Name: rs2227574
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.

rs2227574

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:73917409 (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: delG
Variation Type: Deletion
Frequency: delG=0.499875 (132312/264690, TOPMED)
G=0.490714 (68697/139994, GnomAD)
delG=0.11077 (3130/28258, 14KJPN) (+ 12 more)
delG=0.10817 (1813/16760, 8.3KJPN)
delG=0.3708 (3469/9356, ALFA)
delG=0.3707 (2374/6404, 1000G_30x)
delG=0.3666 (1836/5008, 1000G)
delG=0.4973 (2228/4480, Estonian)
G=0.4362 (1681/3854, ALSPAC)
G=0.4177 (1549/3708, TWINSUK)
delG=0.1108 (203/1832, Korea1K)
G=0.438 (437/998, GoNL)
G=0.453 (272/600, NorthernSweden)
delG=0.098 (21/214, Vietnamese)
G=0.45 (18/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: C10orf55 : Intron Variant
PLAU : 3 Prime UTR 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	9356	G=0.6292	=0.3708	0.449551	0.191107	0.359342	32
European	Sub	7870	G=0.5659	=0.4341	0.356798	0.224905	0.418297	32
African	Sub	912	G=0.965	=0.035	0.940789	0.010965	0.048246	20
African Others	Sub	36	G=0.86	=0.14	0.833333	0.111111	0.055556	6
African American	Sub	876	G=0.969	=0.031	0.945205	0.006849	0.047945	10
Asian	Sub	88	G=0.99	=0.01	0.977273	0.0	0.022727	0
East Asian	Sub	68	G=1.00	=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	20	G=0.95	=0.05	0.9	0.0	0.1	0
Latin American 1	Sub	24	G=1.00	=0.00	1.0	0.0	0.0	N/A
Latin American 2	Sub	230	G=1.000	=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	60	G=0.98	=0.02	0.966667	0.0	0.033333	0
Other	Sub	172	G=0.890	=0.110	0.825581	0.046512	0.127907	6

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	G=0.500125	delG=0.499875
gnomAD - Genomes	Global	Study-wide	139994	G=0.490714	delG=0.509286
gnomAD - Genomes	European	Sub	75838	G=0.43874	delG=0.56126
gnomAD - Genomes	African	Sub	41922	G=0.55322	delG=0.44678
gnomAD - Genomes	American	Sub	13630	G=0.52561	delG=0.47439
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.3900	delG=0.6100
gnomAD - Genomes	East Asian	Sub	3132	G=0.8844	delG=0.1156
gnomAD - Genomes	Other	Sub	2154	G=0.4661	delG=0.5339
14KJPN	JAPANESE	Study-wide	28258	G=0.88923	delG=0.11077
8.3KJPN	JAPANESE	Study-wide	16760	G=0.89183	delG=0.10817
Allele Frequency Aggregator	Total	Global	9356	G=0.6292	delG=0.3708
Allele Frequency Aggregator	European	Sub	7870	G=0.5659	delG=0.4341
Allele Frequency Aggregator	African	Sub	912	G=0.965	delG=0.035
Allele Frequency Aggregator	Latin American 2	Sub	230	G=1.000	delG=0.000
Allele Frequency Aggregator	Other	Sub	172	G=0.890	delG=0.110
Allele Frequency Aggregator	Asian	Sub	88	G=0.99	delG=0.01
Allele Frequency Aggregator	South Asian	Sub	60	G=0.98	delG=0.02
Allele Frequency Aggregator	Latin American 1	Sub	24	G=1.00	delG=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.6293	delG=0.3707
1000Genomes_30x	African	Sub	1786	G=0.5661	delG=0.4339
1000Genomes_30x	Europe	Sub	1266	G=0.3965	delG=0.6035
1000Genomes_30x	South Asian	Sub	1202	G=0.7488	delG=0.2512
1000Genomes_30x	East Asian	Sub	1170	G=0.8675	delG=0.1325
1000Genomes_30x	American	Sub	980	G=0.614	delG=0.386
1000Genomes	Global	Study-wide	5008	G=0.6334	delG=0.3666
1000Genomes	African	Sub	1322	G=0.5537	delG=0.4463
1000Genomes	East Asian	Sub	1008	G=0.8770	delG=0.1230
1000Genomes	Europe	Sub	1006	G=0.3996	delG=0.6004
1000Genomes	South Asian	Sub	978	G=0.751	delG=0.249
1000Genomes	American	Sub	694	G=0.605	delG=0.395
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.5027	delG=0.4973
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.4362	delG=0.5638
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.4177	delG=0.5823
Korean Genome Project	KOREAN	Study-wide	1832	G=0.8892	delG=0.1108
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.438	delG=0.562
Northern Sweden	ACPOP	Study-wide	600	G=0.453	delG=0.547
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.902	delG=0.098
The Danish reference pan genome	Danish	Study-wide	40	G=0.45	delG=0.55

