Name: rs10917041
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.

rs10917041

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:21772447 (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: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.160920 (42594/264690, TOPMED)
T=0.152153 (21236/139570, GnomAD)
T=0.32511 (9187/28258, 14KJPN) (+ 14 more)
T=0.16665 (3148/18890, ALFA)
T=0.33079 (5544/16760, 8.3KJPN)
T=0.1833 (1174/6404, 1000G_30x)
T=0.1877 (940/5008, 1000G)
T=0.1653 (637/3854, ALSPAC)
T=0.1594 (591/3708, TWINSUK)
T=0.4133 (1210/2928, KOREAN)
T=0.4170 (764/1832, Korea1K)
T=0.143 (143/998, GoNL)
T=0.250 (150/600, NorthernSweden)
T=0.056 (12/216, Qatari)
C=0.351 (73/208, SGDP_PRJ)
T=0.28 (11/40, GENOME_DK)
C=0.32 (11/34, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: USP48 : 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	C=0.83335	T=0.16665
European	Sub	14286	C=0.82346	T=0.17654
African	Sub	2946	C=0.9440	T=0.0560
African Others	Sub	114	C=0.982	T=0.018
African American	Sub	2832	C=0.9424	T=0.0576
Asian	Sub	112	C=0.634	T=0.366
East Asian	Sub	86	C=0.64	T=0.36
Other Asian	Sub	26	C=0.62	T=0.38
Latin American 1	Sub	146	C=0.849	T=0.151
Latin American 2	Sub	610	C=0.562	T=0.438
South Asian	Sub	98	C=0.86	T=0.14
Other	Sub	692	C=0.831	T=0.169

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
TopMed	Global	Study-wide	264690	C=0.839080	T=0.160920
gnomAD - Genomes	Global	Study-wide	139570	C=0.847847	T=0.152153
gnomAD - Genomes	European	Sub	75644	C=0.82525	T=0.17475
gnomAD - Genomes	African	Sub	41794	C=0.94928	T=0.05072
gnomAD - Genomes	American	Sub	13558	C=0.69339	T=0.30661
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	C=0.9276	T=0.0724
gnomAD - Genomes	East Asian	Sub	3118	C=0.6260	T=0.3740
gnomAD - Genomes	Other	Sub	2140	C=0.8439	T=0.1561
14KJPN	JAPANESE	Study-wide	28258	C=0.67489	T=0.32511
Allele Frequency Aggregator	Total	Global	18890	C=0.83335	T=0.16665
Allele Frequency Aggregator	European	Sub	14286	C=0.82346	T=0.17654
Allele Frequency Aggregator	African	Sub	2946	C=0.9440	T=0.0560
Allele Frequency Aggregator	Other	Sub	692	C=0.831	T=0.169
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.562	T=0.438
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.849	T=0.151
Allele Frequency Aggregator	Asian	Sub	112	C=0.634	T=0.366
Allele Frequency Aggregator	South Asian	Sub	98	C=0.86	T=0.14
8.3KJPN	JAPANESE	Study-wide	16760	C=0.66921	T=0.33079
1000Genomes_30x	Global	Study-wide	6404	C=0.8167	T=0.1833
1000Genomes_30x	African	Sub	1786	C=0.9782	T=0.0218
1000Genomes_30x	Europe	Sub	1266	C=0.8610	T=0.1390
1000Genomes_30x	South Asian	Sub	1202	C=0.8810	T=0.1190
1000Genomes_30x	East Asian	Sub	1170	C=0.6265	T=0.3735
1000Genomes_30x	American	Sub	980	C=0.613	T=0.387
1000Genomes	Global	Study-wide	5008	C=0.8123	T=0.1877
1000Genomes	African	Sub	1322	C=0.9773	T=0.0227
1000Genomes	East Asian	Sub	1008	C=0.6210	T=0.3790
1000Genomes	Europe	Sub	1006	C=0.8559	T=0.1441
1000Genomes	South Asian	Sub	978	C=0.885	T=0.115
1000Genomes	American	Sub	694	C=0.610	T=0.390
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8347	T=0.1653
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8406	T=0.1594
KOREAN population from KRGDB	KOREAN	Study-wide	2928	C=0.5867	T=0.4133
Korean Genome Project	KOREAN	Study-wide	1832	C=0.5830	T=0.4170
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.857	T=0.143
Northern Sweden	ACPOP	Study-wide	600	C=0.750	T=0.250
Qatari	Global	Study-wide	216	C=0.944	T=0.056
SGDP_PRJ	Global	Study-wide	208	C=0.351	T=0.649
The Danish reference pan genome	Danish	Study-wide	40	C=0.72	T=0.28
Siberian	Global	Study-wide	34	C=0.32	T=0.68

