Name: rs76172507
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.

rs76172507

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:43105976 (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: G>A / G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.004477 (1185/264690, TOPMED)
A=0.000286 (54/188872, ALFA)
A=0.00661 (520/78702, PAGE_STUDY) (+ 8 more)
A=0.00011 (3/28258, 14KJPN)
A=0.00018 (3/16760, 8.3KJPN)
A=0.00515 (67/13004, GO-ESP)
A=0.0061 (39/6404, 1000G_30x)
A=0.0054 (27/5008, 1000G)
A=0.0005 (1/1832, Korea1K)
G=0.5 (2/4, SGDP_PRJ)
A=0.5 (2/4, SGDP_PRJ)

Clinical Significance: Reported in ClinVar
Gene : Consequence: UBR1 : Missense 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	188872	G=0.999714	A=0.000286, C=0.000000, T=0.000000
European	Sub	159580	G=0.999969	A=0.000031, C=0.000000, T=0.000000
African	Sub	5332	G=0.9929	A=0.0071, C=0.0000, T=0.0000
African Others	Sub	174	G=0.989	A=0.011, C=0.000, T=0.000
African American	Sub	5158	G=0.9930	A=0.0070, C=0.0000, T=0.0000
Asian	Sub	6380	G=1.0000	A=0.0000, C=0.0000, T=0.0000
East Asian	Sub	4526	G=1.0000	A=0.0000, C=0.0000, T=0.0000
Other Asian	Sub	1854	G=1.0000	A=0.0000, C=0.0000, T=0.0000
Latin American 1	Sub	828	G=0.996	A=0.004, C=0.000, T=0.000
Latin American 2	Sub	1080	G=1.0000	A=0.0000, C=0.0000, T=0.0000
South Asian	Sub	312	G=1.000	A=0.000, C=0.000, T=0.000
Other	Sub	15360	G=0.99948	A=0.00052, C=0.00000, T=0.00000

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	G=0.995523	A=0.004477
Allele Frequency Aggregator	Total	Global	188872	G=0.999714	A=0.000286, C=0.000000, T=0.000000
Allele Frequency Aggregator	European	Sub	159580	G=0.999969	A=0.000031, C=0.000000, T=0.000000
Allele Frequency Aggregator	Other	Sub	15360	G=0.99948	A=0.00052, C=0.00000, T=0.00000
Allele Frequency Aggregator	Asian	Sub	6380	G=1.0000	A=0.0000, C=0.0000, T=0.0000
Allele Frequency Aggregator	African	Sub	5332	G=0.9929	A=0.0071, C=0.0000, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	1080	G=1.0000	A=0.0000, C=0.0000, T=0.0000
Allele Frequency Aggregator	Latin American 1	Sub	828	G=0.996	A=0.004, C=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	312	G=1.000	A=0.000, C=0.000, T=0.000
The PAGE Study	Global	Study-wide	78702	G=0.99339	A=0.00661
The PAGE Study	AfricanAmerican	Sub	32516	G=0.98635	A=0.01365
The PAGE Study	Mexican	Sub	10810	G=0.99954	A=0.00046
The PAGE Study	Asian	Sub	8318	G=1.0000	A=0.0000
The PAGE Study	PuertoRican	Sub	7918	G=0.9984	A=0.0016
The PAGE Study	NativeHawaiian	Sub	4534	G=1.0000	A=0.0000
The PAGE Study	Cuban	Sub	4230	G=0.9974	A=0.0026
The PAGE Study	Dominican	Sub	3828	G=0.9911	A=0.0089
The PAGE Study	CentralAmerican	Sub	2450	G=0.9971	A=0.0029
The PAGE Study	SouthAmerican	Sub	1982	G=0.9985	A=0.0015
The PAGE Study	NativeAmerican	Sub	1260	G=0.9976	A=0.0024
The PAGE Study	SouthAsian	Sub	856	G=1.000	A=0.000
14KJPN	JAPANESE	Study-wide	28258	G=0.99989	A=0.00011
8.3KJPN	JAPANESE	Study-wide	16760	G=0.99982	A=0.00018
GO Exome Sequencing Project	Global	Study-wide	13004	G=0.99485	A=0.00515
GO Exome Sequencing Project	European American	Sub	8598	G=1.0000	A=0.0000
GO Exome Sequencing Project	African American	Sub	4406	G=0.9848	A=0.0152
1000Genomes_30x	Global	Study-wide	6404	G=0.9939	A=0.0061
1000Genomes_30x	African	Sub	1786	G=0.9787	A=0.0213
1000Genomes_30x	Europe	Sub	1266	G=1.0000	A=0.0000
1000Genomes_30x	South Asian	Sub	1202	G=1.0000	A=0.0000
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	G=0.999	A=0.001
1000Genomes	Global	Study-wide	5008	G=0.9946	A=0.0054
1000Genomes	African	Sub	1322	G=0.9803	A=0.0197
1000Genomes	East Asian	Sub	1008	G=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	G=1.0000	A=0.0000
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
1000Genomes	American	Sub	694	G=0.999	A=0.001
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9995	A=0.0005
SGDP_PRJ	Global	Study-wide	4	G=0.5	A=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 15	NC_000015.10:g.43105976G>A
GRCh38.p14 chr 15	NC_000015.10:g.43105976G>C
GRCh38.p14 chr 15	NC_000015.10:g.43105976G>T
GRCh37.p13 chr 15	NC_000015.9:g.43398174G>A
GRCh37.p13 chr 15	NC_000015.9:g.43398174G>C
GRCh37.p13 chr 15	NC_000015.9:g.43398174G>T
UBR1 RefSeqGene	NG_012182.1:g.5113C>T
UBR1 RefSeqGene	NG_012182.1:g.5113C>G
UBR1 RefSeqGene	NG_012182.1:g.5113C>A

