Name: rs73958618
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.

rs73958618

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:135742905 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.235985 (62463/264690, TOPMED)
G=0.226261 (31662/139936, GnomAD)
G=0.24759 (10985/44368, ALFA) (+ 16 more)
G=0.15367 (4342/28256, 14KJPN)
G=0.15489 (2596/16760, 8.3KJPN)
G=0.2601 (1666/6404, 1000G_30x)
G=0.2638 (1321/5008, 1000G)
G=0.2792 (1251/4480, Estonian)
G=0.1572 (606/3854, ALSPAC)
G=0.1642 (609/3708, TWINSUK)
G=0.1915 (561/2930, KOREAN)
G=0.1916 (351/1832, Korea1K)
G=0.155 (155/998, GoNL)
G=0.140 (84/600, NorthernSweden)
A=0.368 (98/266, SGDP_PRJ)
A=0.394 (85/216, Qatari)
G=0.222 (48/216, Vietnamese)
G=0.15 (6/40, GENOME_DK)
A=0.35 (14/40, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: UBXN4 : Intron Variant
LOC107985946 : 2KB Upstream 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	44368	A=0.75241	G=0.24759
European	Sub	33776	A=0.74929	G=0.25071
African	Sub	5572	A=0.7904	G=0.2096
African Others	Sub	198	A=0.768	G=0.232
African American	Sub	5374	A=0.7912	G=0.2088
Asian	Sub	112	A=0.804	G=0.196
East Asian	Sub	86	A=0.83	G=0.17
Other Asian	Sub	26	A=0.73	G=0.27
Latin American 1	Sub	146	A=0.664	G=0.336
Latin American 2	Sub	610	A=0.685	G=0.315
South Asian	Sub	98	A=0.77	G=0.23
Other	Sub	4054	A=0.7378	G=0.2622

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	A=0.764015	G=0.235985
gnomAD - Genomes	Global	Study-wide	139936	A=0.773739	G=0.226261
gnomAD - Genomes	European	Sub	75814	A=0.79282	G=0.20718
gnomAD - Genomes	African	Sub	41928	A=0.79417	G=0.20583
gnomAD - Genomes	American	Sub	13612	A=0.67257	G=0.32743
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.5220	G=0.4780
gnomAD - Genomes	East Asian	Sub	3120	A=0.7904	G=0.2096
gnomAD - Genomes	Other	Sub	2140	A=0.7075	G=0.2925
Allele Frequency Aggregator	Total	Global	44368	A=0.75241	G=0.24759
Allele Frequency Aggregator	European	Sub	33776	A=0.74929	G=0.25071
Allele Frequency Aggregator	African	Sub	5572	A=0.7904	G=0.2096
Allele Frequency Aggregator	Other	Sub	4054	A=0.7378	G=0.2622
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.685	G=0.315
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.664	G=0.336
Allele Frequency Aggregator	Asian	Sub	112	A=0.804	G=0.196
Allele Frequency Aggregator	South Asian	Sub	98	A=0.77	G=0.23
14KJPN	JAPANESE	Study-wide	28256	A=0.84633	G=0.15367
8.3KJPN	JAPANESE	Study-wide	16760	A=0.84511	G=0.15489
1000Genomes_30x	Global	Study-wide	6404	A=0.7399	G=0.2601
1000Genomes_30x	African	Sub	1786	A=0.7576	G=0.2424
1000Genomes_30x	Europe	Sub	1266	A=0.7370	G=0.2630
1000Genomes_30x	South Asian	Sub	1202	A=0.7121	G=0.2879
1000Genomes_30x	East Asian	Sub	1170	A=0.7846	G=0.2154
1000Genomes_30x	American	Sub	980	A=0.692	G=0.308
1000Genomes	Global	Study-wide	5008	A=0.7362	G=0.2638
1000Genomes	African	Sub	1322	A=0.7572	G=0.2428
1000Genomes	East Asian	Sub	1008	A=0.7907	G=0.2093
1000Genomes	Europe	Sub	1006	A=0.7147	G=0.2853
1000Genomes	South Asian	Sub	978	A=0.708	G=0.292
1000Genomes	American	Sub	694	A=0.689	G=0.311
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7208	G=0.2792
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.8428	G=0.1572
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.8358	G=0.1642
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.8085	G=0.1915
Korean Genome Project	KOREAN	Study-wide	1832	A=0.8084	G=0.1916
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.845	G=0.155
Northern Sweden	ACPOP	Study-wide	600	A=0.860	G=0.140
SGDP_PRJ	Global	Study-wide	266	A=0.368	G=0.632
Qatari	Global	Study-wide	216	A=0.394	G=0.606
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.778	G=0.222
The Danish reference pan genome	Danish	Study-wide	40	A=0.85	G=0.15
Siberian	Global	Study-wide	40	A=0.35	G=0.65

