Name: rs9516430
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.

rs9516430

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:87086209 (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: T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.072844 (19281/264690, TOPMED)
G=0.071733 (9952/138736, GnomAD)
G=0.04769 (3751/78652, PAGE_STUDY) (+ 15 more)
G=0.03065 (866/28258, 14KJPN)
G=0.08337 (1544/18520, ALFA)
G=0.03192 (535/16760, 8.3KJPN)
G=0.0623 (399/6404, 1000G_30x)
G=0.0611 (306/5008, 1000G)
G=0.0786 (352/4480, Estonian)
G=0.0412 (120/2910, KOREAN)
G=0.0413 (75/1814, Korea1K)
G=0.088 (53/600, NorthernSweden)
G=0.102 (22/216, Qatari)
G=0.047 (10/214, Vietnamese)
T=0.43 (30/70, SGDP_PRJ)
G=0.06 (2/32, GENOME_DK)
T=0.5 (3/6, Siberian)
G=0.5 (3/6, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	18520	T=0.91663	G=0.08337
European	Sub	14152	T=0.90341	G=0.09659
African	Sub	2898	T=0.9727	G=0.0273
African Others	Sub	114	T=0.982	G=0.018
African American	Sub	2784	T=0.9723	G=0.0277
Asian	Sub	112	T=0.929	G=0.071
East Asian	Sub	86	T=0.91	G=0.09
Other Asian	Sub	26	T=1.00	G=0.00
Latin American 1	Sub	146	T=0.918	G=0.082
Latin American 2	Sub	610	T=0.956	G=0.044
South Asian	Sub	98	T=0.86	G=0.14
Other	Sub	504	T=0.927	G=0.073

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	T=0.927156	G=0.072844
gnomAD - Genomes	Global	Study-wide	138736	T=0.928267	G=0.071733
gnomAD - Genomes	European	Sub	74898	T=0.90667	G=0.09333
gnomAD - Genomes	African	Sub	41806	T=0.97003	G=0.02997
gnomAD - Genomes	American	Sub	13448	T=0.93605	G=0.06395
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=0.8363	G=0.1637
gnomAD - Genomes	East Asian	Sub	3126	T=0.9543	G=0.0457
gnomAD - Genomes	Other	Sub	2140	T=0.9238	G=0.0762
The PAGE Study	Global	Study-wide	78652	T=0.95231	G=0.04769
The PAGE Study	AfricanAmerican	Sub	32494	T=0.96658	G=0.03342
The PAGE Study	Mexican	Sub	10802	T=0.94668	G=0.05332
The PAGE Study	Asian	Sub	8312	T=0.9696	G=0.0304
The PAGE Study	PuertoRican	Sub	7916	T=0.9296	G=0.0704
The PAGE Study	NativeHawaiian	Sub	4532	T=0.9490	G=0.0510
The PAGE Study	Cuban	Sub	4224	T=0.9096	G=0.0904
The PAGE Study	Dominican	Sub	3828	T=0.9347	G=0.0653
The PAGE Study	CentralAmerican	Sub	2448	T=0.9526	G=0.0474
The PAGE Study	SouthAmerican	Sub	1980	T=0.9455	G=0.0545
The PAGE Study	NativeAmerican	Sub	1260	T=0.9286	G=0.0714
The PAGE Study	SouthAsian	Sub	856	T=0.881	G=0.119
14KJPN	JAPANESE	Study-wide	28258	T=0.96935	G=0.03065
Allele Frequency Aggregator	Total	Global	18520	T=0.91663	G=0.08337
Allele Frequency Aggregator	European	Sub	14152	T=0.90341	G=0.09659
Allele Frequency Aggregator	African	Sub	2898	T=0.9727	G=0.0273
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.956	G=0.044
Allele Frequency Aggregator	Other	Sub	504	T=0.927	G=0.073
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.918	G=0.082
Allele Frequency Aggregator	Asian	Sub	112	T=0.929	G=0.071
Allele Frequency Aggregator	South Asian	Sub	98	T=0.86	G=0.14
8.3KJPN	JAPANESE	Study-wide	16760	T=0.96808	G=0.03192
1000Genomes_30x	Global	Study-wide	6404	T=0.9377	G=0.0623
1000Genomes_30x	African	Sub	1786	T=0.9815	G=0.0185
1000Genomes_30x	Europe	Sub	1266	T=0.9021	G=0.0979
1000Genomes_30x	South Asian	Sub	1202	T=0.8894	G=0.1106
1000Genomes_30x	East Asian	Sub	1170	T=0.9650	G=0.0350
1000Genomes_30x	American	Sub	980	T=0.931	G=0.069
1000Genomes	Global	Study-wide	5008	T=0.9389	G=0.0611
1000Genomes	African	Sub	1322	T=0.9811	G=0.0189
1000Genomes	East Asian	Sub	1008	T=0.9683	G=0.0317
1000Genomes	Europe	Sub	1006	T=0.9076	G=0.0924
1000Genomes	South Asian	Sub	978	T=0.887	G=0.113
1000Genomes	American	Sub	694	T=0.935	G=0.065
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9214	G=0.0786
KOREAN population from KRGDB	KOREAN	Study-wide	2910	T=0.9588	G=0.0412
Korean Genome Project	KOREAN	Study-wide	1814	T=0.9587	G=0.0413
Northern Sweden	ACPOP	Study-wide	600	T=0.912	G=0.088
Qatari	Global	Study-wide	216	T=0.898	G=0.102
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.953	G=0.047
SGDP_PRJ	Global	Study-wide	70	T=0.43	G=0.57
The Danish reference pan genome	Danish	Study-wide	32	T=0.94	G=0.06
Siberian	Global	Study-wide	6	T=0.5	G=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 13	NC_000013.11:g.87086209T>G
GRCh37.p13 chr 13	NC_000013.10:g.87738464T>G