Gene: UBR1, ubiquitin protein ligase E3 component n-recognin 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UBR1 transcript	NM_174916.3:c.47C>T	A [GCG] > V [GTG]	Coding Sequence Variant
E3 ubiquitin-protein ligase UBR1	NP_777576.1:p.Ala16Val	A (Ala) > V (Val)	Missense Variant
UBR1 transcript	NM_174916.3:c.47C>G	A [GCG] > G [GGG]	Coding Sequence Variant
E3 ubiquitin-protein ligase UBR1	NP_777576.1:p.Ala16Gly	A (Ala) > G (Gly)	Missense Variant
UBR1 transcript	NM_174916.3:c.47C>A	A [GCG] > E [GAG]	Coding Sequence Variant
E3 ubiquitin-protein ligase UBR1	NP_777576.1:p.Ala16Glu	A (Ala) > E (Glu)	Missense 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: A (allele ID: 726077 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000886850.5	not provided	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=	A	C	T
GRCh38.p14 chr 15	NC_000015.10:g.43105976=	NC_000015.10:g.43105976G>A	NC_000015.10:g.43105976G>C	NC_000015.10:g.43105976G>T
GRCh37.p13 chr 15	NC_000015.9:g.43398174=	NC_000015.9:g.43398174G>A	NC_000015.9:g.43398174G>C	NC_000015.9:g.43398174G>T
UBR1 RefSeqGene	NG_012182.1:g.5113=	NG_012182.1:g.5113C>T	NG_012182.1:g.5113C>G	NG_012182.1:g.5113C>A
UBR1 transcript	NM_174916.3:c.47=	NM_174916.3:c.47C>T	NM_174916.3:c.47C>G	NM_174916.3:c.47C>A
UBR1 transcript	NM_174916.2:c.47=	NM_174916.2:c.47C>T	NM_174916.2:c.47C>G	NM_174916.2:c.47C>A
E3 ubiquitin-protein ligase UBR1	NP_777576.1:p.Ala16=	NP_777576.1:p.Ala16Val	NP_777576.1:p.Ala16Gly	NP_777576.1:p.Ala16Glu

