Name: rs10919
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.

rs10919

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:156035640 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.487302 (128984/264690, TOPMED)
C=0.495748 (68552/138280, GnomAD)
G=0.17483 (4940/28256, 14KJPN) (+ 10 more)
G=0.17440 (2923/16760, 8.3KJPN)
G=0.3142 (3020/9612, ALFA)
G=0.3944 (2526/6404, 1000G_30x)
G=0.3938 (1972/5008, 1000G)
G=0.1385 (401/2896, KOREAN)
C=0.362 (361/998, GoNL)
C=0.387 (232/600, NorthernSweden)
C=0.298 (102/342, SGDP_PRJ)
C=0.472 (102/216, Qatari)
C=0.30 (12/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: UBQLN4 : 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	9612	C=0.6858	G=0.3142
European	Sub	7672	C=0.6068	G=0.3932
African	Sub	1440	C=1.0000	G=0.0000
African Others	Sub	74	C=1.00	G=0.00
African American	Sub	1366	C=1.0000	G=0.0000
Asian	Sub	94	C=1.00	G=0.00
East Asian	Sub	72	C=1.00	G=0.00
Other Asian	Sub	22	C=1.00	G=0.00
Latin American 1	Sub	32	C=1.00	G=0.00
Latin American 2	Sub	174	C=1.000	G=0.000
South Asian	Sub	20	C=1.00	G=0.00
Other	Sub	180	C=0.983	G=0.017

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	C=0.512698	G=0.487302
gnomAD - Genomes	Global	Study-wide	138280	C=0.495748	G=0.504252
gnomAD - Genomes	European	Sub	74834	C=0.38560	G=0.61440
gnomAD - Genomes	African	Sub	41494	C=0.68617	G=0.31383
gnomAD - Genomes	American	Sub	13434	C=0.45757	G=0.54243
gnomAD - Genomes	Ashkenazi Jewish	Sub	3288	C=0.4161	G=0.5839
gnomAD - Genomes	East Asian	Sub	3098	C=0.8618	G=0.1382
gnomAD - Genomes	Other	Sub	2132	C=0.4873	G=0.5127
14KJPN	JAPANESE	Study-wide	28256	C=0.82517	G=0.17483
8.3KJPN	JAPANESE	Study-wide	16760	C=0.82560	G=0.17440
Allele Frequency Aggregator	Total	Global	9612	C=0.6858	G=0.3142
Allele Frequency Aggregator	European	Sub	7672	C=0.6068	G=0.3932
Allele Frequency Aggregator	African	Sub	1440	C=1.0000	G=0.0000
Allele Frequency Aggregator	Other	Sub	180	C=0.983	G=0.017
Allele Frequency Aggregator	Latin American 2	Sub	174	C=1.000	G=0.000
Allele Frequency Aggregator	Asian	Sub	94	C=1.00	G=0.00
Allele Frequency Aggregator	Latin American 1	Sub	32	C=1.00	G=0.00
Allele Frequency Aggregator	South Asian	Sub	20	C=1.00	G=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.6056	G=0.3944
1000Genomes_30x	African	Sub	1786	C=0.7721	G=0.2279
1000Genomes_30x	Europe	Sub	1266	C=0.3965	G=0.6035
1000Genomes_30x	South Asian	Sub	1202	C=0.4459	G=0.5541
1000Genomes_30x	East Asian	Sub	1170	C=0.8667	G=0.1333
1000Genomes_30x	American	Sub	980	C=0.456	G=0.544
1000Genomes	Global	Study-wide	5008	C=0.6062	G=0.3938
1000Genomes	African	Sub	1322	C=0.7670	G=0.2330
1000Genomes	East Asian	Sub	1008	C=0.8571	G=0.1429
1000Genomes	Europe	Sub	1006	C=0.3976	G=0.6024
1000Genomes	South Asian	Sub	978	C=0.448	G=0.552
1000Genomes	American	Sub	694	C=0.461	G=0.539
KOREAN population from KRGDB	KOREAN	Study-wide	2896	C=0.8615	G=0.1385
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.362	G=0.638
Northern Sweden	ACPOP	Study-wide	600	C=0.387	G=0.613
SGDP_PRJ	Global	Study-wide	342	C=0.298	G=0.702
Qatari	Global	Study-wide	216	C=0.472	G=0.528
The Danish reference pan genome	Danish	Study-wide	40	C=0.30	G=0.70

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.156035640C>G
GRCh37.p13 chr 1	NC_000001.10:g.156005431C>G