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 2	NC_000002.12:g.135742905A>G
GRCh37.p13 chr 2	NC_000002.11:g.136500475A>G

Gene: UBXN4, UBX domain protein 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UBXN4 transcript	NM_014607.4:c.82+894A>G	N/A	Intron Variant

Gene: LOC107985946, uncharacterized LOC107985946 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985946 transcript	NR_163478.1:n.	N/A	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	A=	G
GRCh38.p14 chr 2	NC_000002.12:g.135742905=	NC_000002.12:g.135742905A>G
GRCh37.p13 chr 2	NC_000002.11:g.136500475=	NC_000002.11:g.136500475A>G
LOC107985946 transcript	NM_001365239.1:c.-239=	NM_001365239.1:c.-239T>C
UBXN4 transcript	NM_014607.3:c.82+894=	NM_014607.3:c.82+894A>G
UBXN4 transcript	NM_014607.4:c.82+894=	NM_014607.4:c.82+894A>G

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, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ILLUMINA-UK	ss117888107	Feb 14, 2009 (130)
2	1000GENOMES	ss211004551	Jul 14, 2010 (132)
3	1000GENOMES	ss219528200	Jul 14, 2010 (132)
4	1000GENOMES	ss231373679	Jul 14, 2010 (132)
5	1000GENOMES	ss238880231	Jul 15, 2010 (132)
6	TISHKOFF	ss555895676	Apr 25, 2013 (138)
7	SSMP	ss649524212	Apr 25, 2013 (138)
8	EVA-GONL	ss977390431	Aug 21, 2014 (142)
9	JMKIDD_LAB	ss1069519630	Aug 21, 2014 (142)
10	1000GENOMES	ss1299457952	Aug 21, 2014 (142)
11	DDI	ss1428749912	Apr 01, 2015 (144)
12	EVA_GENOME_DK	ss1579099106	Apr 01, 2015 (144)
13	EVA_DECODE	ss1586819073	Apr 01, 2015 (144)
14	EVA_UK10K_ALSPAC	ss1604630937	Apr 01, 2015 (144)
15	EVA_UK10K_TWINSUK	ss1647624970	Apr 01, 2015 (144)
16	HAMMER_LAB	ss1797577432	Sep 08, 2015 (146)
17	WEILL_CORNELL_DGM	ss1920649546	Feb 12, 2016 (147)
18	GENOMED	ss1968895931	Jul 19, 2016 (147)
19	JJLAB	ss2020847903	Sep 14, 2016 (149)
20	USC_VALOUEV	ss2148914635	Dec 20, 2016 (150)
21	HUMAN_LONGEVITY	ss2234541899	Dec 20, 2016 (150)
22	SYSTEMSBIOZJU	ss2624930338	Nov 08, 2017 (151)
23	GRF	ss2703539690	Nov 08, 2017 (151)
24	GNOMAD	ss2780034278	Nov 08, 2017 (151)
25	SWEGEN	ss2990480540	Nov 08, 2017 (151)
26	BIOINF_KMB_FNS_UNIBA	ss3024187352	Nov 08, 2017 (151)
27	CSHL	ss3344495419	Nov 08, 2017 (151)
28	EGCUT_WGS	ss3658323649	Jul 13, 2019 (153)
29	EVA_DECODE	ss3704953730	Jul 13, 2019 (153)
30	ACPOP	ss3728894481	Jul 13, 2019 (153)
31	ILLUMINA	ss3744480742	Jul 13, 2019 (153)
32	EVA	ss3757421439	Jul 13, 2019 (153)
33	PACBIO	ss3784002395	Jul 13, 2019 (153)
34	PACBIO	ss3789564529	Jul 13, 2019 (153)
35	PACBIO	ss3794437450	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3801788457	Jul 13, 2019 (153)
37	EVA	ss3827236404	Apr 25, 2020 (154)
38	SGDP_PRJ	ss3853482669	Apr 25, 2020 (154)
39	KRGDB	ss3899046232	Apr 25, 2020 (154)
40	KOGIC	ss3949034638	Apr 25, 2020 (154)
41	TOPMED	ss4525066365	Apr 27, 2021 (155)
42	TOMMO_GENOMICS	ss5154017313	Apr 27, 2021 (155)
43	1000G_HIGH_COVERAGE	ss5250130287	Oct 12, 2022 (156)
44	HUGCELL_USP	ss5449930382	Oct 12, 2022 (156)
45	EVA	ss5506600193	Oct 12, 2022 (156)