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, 17 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	ILLUMINA	ss161050958	Dec 01, 2009 (131)
2	1000GENOMES	ss226863613	Jul 14, 2010 (132)
3	NHLBI-ESP	ss342401558	May 09, 2011 (134)
4	ILLUMINA	ss479266212	Sep 08, 2015 (146)
5	ILLUMINA	ss482021077	May 04, 2012 (137)
6	ILLUMINA	ss483394167	May 04, 2012 (137)
7	1000GENOMES	ss491081482	May 04, 2012 (137)
8	EXOME_CHIP	ss491493449	May 04, 2012 (137)
9	ILLUMINA	ss534471528	Sep 08, 2015 (146)
10	TISHKOFF	ss564445809	Apr 25, 2013 (138)
11	ILLUMINA	ss781627606	Sep 08, 2015 (146)
12	ILLUMINA	ss834127152	Sep 08, 2015 (146)
13	1000GENOMES	ss1353224409	Aug 21, 2014 (142)
14	EVA_EXAC	ss1691791913	Apr 01, 2015 (144)
15	EVA_EXAC	ss1691791914	Apr 01, 2015 (144)
16	ILLUMINA	ss1752160163	Sep 08, 2015 (146)
17	ILLUMINA	ss1917895538	Feb 12, 2016 (147)
18	ILLUMINA	ss1946391880	Feb 12, 2016 (147)
19	ILLUMINA	ss1959607772	Feb 12, 2016 (147)
20	HUMAN_LONGEVITY	ss2206297163	Dec 20, 2016 (150)
21	ILLUMINA	ss2633221999	Nov 08, 2017 (151)
22	GNOMAD	ss2741188080	Nov 08, 2017 (151)
23	GNOMAD	ss2749288323	Nov 08, 2017 (151)
24	GNOMAD	ss2934201749	Nov 08, 2017 (151)
25	AFFY	ss2985039621	Nov 08, 2017 (151)
26	ILLUMINA	ss3021627395	Nov 08, 2017 (151)
27	ILLUMINA	ss3627347702	Oct 12, 2018 (152)
28	ILLUMINA	ss3631215460	Oct 12, 2018 (152)
29	ILLUMINA	ss3634603723	Oct 12, 2018 (152)
30	ILLUMINA	ss3636293788	Oct 12, 2018 (152)
31	ILLUMINA	ss3640311047	Oct 12, 2018 (152)
32	ILLUMINA	ss3644644988	Oct 12, 2018 (152)
33	ILLUMINA	ss3652027632	Oct 12, 2018 (152)
34	ILLUMINA	ss3653811033	Oct 12, 2018 (152)
35	ILLUMINA	ss3725494476	Jul 13, 2019 (153)
36	ILLUMINA	ss3744419097	Jul 13, 2019 (153)
37	ILLUMINA	ss3744904270	Jul 13, 2019 (153)
38	PAGE_CC	ss3771826210	Jul 13, 2019 (153)
39	ILLUMINA	ss3772402935	Jul 13, 2019 (153)
40	EVA	ss3824912117	Apr 27, 2020 (154)
41	SGDP_PRJ	ss3882792723	Apr 27, 2020 (154)
42	KOGIC	ss3976021772	Apr 27, 2020 (154)
43	TOPMED	ss4989222951	Apr 26, 2021 (155)
44	TOMMO_GENOMICS	ss5215909166	Apr 26, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5298232690	Oct 16, 2022 (156)
46	EVA	ss5418852235	Oct 16, 2022 (156)
47	HUGCELL_USP	ss5491985469	Oct 16, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5599527318	Oct 16, 2022 (156)
49	SANFORD_IMAGENETICS	ss5657391890	Oct 16, 2022 (156)
50	TOMMO_GENOMICS	ss5769630784	Oct 16, 2022 (156)
51	EVA	ss5847740579	Oct 16, 2022 (156)
52	EVA	ss5875638525	Oct 16, 2022 (156)
53	EVA	ss5948789261	Oct 16, 2022 (156)
54	EVA	ss5979459075	Oct 16, 2022 (156)
55	1000Genomes	NC_000015.9 - 43398174	Oct 12, 2018 (152)
56	1000Genomes_30x	NC_000015.10 - 43105976	Oct 16, 2022 (156)
57	ExAC Submission ignored due to conflicting rows: Row 2162605 (NC_000015.9:43398173:G:G 118546/118696, NC_000015.9:43398173:G:A 150/118696) Row 2162606 (NC_000015.9:43398173:G:G 118695/118696, NC_000015.9:43398173:G:T 1/118696)	-	Oct 12, 2018 (152)
58	ExAC Submission ignored due to conflicting rows: Row 2162605 (NC_000015.9:43398173:G:G 118546/118696, NC_000015.9:43398173:G:A 150/118696) Row 2162606 (NC_000015.9:43398173:G:G 118695/118696, NC_000015.9:43398173:G:T 1/118696)	-	Oct 12, 2018 (152)