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 1	NC_000001.11:g.21772447C>T
GRCh37.p13 chr 1	NC_000001.10:g.22098940C>T
USP48 RefSeqGene	NG_047203.1:g.15753G>A

Gene: USP48, ubiquitin specific peptidase 48 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
USP48 transcript variant 2	NM_001032730.3:c.134+1037… NM_001032730.3:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant 3	NM_001330394.3:c.134+1037… NM_001330394.3:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant 4	NM_001350164.2:c.134+1037… NM_001350164.2:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant 5	NM_001350166.2:c.134+1037… NM_001350166.2:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant 6	NM_001350167.2:c.134+1037… NM_001350167.2:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant 7	NM_001350168.2:c.134+1037… NM_001350168.2:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant 1	NM_032236.8:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant X3	XM_006710955.5:c.134+1037… XM_006710955.5:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant X1	XM_047432026.1:c.134+1037… XM_047432026.1:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant X2	XM_047432027.1:c.134+1037… XM_047432027.1:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant X4	XM_047432029.1:c.134+1037… XM_047432029.1:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant X6	XM_047432030.1:c.134+1037… XM_047432030.1:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant X7	XM_047432031.1:c.134+1037… XM_047432031.1:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant X8	XM_047432032.1:c.134+1037… XM_047432032.1:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant X9	XM_047432033.1:c.134+1037… XM_047432033.1:c.134+10377G>A	N/A	Intron Variant
USP48 transcript variant X5	XM_011542264.2:c.	N/A	Genic Upstream Transcript Variant
USP48 transcript variant X10	XM_011542267.4:c.	N/A	Genic Upstream Transcript Variant
USP48 transcript variant X11	XM_011542268.3: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	C=	T
GRCh38.p14 chr 1	NC_000001.11:g.21772447=	NC_000001.11:g.21772447C>T
GRCh37.p13 chr 1	NC_000001.10:g.22098940=	NC_000001.10:g.22098940C>T
USP48 RefSeqGene	NG_047203.1:g.15753=	NG_047203.1:g.15753G>A
USP48 transcript variant 2	NM_001032730.1:c.134+10377=	NM_001032730.1:c.134+10377G>A
USP48 transcript variant 2	NM_001032730.3:c.134+10377=	NM_001032730.3:c.134+10377G>A
USP48 transcript variant 3	NM_001330394.3:c.134+10377=	NM_001330394.3:c.134+10377G>A
USP48 transcript variant 4	NM_001350164.2:c.134+10377=	NM_001350164.2:c.134+10377G>A
USP48 transcript variant 5	NM_001350166.2:c.134+10377=	NM_001350166.2:c.134+10377G>A
USP48 transcript variant 6	NM_001350167.2:c.134+10377=	NM_001350167.2:c.134+10377G>A
USP48 transcript variant 7	NM_001350168.2:c.134+10377=	NM_001350168.2:c.134+10377G>A
USP48 transcript variant 1	NM_032236.5:c.134+10377=	NM_032236.5:c.134+10377G>A
USP48 transcript variant 1	NM_032236.8:c.134+10377=	NM_032236.8:c.134+10377G>A
USP48 transcript variant X1	XM_005246006.1:c.134+10377=	XM_005246006.1:c.134+10377G>A
USP48 transcript variant X2	XM_005246007.1:c.134+10377=	XM_005246007.1:c.134+10377G>A
USP48 transcript variant X3	XM_005246008.1:c.134+10377=	XM_005246008.1:c.134+10377G>A
USP48 transcript variant X4	XM_005246009.1:c.134+10377=	XM_005246009.1:c.134+10377G>A
USP48 transcript variant X5	XM_005246010.1:c.134+10377=	XM_005246010.1:c.134+10377G>A
USP48 transcript variant X3	XM_006710955.5:c.134+10377=	XM_006710955.5:c.134+10377G>A
USP48 transcript variant X1	XM_047432026.1:c.134+10377=	XM_047432026.1:c.134+10377G>A
USP48 transcript variant X2	XM_047432027.1:c.134+10377=	XM_047432027.1:c.134+10377G>A
USP48 transcript variant X4	XM_047432029.1:c.134+10377=	XM_047432029.1:c.134+10377G>A
USP48 transcript variant X6	XM_047432030.1:c.134+10377=	XM_047432030.1:c.134+10377G>A
USP48 transcript variant X7	XM_047432031.1:c.134+10377=	XM_047432031.1:c.134+10377G>A
USP48 transcript variant X8	XM_047432032.1:c.134+10377=	XM_047432032.1:c.134+10377G>A
USP48 transcript variant X9	XM_047432033.1:c.134+10377=	XM_047432033.1:c.134+10377G>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#.