Gene: UBQLN4, ubiquilin 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UBQLN4 transcript variant 1	NM_020131.5:c.*1338=	N/A	3 Prime UTR Variant
UBQLN4 transcript variant 2	NM_001304342.2:c.*1338=	N/A	3 Prime UTR Variant
UBQLN4 transcript variant X1	XM_024448469.2:c.1654-236… XM_024448469.2:c.1654-2364G>C	N/A	Intron Variant
UBQLN4 transcript variant X3	XM_047425666.1:c.*1338=	N/A	3 Prime UTR Variant
UBQLN4 transcript variant X2	XM_005245348.5:c.	N/A	Genic Downstream Transcript Variant
UBQLN4 transcript variant X4	XR_007061984.1:n.	N/A	Genic Downstream 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=	G
GRCh38.p14 chr 1	NC_000001.11:g.156035640=	NC_000001.11:g.156035640C>G
GRCh37.p13 chr 1	NC_000001.10:g.156005431=	NC_000001.10:g.156005431C>G
UBQLN4 transcript variant 1	NM_020131.5:c.*1338=	NM_020131.5:c.*1338G>C
UBQLN4 transcript variant 1	NM_020131.4:c.*1338=	NM_020131.4:c.*1338G>C
UBQLN4 transcript	NM_020131.3:c.*1338=	NM_020131.3:c.*1338G>C
UBQLN4 transcript variant 2	NM_001304342.2:c.*1338=	NM_001304342.2:c.*1338G>C
UBQLN4 transcript variant 2	NM_001304342.1:c.*1338=	NM_001304342.1:c.*1338G>C
UBQLN4 transcript variant X3	XM_047425666.1:c.*1338=	XM_047425666.1:c.*1338G>C
UBQLN4 transcript variant X2	XM_005245347.1:c.1654-2364=	XM_005245347.1:c.1654-2364G>C
UBQLN4 transcript variant X1	XM_024448469.2:c.1654-2364=	XM_024448469.2:c.1654-2364G>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#.

54 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	LEE	ss1524307	Oct 04, 2000 (86)
2	LEE	ss4415225	May 29, 2002 (106)
3	BCM_SSAHASNP	ss9889964	Jul 11, 2003 (116)
4	BCM_SSAHASNP	ss13539968	Dec 05, 2003 (120)
5	SEQUENOM	ss24790887	Sep 21, 2004 (123)
6	SEQUENOM	ss24816732	Sep 21, 2004 (123)
7	SSAHASNP	ss35163025	May 24, 2005 (125)
8	ABI	ss41058362	Mar 14, 2006 (126)
9	SI_EXO	ss76897982	Dec 07, 2007 (144)
10	HGSV	ss77448402	Dec 06, 2007 (129)
11	BCMHGSC_JDW	ss87826892	Mar 23, 2008 (129)
12	HUMANGENOME_JCVI	ss99251725	Feb 04, 2009 (130)
13	BGI	ss102786313	Dec 01, 2009 (131)
14	ENSEMBL	ss144372892	Dec 01, 2009 (131)
15	BL	ss253514290	May 09, 2011 (144)
16	GMI	ss276053687	May 04, 2012 (144)
17	PJP	ss290638431	May 09, 2011 (144)
18	TISHKOFF	ss554710207	Apr 25, 2013 (144)
19	SSMP	ss648418926	Apr 25, 2013 (144)
20	EVA-GONL	ss975690991	Aug 21, 2014 (144)
21	1000GENOMES	ss1292961528	Aug 21, 2014 (144)
22	DDI	ss1425980532	Apr 01, 2015 (144)
23	EVA_GENOME_DK	ss1574396179	Apr 01, 2015 (144)
24	WEILL_CORNELL_DGM	ss1918924577	Feb 12, 2016 (147)
25	JJLAB	ss2019977334	Sep 14, 2016 (149)
26	ILLUMINA	ss2094849700	Dec 20, 2016 (150)
27	GRF	ss2697975487	Nov 08, 2017 (151)
28	GNOMAD	ss2761429788	Nov 08, 2017 (151)
29	SWEGEN	ss2987767371	Nov 08, 2017 (151)
30	CSHL	ss3343713793	Nov 08, 2017 (151)
31	OMUKHERJEE_ADBS	ss3646246433	Oct 11, 2018 (152)
32	URBANLAB	ss3646792955	Oct 11, 2018 (152)
33	ACPOP	ss3727492288	Jul 12, 2019 (153)
34	PACBIO	ss3783568892	Jul 12, 2019 (153)
35	PACBIO	ss3789199778	Jul 12, 2019 (153)
36	PACBIO	ss3794071783	Jul 12, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3799818360	Jul 12, 2019 (153)
38	EVA	ss3836608513	Apr 25, 2020 (154)
39	EVA	ss3842017786	Apr 25, 2020 (154)
40	SGDP_PRJ	ss3850023678	Apr 25, 2020 (154)
41	KRGDB	ss3895237569	Apr 25, 2020 (154)
42	FSA-LAB	ss3983948010	Apr 25, 2021 (155)
43	FSA-LAB	ss3983948011	Apr 25, 2021 (155)
44	EVA	ss3986013266	Apr 25, 2021 (155)
45	TOPMED	ss4468649065	Apr 25, 2021 (155)
46	TOMMO_GENOMICS	ss5146531048	Apr 25, 2021 (155)
47	1000G_HIGH_COVERAGE	ss5244325110	Oct 12, 2022 (156)
48	EVA	ss5322109188	Oct 12, 2022 (156)
49	EVA	ss5506031684	Oct 12, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5517669562	Oct 12, 2022 (156)
51	SANFORD_IMAGENETICS	ss5626608005	Oct 12, 2022 (156)
52	TOMMO_GENOMICS	ss5673743603	Oct 12, 2022 (156)
53	YY_MCH	ss5801267114	Oct 12, 2022 (156)
54	EVA	ss5832677036	Oct 12, 2022 (156)
55	1000Genomes	NC_000001.10 - 156005431	Oct 11, 2018 (152)
56	1000Genomes_30x	NC_000001.11 - 156035640	Oct 12, 2022 (156)
57	The Danish reference pan genome	NC_000001.10 - 156005431	Apr 25, 2020 (154)
58	gnomAD - Genomes	NC_000001.11 - 156035640	Apr 25, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000001.10 - 156005431	Apr 25, 2020 (154)
60	KOREAN population from KRGDB	NC_000001.10 - 156005431	Apr 25, 2020 (154)
61	Northern Sweden	NC_000001.10 - 156005431	Jul 12, 2019 (153)
62	Qatari	NC_000001.10 - 156005431	Apr 25, 2020 (154)
63	SGDP_PRJ	NC_000001.10 - 156005431	Apr 25, 2020 (154)
64	8.3KJPN	NC_000001.10 - 156005431	Apr 25, 2021 (155)
65	14KJPN	NC_000001.11 - 156035640	Oct 12, 2022 (156)
66	TopMed	NC_000001.11 - 156035640	Apr 25, 2021 (155)
67	ALFA	NC_000001.11 - 156035640	Apr 25, 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).