59	gnomAD - Genomes Submission ignored due to conflicting rows: Row 467277281 (NC_000015.10:43105975:G:A 627/140134) Row 467277282 (NC_000015.10:43105975:G:C 1/140138) Row 467277283 (NC_000015.10:43105975:G:T 0/140138)	-	Apr 26, 2021 (155)
60	gnomAD - Genomes Submission ignored due to conflicting rows: Row 467277281 (NC_000015.10:43105975:G:A 627/140134) Row 467277282 (NC_000015.10:43105975:G:C 1/140138) Row 467277283 (NC_000015.10:43105975:G:T 0/140138)	-	Apr 26, 2021 (155)
61	gnomAD - Genomes Submission ignored due to conflicting rows: Row 467277281 (NC_000015.10:43105975:G:A 627/140134) Row 467277282 (NC_000015.10:43105975:G:C 1/140138) Row 467277283 (NC_000015.10:43105975:G:T 0/140138)	-	Apr 26, 2021 (155)
62	gnomAD - Exomes Submission ignored due to conflicting rows: Row 10451654 (NC_000015.9:43398173:G:G 250608/250886, NC_000015.9:43398173:G:A 278/250886) Row 10451655 (NC_000015.9:43398173:G:G 250885/250886, NC_000015.9:43398173:G:T 1/250886)	-	Jul 13, 2019 (153)
63	gnomAD - Exomes Submission ignored due to conflicting rows: Row 10451654 (NC_000015.9:43398173:G:G 250608/250886, NC_000015.9:43398173:G:A 278/250886) Row 10451655 (NC_000015.9:43398173:G:G 250885/250886, NC_000015.9:43398173:G:T 1/250886)	-	Jul 13, 2019 (153)
64	GO Exome Sequencing Project	NC_000015.9 - 43398174	Oct 12, 2018 (152)
65	Korean Genome Project	NC_000015.10 - 43105976	Apr 27, 2020 (154)
66	The PAGE Study	NC_000015.10 - 43105976	Jul 13, 2019 (153)
67	SGDP_PRJ	NC_000015.9 - 43398174	Apr 27, 2020 (154)
68	8.3KJPN	NC_000015.9 - 43398174	Apr 26, 2021 (155)
69	14KJPN	NC_000015.10 - 43105976	Oct 16, 2022 (156)
70	TopMed	NC_000015.10 - 43105976	Apr 26, 2021 (155)
71	ALFA	NC_000015.10 - 43105976	Apr 26, 2021 (155)
72	ClinVar	RCV000886850.5	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss483394167	NC_000015.8:41185465:G:A	NC_000015.10:43105975:G:A	(self)
66287578, 1369390, 34809703, 73878473, ss226863613, ss342401558, ss479266212, ss482021077, ss491081482, ss491493449, ss534471528, ss564445809, ss781627606, ss834127152, ss1353224409, ss1691791913, ss1752160163, ss1917895538, ss1946391880, ss1959607772, ss2633221999, ss2741188080, ss2749288323, ss2934201749, ss2985039621, ss3021627395, ss3627347702, ss3631215460, ss3634603723, ss3636293788, ss3640311047, ss3644644988, ss3652027632, ss3653811033, ss3744419097, ss3744904270, ss3772402935, ss3824912117, ss3882792723, ss5215909166, ss5418852235, ss5657391890, ss5847740579, ss5948789261, ss5979459075	NC_000015.9:43398173:G:A	NC_000015.10:43105975:G:A	(self)
RCV000886850.5, 87053253, 32399773, 1047679, 103467888, 204768611, 13664177697, ss2206297163, ss3725494476, ss3771826210, ss3976021772, ss4989222951, ss5298232690, ss5491985469, ss5599527318, ss5769630784, ss5875638525	NC_000015.10:43105975:G:A	NC_000015.10:43105975:G:A	(self)
ss161050958	NT_010194.17:14188730:G:A	NC_000015.10:43105975:G:A	(self)
ss2749288323, ss2934201749	NC_000015.9:43398173:G:C	NC_000015.10:43105975:G:C	(self)
13664177697	NC_000015.10:43105975:G:C	NC_000015.10:43105975:G:C	(self)
ss1691791914, ss2741188080	NC_000015.9:43398173:G:T	NC_000015.10:43105975:G:T	(self)
13664177697	NC_000015.10:43105975:G:T	NC_000015.10:43105975:G: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 rs76172507

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

rs76172507