693
African American	Sub	2832	T=0.4333	A=0.5667
Asian	Sub	112	T=0.482	A=0.518
East Asian	Sub	86	T=0.51	A=0.49
Other Asian	Sub	26	T=0.38	A=0.62
Latin American 1	Sub	146	T=0.616	A=0.384
Latin American 2	Sub	610	T=0.659	A=0.341
South Asian	Sub	98	T=0.61	A=0.39
Other	Sub	692	T=0.590	A=0.410

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=0.586841	A=0.413159
gnomAD - Genomes	Global	Study-wide	140034	T=0.591292	A=0.408708
gnomAD - Genomes	European	Sub	75858	T=0.67085	A=0.32915
gnomAD - Genomes	African	Sub	41948	T=0.43647	A=0.56353
gnomAD - Genomes	American	Sub	13640	T=0.62295	A=0.37705
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.7301	A=0.2699
gnomAD - Genomes	East Asian	Sub	3122	T=0.4404	A=0.5596
gnomAD - Genomes	Other	Sub	2146	T=0.6090	A=0.3910
14KJPN	JAPANESE	Study-wide	28258	T=0.53967	A=0.46033
Allele Frequency Aggregator	Total	Global	18890	T=0.64320	A=0.35680
Allele Frequency Aggregator	European	Sub	14286	T=0.69117	A=0.30883
Allele Frequency Aggregator	African	Sub	2946	T=0.4284	A=0.5716
Allele Frequency Aggregator	Other	Sub	692	T=0.590	A=0.410
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.659	A=0.341
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.616	A=0.384
Allele Frequency Aggregator	Asian	Sub	112	T=0.482	A=0.518
Allele Frequency Aggregator	South Asian	Sub	98	T=0.61	A=0.39
8.3KJPN	JAPANESE	Study-wide	16760	T=0.54242	A=0.45758
1000Genomes_30x	Global	Study-wide	6404	T=0.5387	A=0.4613
1000Genomes_30x	African	Sub	1786	T=0.4026	A=0.5974
1000Genomes_30x	Europe	Sub	1266	T=0.7062	A=0.2938
1000Genomes_30x	South Asian	Sub	1202	T=0.6240	A=0.3760
1000Genomes_30x	East Asian	Sub	1170	T=0.4462	A=0.5538
1000Genomes_30x	American	Sub	980	T=0.577	A=0.423
1000Genomes	Global	Study-wide	5008	T=0.5447	A=0.4553
1000Genomes	African	Sub	1322	T=0.4009	A=0.5991
1000Genomes	East Asian	Sub	1008	T=0.4544	A=0.5456
1000Genomes	Europe	Sub	1006	T=0.7127	A=0.2873
1000Genomes	South Asian	Sub	978	T=0.630	A=0.370
1000Genomes	American	Sub	694	T=0.586	A=0.414
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.7049	A=0.2951
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.6637	A=0.3363
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.6713	A=0.3287
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.5116	A=0.4884
Korean Genome Project	KOREAN	Study-wide	1832	T=0.5136	A=0.4864
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.670	A=0.330
Northern Sweden	ACPOP	Study-wide	600	T=0.687	A=0.313
SGDP_PRJ	Global	Study-wide	344	T=0.358	A=0.642
Qatari	Global	Study-wide	216	T=0.708	A=0.292
The Danish reference pan genome	Danish	Study-wide	40	T=0.68	A=0.33
Siberian	Global	Study-wide	28	T=0.36	A=0.64

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.54887070T>A
GRCh38.p14 chr 14	NC_000014.9:g.54887070T>G
GRCh37.p13 chr 14	NC_000014.8:g.55353788T>A
GRCh37.p13 chr 14	NC_000014.8:g.55353788T>G
GCH1 RefSeqGene	NG_008647.1:g.20755A>T
GCH1 RefSeqGene	NG_008647.1:g.20755A>C