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 10	NC_000010.11:g.73917409del
GRCh37.p13 chr 10	NC_000010.10:g.75677167del
PLAU RefSeqGene (LRG_593)	NG_011904.1:g.11306del

Gene: PLAU, plasminogen activator, urokinase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PLAU transcript variant 2	NM_001145031.3:c.*844=	N/A	3 Prime UTR Variant
PLAU transcript variant 1	NM_002658.6:c.*844=	N/A	3 Prime UTR Variant
PLAU transcript variant 3	NM_001319191.2:c.*844=	N/A	3 Prime UTR Variant
PLAU transcript variant X1	XM_047425353.1:c.*844=	N/A	3 Prime UTR Variant
PLAU transcript variant X2	XM_011539866.3:c.*844=	N/A	3 Prime UTR Variant

Gene: C10orf55, chromosome 10 putative open reading frame 55 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
C10orf55 transcript variant 1	NR_160937.1:n.	N/A	Intron Variant
C10orf55 transcript variant 2	NR_160938.1: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.

Allele: delG (allele ID: 316340 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000406801.3	Quebec platelet disorder	Benign

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=	delG
GRCh38.p14 chr 10	NC_000010.11:g.73917409=	NC_000010.11:g.73917409del
GRCh37.p13 chr 10	NC_000010.10:g.75677167=	NC_000010.10:g.75677167del
PLAU RefSeqGene (LRG_593)	NG_011904.1:g.11306=	NG_011904.1:g.11306del
PLAU transcript variant 1	NM_002658.6:c.*844=	NM_002658.6:c.*844del
PLAU transcript variant 1	NM_002658.5:c.*844=	NM_002658.5:c.*844del
PLAU transcript variant 1	NM_002658.4:c.*844=	NM_002658.4:c.*844del
PLAU transcript variant 1	NM_002658.3:c.*844=	NM_002658.3:c.*844del
PLAU transcript variant 2	NM_001145031.3:c.*844=	NM_001145031.3:c.*844del
PLAU transcript variant 2	NM_001145031.2:c.*844=	NM_001145031.2:c.*844del
PLAU transcript variant 2	NM_001145031.1:c.*844=	NM_001145031.1:c.*844del
PLAU transcript variant 3	NM_001319191.2:c.*844=	NM_001319191.2:c.*844del
PLAU transcript variant 3	NM_001319191.1:c.*844=	NM_001319191.1:c.*844del
PLAU transcript variant X2	XM_011539866.3:c.*844=	XM_011539866.3:c.*844del
PLAU transcript variant X1	XM_011539866.2:c.*844=	XM_011539866.2:c.*844del
PLAU transcript variant X1	XM_011539866.1:c.*844=	XM_011539866.1:c.*844del
PLAU transcript variant X1	XM_047425353.1:c.*844=	XM_047425353.1:c.*844del
C10orf55 transcript	NM_001001791.2:c.-196-768=	NM_001001791.2:c.-196-768del

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#.

