Name: rs73810453
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.

rs73810453

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:41992690 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.051543 (13643/264690, TOPMED)
T=0.048980 (6863/140118, GnomAD)
T=0.04330 (818/18890, ALFA) (+ 9 more)
T=0.0437 (219/5008, 1000G)
T=0.0170 (76/4480, Estonian)
T=0.0439 (169/3854, ALSPAC)
T=0.0456 (169/3708, TWINSUK)
T=0.0003 (1/2922, KOREAN)
T=0.033 (20/600, NorthernSweden)
T=0.079 (17/216, Qatari)
A=0.48 (22/46, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC30A9 : 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	A=0.95670	T=0.04330
European	Sub	14286	A=0.96521	T=0.03479
African	Sub	2946	A=0.9179	T=0.0821
African Others	Sub	114	A=0.895	T=0.105
African American	Sub	2832	A=0.9188	T=0.0812
Asian	Sub	112	A=0.991	T=0.009
East Asian	Sub	86	A=1.00	T=0.00
Other Asian	Sub	26	A=0.96	T=0.04
Latin American 1	Sub	146	A=0.918	T=0.082
Latin American 2	Sub	610	A=0.974	T=0.026
South Asian	Sub	98	A=0.94	T=0.06
Other	Sub	692	A=0.936	T=0.064

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	A=0.948457	T=0.051543
gnomAD - Genomes	Global	Study-wide	140118	A=0.951020	T=0.048980
gnomAD - Genomes	European	Sub	75890	A=0.96411	T=0.03589
gnomAD - Genomes	African	Sub	41990	A=0.92339	T=0.07661
gnomAD - Genomes	American	Sub	13632	A=0.96332	T=0.03668
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.9106	T=0.0894
gnomAD - Genomes	East Asian	Sub	3132	A=0.9997	T=0.0003
gnomAD - Genomes	Other	Sub	2150	A=0.9423	T=0.0577
Allele Frequency Aggregator	Total	Global	18890	A=0.95670	T=0.04330
Allele Frequency Aggregator	European	Sub	14286	A=0.96521	T=0.03479
Allele Frequency Aggregator	African	Sub	2946	A=0.9179	T=0.0821
Allele Frequency Aggregator	Other	Sub	692	A=0.936	T=0.064
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.974	T=0.026
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.918	T=0.082
Allele Frequency Aggregator	Asian	Sub	112	A=0.991	T=0.009
Allele Frequency Aggregator	South Asian	Sub	98	A=0.94	T=0.06
1000Genomes	Global	Study-wide	5008	A=0.9563	T=0.0437
1000Genomes	African	Sub	1322	A=0.9130	T=0.0870
1000Genomes	East Asian	Sub	1008	A=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	A=0.9612	T=0.0388
1000Genomes	South Asian	Sub	978	A=0.962	T=0.038
1000Genomes	American	Sub	694	A=0.960	T=0.040
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9830	T=0.0170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9561	T=0.0439
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9544	T=0.0456
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.9997	T=0.0003
Northern Sweden	ACPOP	Study-wide	600	A=0.967	T=0.033
Qatari	Global	Study-wide	216	A=0.921	T=0.079
SGDP_PRJ	Global	Study-wide	46	A=0.48	T=0.52
The Danish reference pan genome	Danish	Study-wide	40	A=0.97	T=0.03

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 4	NC_000004.12:g.41992690A>T
GRCh37.p13 chr 4	NC_000004.11:g.41994707A>T

Gene: SLC30A9, solute carrier family 30 member 9 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC30A9 transcript	NM_006345.4:c.109+1930A>T	N/A	Intron Variant
SLC30A9 transcript variant X1	XM_047449525.1:c.109+1930… XM_047449525.1:c.109+1930A>T	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.

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=	T
GRCh38.p14 chr 4	NC_000004.12:g.41992690=	NC_000004.12:g.41992690A>T
GRCh37.p13 chr 4	NC_000004.11:g.41994707=	NC_000004.11:g.41994707A>T
SLC30A9 transcript	NM_006345.3:c.109+1930=	NM_006345.3:c.109+1930A>T
SLC30A9 transcript	NM_006345.4:c.109+1930=	NM_006345.4:c.109+1930A>T
SLC30A9 transcript variant X1	XM_005248044.1:c.109+1930=	XM_005248044.1:c.109+1930A>T
SLC30A9 transcript variant X2	XM_005248045.1:c.-729+1930=	XM_005248045.1:c.-729+1930A>T
SLC30A9 transcript variant X1	XM_047449525.1:c.109+1930=	XM_047449525.1:c.109+1930A>T

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#.