50 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss16041262	Feb 27, 2004 (120)
2	SC_SNP	ss18404532	Feb 27, 2004 (120)
3	HGSV	ss78106011	Dec 06, 2007 (129)
4	BCMHGSC_JDW	ss87289620	Mar 23, 2008 (129)
5	ENSEMBL	ss137838698	Dec 01, 2009 (131)
6	GMI	ss154750569	Dec 01, 2009 (131)
7	BCM-HGSC-SUB	ss205513860	Jul 04, 2010 (132)
8	GMI	ss275748475	May 04, 2012 (137)
9	1000GENOMES	ss328468305	May 09, 2011 (134)
10	SSMP	ss647632234	Apr 25, 2013 (138)
11	EVA-GONL	ss974934779	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1067726622	Aug 21, 2014 (142)
13	1000GENOMES	ss1289990459	Aug 21, 2014 (142)
14	DDI	ss1425741850	Apr 01, 2015 (144)
15	EVA_GENOME_DK	ss1573934213	Apr 01, 2015 (144)
16	EVA_DECODE	ss1584293110	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1599703862	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1642697895	Apr 01, 2015 (144)
19	WEILL_CORNELL_DGM	ss1918146371	Feb 12, 2016 (147)
20	JJLAB	ss2019585150	Sep 14, 2016 (149)
21	USC_VALOUEV	ss2147589437	Dec 20, 2016 (150)
22	HUMAN_LONGEVITY	ss2160631420	Dec 20, 2016 (150)
23	SYSTEMSBIOZJU	ss2624308935	Nov 08, 2017 (151)
24	GRF	ss2697494041	Nov 08, 2017 (151)
25	GNOMAD	ss2752537073	Nov 08, 2017 (151)
26	SWEGEN	ss2986447387	Nov 08, 2017 (151)
27	CSHL	ss3343362192	Nov 08, 2017 (151)
28	EVA_DECODE	ss3686322774	Jul 12, 2019 (153)
29	ACPOP	ss3726859747	Jul 12, 2019 (153)
30	EVA	ss3745926830	Jul 12, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3798946318	Jul 12, 2019 (153)
32	EVA	ss3826065149	Apr 25, 2020 (154)
33	EVA	ss3836420215	Apr 25, 2020 (154)
34	EVA	ss3841824761	Apr 25, 2020 (154)
35	SGDP_PRJ	ss3848382271	Apr 25, 2020 (154)
36	KRGDB	ss3893294588	Apr 25, 2020 (154)
37	KOGIC	ss3944008564	Apr 25, 2020 (154)
38	TOPMED	ss4441747324	Apr 27, 2021 (155)
39	TOMMO_GENOMICS	ss5142875185	Apr 27, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5241467815	Oct 17, 2022 (156)
41	HUGCELL_USP	ss5442622058	Oct 17, 2022 (156)
42	EVA	ss5505786691	Oct 17, 2022 (156)
43	1000G_HIGH_COVERAGE	ss5513356360	Oct 17, 2022 (156)
44	SANFORD_IMAGENETICS	ss5625089549	Oct 17, 2022 (156)
45	TOMMO_GENOMICS	ss5667295507	Oct 17, 2022 (156)
46	YY_MCH	ss5800402052	Oct 17, 2022 (156)
47	EVA	ss5831653096	Oct 17, 2022 (156)
48	EVA	ss5848818043	Oct 17, 2022 (156)
49	EVA	ss5907349509	Oct 17, 2022 (156)
50	EVA	ss5936905714	Oct 17, 2022 (156)
51	1000Genomes	NC_000001.10 - 22098940	Oct 11, 2018 (152)