52 SubSNP, 15 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	PGA-UW-FHCRC	ss3172143	Aug 15, 2001 (98)
2	ABI	ss39763816	Mar 14, 2006 (126)
3	CGM_KYOTO	ss76876481	Dec 06, 2007 (129)
4	HUMANGENOME_JCVI	ss95545947	Feb 04, 2009 (130)
5	BUSHMAN	ss193192141	Jul 04, 2010 (132)
6	GMI	ss287861798	May 09, 2011 (134)
7	GMI	ss289023720	May 04, 2012 (137)
8	PJP	ss294664214	May 09, 2011 (134)
9	1000GENOMES	ss327255152	May 09, 2011 (137)
10	1000GENOMES	ss327335704	May 09, 2011 (137)
11	1000GENOMES	ss327720517	May 09, 2011 (137)
12	1000GENOMES	ss499264194	May 04, 2012 (137)
13	LUNTER	ss552040888	Apr 25, 2013 (138)
14	LUNTER	ss552289699	Apr 25, 2013 (138)
15	LUNTER	ss553417923	Apr 25, 2013 (138)
16	TISHKOFF	ss554534585	Apr 25, 2013 (138)
17	SSMP	ss664002404	Apr 01, 2015 (144)
18	BILGI_BIOE	ss666507618	Apr 25, 2013 (138)
19	EVA-GONL	ss987649576	Aug 21, 2014 (142)
20	1000GENOMES	ss1369740086	Aug 21, 2014 (142)
21	EVA_GENOME_DK	ss1574228083	Apr 01, 2015 (144)
22	EVA_DECODE	ss1597322410	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1706801661	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1706801777	Apr 01, 2015 (144)
25	HAMMER_LAB	ss1806459045	Sep 08, 2015 (146)
26	JJLAB	ss2031028231	Sep 14, 2016 (149)
27	GNOMAD	ss2890481204	Nov 08, 2017 (151)
28	SWEGEN	ss3006727582	Nov 08, 2017 (151)
29	MCHAISSO	ss3064481092	Nov 08, 2017 (151)
30	MCHAISSO	ss3065391121	Nov 08, 2017 (151)
31	BEROUKHIMLAB	ss3644302647	Oct 12, 2018 (152)
32	BIOINF_KMB_FNS_UNIBA	ss3645148473	Oct 12, 2018 (152)
33	URBANLAB	ss3649408186	Oct 12, 2018 (152)
34	EGCUT_WGS	ss3674143440	Jul 13, 2019 (153)
35	EVA_DECODE	ss3690180127	Jul 13, 2019 (153)
36	ACPOP	ss3737457932	Jul 13, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3813660475	Jul 13, 2019 (153)
38	EVA	ss3832204458	Apr 26, 2020 (154)
39	EVA	ss3839641104	Apr 26, 2020 (154)
40	EVA	ss3845114035	Apr 26, 2020 (154)
41	KOGIC	ss3968178415	Apr 26, 2020 (154)
42	TOPMED	ss4857596815	Apr 27, 2021 (155)
43	TOMMO_GENOMICS	ss5198315236	Apr 27, 2021 (155)
44	1000G_HIGH_COVERAGE	ss5284582855	Oct 16, 2022 (156)
45	HUGCELL_USP	ss5480105012	Oct 16, 2022 (156)
46	1000G_HIGH_COVERAGE	ss5578795290	Oct 16, 2022 (156)
47	SANFORD_IMAGENETICS	ss5649594155	Oct 16, 2022 (156)
48	TOMMO_GENOMICS	ss5744345663	Oct 16, 2022 (156)
49	YY_MCH	ss5811665302	Oct 16, 2022 (156)
50	EVA	ss5824608065	Oct 16, 2022 (156)
51	EVA	ss5879511114	Oct 16, 2022 (156)
52	EVA	ss5940872022	Oct 16, 2022 (156)
53	1000Genomes	NC_000010.10 - 75677167	Oct 12, 2018 (152)
54	1000Genomes_30x	NC_000010.11 - 73917409	Oct 16, 2022 (156)
55	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 75677167	Oct 12, 2018 (152)
56	Genetic variation in the Estonian population	NC_000010.10 - 75677167	Oct 12, 2018 (152)
57	The Danish reference pan genome	NC_000010.10 - 75677167	Apr 26, 2020 (154)
58	gnomAD - Genomes	NC_000010.11 - 73917409	Apr 27, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000010.10 - 75677167	Apr 26, 2020 (154)
60	Korean Genome Project	NC_000010.11 - 73917409	Apr 26, 2020 (154)
61	Northern Sweden	NC_000010.10 - 75677167	Jul 13, 2019 (153)
62	8.3KJPN	NC_000010.10 - 75677167	Apr 27, 2021 (155)
63	14KJPN	NC_000010.11 - 73917409	Oct 16, 2022 (156)
64	TopMed	NC_000010.11 - 73917409	Apr 27, 2021 (155)
65	UK 10K study - Twins	NC_000010.10 - 75677167	Oct 12, 2018 (152)
66	A Vietnamese Genetic Variation Database	NC_000010.10 - 75677167	Jul 13, 2019 (153)
67	ALFA	NC_000010.11 - 73917409	Apr 27, 2021 (155)
68	ClinVar	RCV000406801.3	Oct 16, 2022 (156)

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)
rs147642011	May 04, 2012 (137)
rs369687320	May 13, 2013 (138)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss289023720, ss294664214, ss327255152, ss327335704, ss327720517, ss552040888, ss552289699, ss553417923, ss1597322410	NC_000010.9:75347172:G:	NC_000010.11:73917408:G:	(self)
50454237, 28006829, 19881688, 249379, 12488687, 10742797, 56284543, 28006829, 6220008, ss499264194, ss554534585, ss664002404, ss666507618, ss987649576, ss1369740086, ss1574228083, ss1706801661, ss1706801777, ss1806459045, ss2031028231, ss2890481204, ss3006727582, ss3644302647, ss3674143440, ss3737457932, ss3832204458, ss3839641104, ss5198315236, ss5649594155, ss5824608065, ss5940872022	NC_000010.10:75677166:G:	NC_000010.11:73917408:G:	(self)
RCV000406801.3, 66321225, 356555227, 24556416, 78182767, 73142470, 5714765083, ss3064481092, ss3065391121, ss3645148473, ss3649408186, ss3690180127, ss3813660475, ss3845114035, ss3968178415, ss4857596815, ss5284582855, ss5480105012, ss5578795290, ss5744345663, ss5811665302, ss5879511114	NC_000010.11:73917408:G:	NC_000010.11:73917408:G:	(self)
ss3172143, ss39763816, ss76876481, ss95545947, ss287861798	NT_030059.13:26481630:G:	NC_000010.11:73917408:G:	(self)
ss193192141	NT_030059.14:32223887:G:	NC_000010.11:73917408: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 rs2227574

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

rs2227574