Gene: GCH1, GTP cyclohydrolase 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GCH1 transcript variant 1	NM_000161.3:c.343+15251A>T	N/A	Intron Variant
GCH1 transcript variant 2	NM_001024024.2:c.343+1525… NM_001024024.2:c.343+15251A>T	N/A	Intron Variant
GCH1 transcript variant 3	NM_001024070.2:c.343+1525… NM_001024070.2:c.343+15251A>T	N/A	Intron Variant
GCH1 transcript variant 4	NM_001024071.2:c.343+1525… NM_001024071.2:c.343+15251A>T	N/A	Intron Variant
GCH1 transcript variant X1	XM_047431261.1:c.343+1525… XM_047431261.1:c.343+15251A>T	N/A	Intron Variant
GCH1 transcript variant X2	XM_017021218.2:c.	N/A	Genic Upstream Transcript 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=	A	G
GRCh38.p14 chr 14	NC_000014.9:g.54887070=	NC_000014.9:g.54887070T>A	NC_000014.9:g.54887070T>G
GRCh37.p13 chr 14	NC_000014.8:g.55353788=	NC_000014.8:g.55353788T>A	NC_000014.8:g.55353788T>G
GCH1 RefSeqGene	NG_008647.1:g.20755=	NG_008647.1:g.20755A>T	NG_008647.1:g.20755A>C
GCH1 transcript variant 1	NM_000161.2:c.343+15251=	NM_000161.2:c.343+15251A>T	NM_000161.2:c.343+15251A>C
GCH1 transcript variant 1	NM_000161.3:c.343+15251=	NM_000161.3:c.343+15251A>T	NM_000161.3:c.343+15251A>C
GCH1 transcript variant 2	NM_001024024.1:c.343+15251=	NM_001024024.1:c.343+15251A>T	NM_001024024.1:c.343+15251A>C
GCH1 transcript variant 2	NM_001024024.2:c.343+15251=	NM_001024024.2:c.343+15251A>T	NM_001024024.2:c.343+15251A>C
GCH1 transcript variant 3	NM_001024070.1:c.343+15251=	NM_001024070.1:c.343+15251A>T	NM_001024070.1:c.343+15251A>C
GCH1 transcript variant 3	NM_001024070.2:c.343+15251=	NM_001024070.2:c.343+15251A>T	NM_001024070.2:c.343+15251A>C
GCH1 transcript variant 4	NM_001024071.1:c.343+15251=	NM_001024071.1:c.343+15251A>T	NM_001024071.1:c.343+15251A>C
GCH1 transcript variant 4	NM_001024071.2:c.343+15251=	NM_001024071.2:c.343+15251A>T	NM_001024071.2:c.343+15251A>C
GCH1 transcript variant X2	XM_005267530.1:c.343+15251=	XM_005267530.1:c.343+15251A>T	XM_005267530.1:c.343+15251A>C
GCH1 transcript variant X1	XM_047431261.1:c.343+15251=	XM_047431261.1:c.343+15251A>T	XM_047431261.1:c.343+15251A>C

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#.