52	1000Genomes_30x	NC_000001.11 - 21772447	Oct 17, 2022 (156)
53	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 22098940	Oct 11, 2018 (152)
54	The Danish reference pan genome	NC_000001.10 - 22098940	Apr 25, 2020 (154)
55	gnomAD - Genomes	NC_000001.11 - 21772447	Apr 27, 2021 (155)
56	Genome of the Netherlands Release 5	NC_000001.10 - 22098940	Apr 25, 2020 (154)
57	KOREAN population from KRGDB	NC_000001.10 - 22098940	Apr 25, 2020 (154)
58	Korean Genome Project	NC_000001.11 - 21772447	Apr 25, 2020 (154)
59	Northern Sweden	NC_000001.10 - 22098940	Jul 12, 2019 (153)
60	Qatari	NC_000001.10 - 22098940	Apr 25, 2020 (154)
61	SGDP_PRJ	NC_000001.10 - 22098940	Apr 25, 2020 (154)
62	Siberian	NC_000001.10 - 22098940	Apr 25, 2020 (154)
63	8.3KJPN	NC_000001.10 - 22098940	Apr 27, 2021 (155)
64	14KJPN	NC_000001.11 - 21772447	Oct 17, 2022 (156)
65	TopMed	NC_000001.11 - 21772447	Apr 27, 2021 (155)
66	UK 10K study - Twins	NC_000001.10 - 22098940	Oct 11, 2018 (152)
67	ALFA	NC_000001.11 - 21772447	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
ss78106011	NC_000001.8:21844245:C:T	NC_000001.11:21772446:C:T	(self)
ss87289620, ss205513860, ss275748475, ss1584293110	NC_000001.9:21971526:C:T	NC_000001.11:21772446:C:T	(self)
677005, 358271, 1421445, 155501, 471982, 144612, 188301, 399251, 105791, 844492, 358271, ss328468305, ss647632234, ss974934779, ss1067726622, ss1289990459, ss1425741850, ss1573934213, ss1599703862, ss1642697895, ss1918146371, ss2019585150, ss2147589437, ss2624308935, ss2697494041, ss2752537073, ss2986447387, ss3343362192, ss3726859747, ss3745926830, ss3826065149, ss3836420215, ss3848382271, ss3893294588, ss5142875185, ss5505786691, ss5625089549, ss5831653096, ss5936905714	NC_000001.10:22098939:C:T	NC_000001.11:21772446:C:T	(self)
882295, 4713768, 386565, 1132611, 5353659, 9826488475, ss2160631420, ss3686322774, ss3798946318, ss3841824761, ss3944008564, ss4441747324, ss5241467815, ss5442622058, ss5513356360, ss5667295507, ss5800402052, ss5848818043, ss5907349509	NC_000001.11:21772446:C:T	NC_000001.11:21772446:C:T	(self)
ss16041262, ss18404532	NT_004610.16:2902189:C:T	NC_000001.11:21772446:C:T	(self)
ss137838698, ss154750569	NT_004610.19:8779027:C:T	NC_000001.11:21772446:C:T	(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 rs10917041

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

rs10917041