34 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ILLUMINA-UK	ss116966877	Feb 14, 2009 (130)
2	1000GENOMES	ss220880112	Jul 14, 2010 (132)
3	1000GENOMES	ss232359421	Jul 14, 2010 (132)
4	1000GENOMES	ss1309371913	Aug 21, 2014 (142)
5	DDI	ss1429851986	Apr 01, 2015 (144)
6	EVA_GENOME_DK	ss1580519253	Apr 01, 2015 (144)
7	EVA_DECODE	ss1589516405	Apr 01, 2015 (144)
8	EVA_UK10K_ALSPAC	ss1609908857	Apr 01, 2015 (144)
9	EVA_UK10K_TWINSUK	ss1652902890	Apr 01, 2015 (144)
10	WEILL_CORNELL_DGM	ss1923253180	Feb 12, 2016 (147)
11	JJLAB	ss2022211384	Sep 14, 2016 (149)
12	HUMAN_LONGEVITY	ss2262336292	Dec 20, 2016 (150)
13	SWEGEN	ss2994521298	Nov 08, 2017 (151)
14	CSHL	ss3345661362	Nov 08, 2017 (151)
15	EGCUT_WGS	ss3662441675	Jul 13, 2019 (153)
16	EVA_DECODE	ss3711877817	Jul 13, 2019 (153)
17	ACPOP	ss3731072096	Jul 13, 2019 (153)
18	EVA	ss3761694357	Jul 13, 2019 (153)
19	KHV_HUMAN_GENOMES	ss3804827014	Jul 13, 2019 (153)
20	EVA	ss3828495661	Apr 26, 2020 (154)
21	EVA	ss3837683813	Apr 26, 2020 (154)
22	EVA	ss3843118969	Apr 26, 2020 (154)
23	SGDP_PRJ	ss3858721687	Apr 26, 2020 (154)
24	KRGDB	ss3904904563	Apr 26, 2020 (154)
25	GNOMAD	ss4094572640	Apr 26, 2021 (155)
26	TOPMED	ss4610766351	Apr 26, 2021 (155)
27	1000G_HIGH_COVERAGE	ss5258870758	Oct 17, 2022 (156)
28	EVA	ss5348397620	Oct 17, 2022 (156)
29	HUGCELL_USP	ss5457690377	Oct 17, 2022 (156)
30	EVA	ss5507478265	Oct 17, 2022 (156)
31	SANFORD_IMAGENETICS	ss5634831046	Oct 17, 2022 (156)
32	EVA	ss5843873721	Oct 17, 2022 (156)
33	EVA	ss5863093555	Oct 17, 2022 (156)
34	EVA	ss5963224323	Oct 17, 2022 (156)
35	1000Genomes	NC_000004.11 - 41994707	Oct 12, 2018 (152)
36	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 41994707	Oct 12, 2018 (152)
37	Genetic variation in the Estonian population	NC_000004.11 - 41994707	Oct 12, 2018 (152)
38	The Danish reference pan genome	NC_000004.11 - 41994707	Apr 26, 2020 (154)
39	gnomAD - Genomes	NC_000004.12 - 41992690	Apr 26, 2021 (155)
40	KOREAN population from KRGDB	NC_000004.11 - 41994707	Apr 26, 2020 (154)
41	Northern Sweden	NC_000004.11 - 41994707	Jul 13, 2019 (153)
42	Qatari	NC_000004.11 - 41994707	Apr 26, 2020 (154)
43	SGDP_PRJ	NC_000004.11 - 41994707	Apr 26, 2020 (154)
44	TopMed	NC_000004.12 - 41992690	Apr 26, 2021 (155)
45	UK 10K study - Twins	NC_000004.11 - 41994707	Oct 12, 2018 (152)
46	ALFA	NC_000004.12 - 41992690	Apr 26, 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
ss116966877, ss1589516405	NC_000004.10:41689463:A:T	NC_000004.12:41992689:A:T	(self)
20754989, 11565135, 8179923, 6684192, 12081957, 4356961, 5295110, 10738667, 11565135, ss220880112, ss232359421, ss1309371913, ss1429851986, ss1580519253, ss1609908857, ss1652902890, ss1923253180, ss2022211384, ss2994521298, ss3345661362, ss3662441675, ss3731072096, ss3761694357, ss3828495661, ss3837683813, ss3858721687, ss3904904563, ss5348397620, ss5507478265, ss5634831046, ss5843873721, ss5963224323	NC_000004.11:41994706:A:T	NC_000004.12:41992689:A:T	(self)
146942297, 448143907, 7162670770, ss2262336292, ss3711877817, ss3804827014, ss3843118969, ss4094572640, ss4610766351, ss5258870758, ss5457690377, ss5863093555	NC_000004.12:41992689:A:T	NC_000004.12:41992689:A: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 rs73810453

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

rs73810453