61 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss35150531	May 24, 2005 (125)
2	BGI	ss106389360	Feb 05, 2009 (130)
3	1000GENOMES	ss108355273	Jan 23, 2009 (130)
4	1000GENOMES	ss113348750	Jan 25, 2009 (130)
5	ILLUMINA-UK	ss118485509	Feb 14, 2009 (130)
6	GMI	ss155823098	Dec 01, 2009 (131)
7	COMPLETE_GENOMICS	ss169579292	Jul 04, 2010 (132)
8	BUSHMAN	ss200101509	Jul 04, 2010 (132)
9	BCM-HGSC-SUB	ss206928384	Jul 04, 2010 (132)
10	1000GENOMES	ss226581203	Jul 14, 2010 (132)
11	1000GENOMES	ss236549998	Jul 15, 2010 (132)
12	1000GENOMES	ss242982682	Jul 15, 2010 (132)
13	BL	ss255003237	May 09, 2011 (134)
14	GMI	ss282012450	May 04, 2012 (137)
15	GMI	ss286846087	Apr 25, 2013 (138)
16	TISHKOFF	ss564105280	Apr 25, 2013 (138)
17	SSMP	ss659784761	Apr 25, 2013 (138)
18	EVA-GONL	ss991168367	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1079671486	Aug 21, 2014 (142)
20	1000GENOMES	ss1351091890	Aug 21, 2014 (142)
21	DDI	ss1427430821	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1577268334	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1631778963	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1674772996	Apr 01, 2015 (144)
25	EVA_DECODE	ss1695167721	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1807933324	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1934544618	Feb 12, 2016 (147)
28	GENOMED	ss1967968368	Jul 19, 2016 (147)
29	JJLAB	ss2028049832	Sep 14, 2016 (149)
30	USC_VALOUEV	ss2156424117	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2202158623	Dec 20, 2016 (150)
32	SYSTEMSBIOZJU	ss2628515140	Nov 08, 2017 (151)
33	GRF	ss2700849132	Nov 08, 2017 (151)
34	GNOMAD	ss2927944114	Nov 08, 2017 (151)
35	SWEGEN	ss3012236849	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3027850264	Nov 08, 2017 (151)
37	CSHL	ss3350816684	Nov 08, 2017 (151)
38	EGCUT_WGS	ss3679484697	Jul 13, 2019 (153)
39	EVA_DECODE	ss3696721175	Jul 13, 2019 (153)
40	ACPOP	ss3740400625	Jul 13, 2019 (153)
41	EVA	ss3752347961	Jul 13, 2019 (153)
42	KHV_HUMAN_GENOMES	ss3817681242	Jul 13, 2019 (153)
43	KHV_HUMAN_GENOMES	ss3817681243	Jul 13, 2019 (153)
44	EVA	ss3833930661	Apr 27, 2020 (154)
45	EVA	ss3840559008	Apr 27, 2020 (154)
46	EVA	ss3846047989	Apr 27, 2020 (154)
47	SGDP_PRJ	ss3881552183	Apr 27, 2020 (154)
48	KRGDB	ss3930569639	Apr 27, 2020 (154)
49	KOGIC	ss3974970076	Apr 27, 2020 (154)
50	TOPMED	ss4971403562	Apr 26, 2021 (155)
51	TOMMO_GENOMICS	ss5213330140	Apr 26, 2021 (155)
52	1000G_HIGH_COVERAGE	ss5296300335	Oct 16, 2022 (156)
53	HUGCELL_USP	ss5490335281	Oct 16, 2022 (156)
54	1000G_HIGH_COVERAGE	ss5596624446	Oct 16, 2022 (156)
55	SANFORD_IMAGENETICS	ss5656266204	Oct 16, 2022 (156)
56	TOMMO_GENOMICS	ss5766160679	Oct 16, 2022 (156)
57	YY_MCH	ss5814771253	Oct 16, 2022 (156)
58	EVA	ss5841137484	Oct 16, 2022 (156)
59	EVA	ss5851041817	Oct 16, 2022 (156)
60	EVA	ss5901427537	Oct 16, 2022 (156)
61	EVA	ss5947696411	Oct 16, 2022 (156)
62	1000Genomes	NC_000014.8 - 55353788	Oct 12, 2018 (152)
63	1000Genomes_30x	NC_000014.9 - 54887070	Oct 16, 2022 (156)
64	The Avon Longitudinal Study of Parents and Children	NC_000014.8 - 55353788	Oct 12, 2018 (152)
65	Genetic variation in the Estonian population	NC_000014.8 - 55353788	Oct 12, 2018 (152)
66	The Danish reference pan genome	NC_000014.8 - 55353788	Apr 27, 2020 (154)
67	gnomAD - Genomes	NC_000014.9 - 54887070	Apr 26, 2021 (155)
68	Genome of the Netherlands Release 5	NC_000014.8 - 55353788	Apr 27, 2020 (154)
69	KOREAN population from KRGDB	NC_000014.8 - 55353788	Apr 27, 2020 (154)
70	Korean Genome Project	NC_000014.9 - 54887070	Apr 27, 2020 (154)
71	Northern Sweden	NC_000014.8 - 55353788	Jul 13, 2019 (153)
72	Qatari	NC_000014.8 - 55353788	Apr 27, 2020 (154)
73	SGDP_PRJ	NC_000014.8 - 55353788	Apr 27, 2020 (154)
74	Siberian	NC_000014.8 - 55353788	Apr 27, 2020 (154)
75	8.3KJPN	NC_000014.8 - 55353788	Apr 26, 2021 (155)
76	14KJPN	NC_000014.9 - 54887070	Oct 16, 2022 (156)
77	TopMed	NC_000014.9 - 54887070	Apr 26, 2021 (155)
78	UK 10K study - Twins	NC_000014.8 - 55353788	Oct 12, 2018 (152)
79	A Vietnamese Genetic Variation Database Submission ignored due to conflicting rows: Row 7919084 (NC_000014.8:55353787:T:T 80/81, NC_000014.8:55353787:T:G 1/81) Row 7919085 (NC_000014.8:55353787:T:T 80/213, NC_000014.8:55353787:T:A 133/213)	-	Jul 13, 2019 (153)
80	A Vietnamese Genetic Variation Database Submission ignored due to conflicting rows: Row 7919084 (NC_000014.8:55353787:T:T 80/81, NC_000014.8:55353787:T:G 1/81) Row 7919085 (NC_000014.8:55353787:T:T 80/213, NC_000014.8:55353787:T:A 133/213)	-	Jul 13, 2019 (153)
81	ALFA	NC_000014.9 - 54887070	Apr 26, 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
ss35150531, ss108355273, ss113348750, ss118485509, ss169579292, ss200101509, ss206928384, ss255003237, ss282012450, ss286846087, ss1695167721	NC_000014.7:54423537:T:A	NC_000014.9:54887069:T:A	(self)
64075836, 35592025, 25222945, 3612447, 15898774, 37747033, 13685490, 16586548, 33569163, 8940471, 71299447, 35592025, ss226581203, ss236549998, ss242982682, ss564105280, ss659784761, ss991168367, ss1079671486, ss1351091890, ss1427430821, ss1577268334, ss1631778963, ss1674772996, ss1807933324, ss1934544618, ss1967968368, ss2028049832, ss2156424117, ss2628515140, ss2700849132, ss2927944114, ss3012236849, ss3350816684, ss3679484697, ss3740400625, ss3752347961, ss3833930661, ss3840559008, ss3881552183, ss3930569639, ss5213330140, ss5656266204, ss5841137484, ss5947696411	NC_000014.8:55353787:T:A	NC_000014.9:54887069:T:A	(self)
84150381, 451809243, 31348077, 99997783, 186949221, 6643600863, ss2202158623, ss3027850264, ss3696721175, ss3817681242, ss3846047989, ss3974970076, ss4971403562, ss5296300335, ss5490335281, ss5596624446, ss5766160679, ss5814771253, ss5851041817, ss5901427537	NC_000014.9:54887069:T:A	NC_000014.9:54887069:T:A	(self)
ss106389360, ss155823098	NT_026437.12:36353787:T:A	NC_000014.9:54887069:T:A	(self)
	NC_000014.8:55353787:T:G	NC_000014.9:54887069:T:G	(self)
ss3817681243	NC_000014.9:54887069:T:G	NC_000014.9:54887069:T:G	(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 rs28417208

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs28417208