46	1000G_HIGH_COVERAGE	ss5526457245	Oct 12, 2022 (156)
47	SANFORD_IMAGENETICS	ss5629873792	Oct 12, 2022 (156)
48	TOMMO_GENOMICS	ss5684187512	Oct 12, 2022 (156)
49	YY_MCH	ss5802751992	Oct 12, 2022 (156)
50	EVA	ss5820849962	Oct 12, 2022 (156)
51	EVA	ss5852727331	Oct 12, 2022 (156)
52	EVA	ss5932501329	Oct 12, 2022 (156)
53	EVA	ss5956074875	Oct 12, 2022 (156)
54	EVA	ss5980085007	Oct 12, 2022 (156)
55	1000Genomes	NC_000002.11 - 136500475	Oct 11, 2018 (152)
56	1000Genomes_30x	NC_000002.12 - 135742905	Oct 12, 2022 (156)
57	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 136500475	Oct 11, 2018 (152)
58	Genetic variation in the Estonian population	NC_000002.11 - 136500475	Oct 11, 2018 (152)
59	The Danish reference pan genome	NC_000002.11 - 136500475	Apr 25, 2020 (154)
60	gnomAD - Genomes	NC_000002.12 - 135742905	Apr 27, 2021 (155)
61	Genome of the Netherlands Release 5	NC_000002.11 - 136500475	Apr 25, 2020 (154)
62	KOREAN population from KRGDB	NC_000002.11 - 136500475	Apr 25, 2020 (154)
63	Korean Genome Project	NC_000002.12 - 135742905	Apr 25, 2020 (154)
64	Northern Sweden	NC_000002.11 - 136500475	Jul 13, 2019 (153)
65	Qatari	NC_000002.11 - 136500475	Apr 25, 2020 (154)
66	SGDP_PRJ	NC_000002.11 - 136500475	Apr 25, 2020 (154)
67	Siberian	NC_000002.11 - 136500475	Apr 25, 2020 (154)
68	8.3KJPN	NC_000002.11 - 136500475	Apr 27, 2021 (155)
69	14KJPN	NC_000002.12 - 135742905	Oct 12, 2022 (156)
70	TopMed	NC_000002.12 - 135742905	Apr 27, 2021 (155)
71	UK 10K study - Twins	NC_000002.11 - 136500475	Oct 11, 2018 (152)
72	A Vietnamese Genetic Variation Database	NC_000002.11 - 136500475	Jul 13, 2019 (153)
73	ALFA	NC_000002.12 - 135742905	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
ss117888107, ss211004551, ss1586819073	NC_000002.10:136216944:A:G	NC_000002.12:135742904:A:G	(self)
10478444, 5769570, 4061897, 5264045, 2536292, 6223626, 2179346, 2691476, 5499649, 1430989, 11986620, 5769570, 1248554, ss219528200, ss231373679, ss238880231, ss555895676, ss649524212, ss977390431, ss1069519630, ss1299457952, ss1428749912, ss1579099106, ss1604630937, ss1647624970, ss1797577432, ss1920649546, ss1968895931, ss2020847903, ss2148914635, ss2624930338, ss2703539690, ss2780034278, ss2990480540, ss3344495419, ss3658323649, ss3728894481, ss3744480742, ss3757421439, ss3784002395, ss3789564529, ss3794437450, ss3827236404, ss3853482669, ss3899046232, ss5154017313, ss5506600193, ss5629873792, ss5820849962, ss5956074875, ss5980085007	NC_000002.11:136500474:A:G	NC_000002.12:135742904:A:G	(self)
13983180, 74709503, 5412639, 18024616, 328889244, 579132644, ss2234541899, ss3024187352, ss3704953730, ss3801788457, ss3949034638, ss4525066365, ss5250130287, ss5449930382, ss5526457245, ss5684187512, ss5802751992, ss5852727331, ss5932501329	NC_000002.12:135742904:A:G	NC_000002.12:135742904:A: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 rs73958618

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

rs73958618