Associated ID	History Updated (Build)
rs3190308	Jul 03, 2002 (106)
rs9728822	Feb 27, 2004 (120)
rs13071797	Dec 02, 2004 (124)
rs28508442	May 23, 2008 (130)
rs56061854	Jul 01, 2015 (144)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss35163025, ss77448402	NC_000001.8:152818503:C:G	NC_000001.11:156035639:C:G	(self)
ss87826892, ss253514290, ss276053687, ss290638431, ss2094849700	NC_000001.9:154272054:C:G	NC_000001.11:156035639:C:G	(self)
3754830, 1711200, 886008, 2414963, 777153, 966507, 2040658, 4500355, ss554710207, ss648418926, ss975690991, ss1292961528, ss1425980532, ss1574396179, ss1918924577, ss2019977334, ss2697975487, ss2761429788, ss2987767371, ss3343713793, ss3646246433, ss3727492288, ss3783568892, ss3789199778, ss3794071783, ss3836608513, ss3850023678, ss3895237569, ss3983948010, ss3983948011, ss3986013266, ss5146531048, ss5322109188, ss5506031684, ss5626608005, ss5832677036	NC_000001.10:156005430:C:G	NC_000001.11:156035639:C:G	(self)
5195497, 27344822, 7580707, 32255400, 2998983605, ss3646792955, ss3799818360, ss3842017786, ss4468649065, ss5244325110, ss5517669562, ss5673743603, ss5801267114	NC_000001.11:156035639:C:G	NC_000001.11:156035639:C:G	(self)
ss76897982	NT_004487.18:6495785:C:G	NC_000001.11:156035639:C:G	(self)
ss1524307, ss4415225, ss24790887, ss24816732, ss41058362, ss99251725, ss102786313, ss144372892	NT_004487.19:7494072:C:G	NC_000001.11:156035639:C:G	(self)
ss9889964	NT_004668.15:2457831:C:G	NC_000001.11:156035639:C:G	(self)
ss13539968	NT_079484.1:2455262:C:G	NC_000001.11:156035639:C: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 rs10919

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

rs10919