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	T=	G
GRCh38.p14 chr 13	NC_000013.11:g.87086209=	NC_000013.11:g.87086209T>G
GRCh37.p13 chr 13	NC_000013.10:g.87738464=	NC_000013.10:g.87738464T>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#.

45 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss13179301	Dec 05, 2003 (119)
2	1000GENOMES	ss236362262	Jul 15, 2010 (132)
3	PJP	ss291499172	May 09, 2011 (134)
4	SSMP	ss659454285	Apr 25, 2013 (138)
5	EVA-GONL	ss990674546	Aug 21, 2014 (142)
6	1000GENOMES	ss1349241888	Aug 21, 2014 (142)
7	DDI	ss1427273616	Apr 01, 2015 (144)
8	EVA_GENOME_DK	ss1576956627	Apr 01, 2015 (144)
9	WEILL_CORNELL_DGM	ss1934033997	Feb 12, 2016 (147)
10	ILLUMINA	ss1959518068	Feb 12, 2016 (147)
11	GENOMED	ss1967851943	Jul 19, 2016 (147)
12	JJLAB	ss2027790024	Sep 14, 2016 (149)
13	USC_VALOUEV	ss2156155615	Dec 20, 2016 (150)
14	HUMAN_LONGEVITY	ss2198487095	Dec 20, 2016 (150)
15	GRF	ss2700547319	Nov 08, 2017 (151)
16	GNOMAD	ss2922582952	Nov 08, 2017 (151)
17	SWEGEN	ss3011444881	Nov 08, 2017 (151)
18	ILLUMINA	ss3021527326	Nov 08, 2017 (151)
19	BIOINF_KMB_FNS_UNIBA	ss3027714730	Nov 08, 2017 (151)
20	CSHL	ss3350583860	Nov 08, 2017 (151)
21	ILLUMINA	ss3651916144	Oct 12, 2018 (152)
22	EGCUT_WGS	ss3678725628	Jul 13, 2019 (153)
23	EVA_DECODE	ss3695801447	Jul 13, 2019 (153)
24	ACPOP	ss3739980865	Jul 13, 2019 (153)
25	EVA	ss3751780351	Jul 13, 2019 (153)
26	PAGE_CC	ss3771759579	Jul 13, 2019 (153)
27	KHV_HUMAN_GENOMES	ss3817110470	Jul 13, 2019 (153)
28	EVA	ss3833683373	Apr 27, 2020 (154)
29	SGDP_PRJ	ss3880514814	Apr 27, 2020 (154)
30	KRGDB	ss3929426572	Apr 27, 2020 (154)
31	KOGIC	ss3974045379	Apr 27, 2020 (154)
32	TOPMED	ss4955560007	Apr 26, 2021 (155)
33	TOMMO_GENOMICS	ss5211157619	Apr 26, 2021 (155)
34	1000G_HIGH_COVERAGE	ss5294628243	Oct 16, 2022 (156)
35	EVA	ss5412402177	Oct 16, 2022 (156)
36	HUGCELL_USP	ss5488902544	Oct 16, 2022 (156)
37	EVA	ss5511086573	Oct 16, 2022 (156)
38	1000G_HIGH_COVERAGE	ss5594101073	Oct 16, 2022 (156)
39	SANFORD_IMAGENETICS	ss5655296735	Oct 16, 2022 (156)
40	TOMMO_GENOMICS	ss5763351379	Oct 16, 2022 (156)
41	YY_MCH	ss5814342498	Oct 16, 2022 (156)
42	EVA	ss5839834466	Oct 16, 2022 (156)
43	EVA	ss5850841569	Oct 16, 2022 (156)
44	EVA	ss5926129197	Oct 16, 2022 (156)
45	EVA	ss5946730978	Oct 16, 2022 (156)
46	1000Genomes	NC_000013.10 - 87738464	Oct 12, 2018 (152)
47	1000Genomes_30x	NC_000013.11 - 87086209	Oct 16, 2022 (156)
48	Genetic variation in the Estonian population	NC_000013.10 - 87738464	Oct 12, 2018 (152)
49	The Danish reference pan genome	NC_000013.10 - 87738464	Apr 27, 2020 (154)
50	gnomAD - Genomes	NC_000013.11 - 87086209	Apr 26, 2021 (155)
51	KOREAN population from KRGDB	NC_000013.10 - 87738464	Apr 27, 2020 (154)
52	Korean Genome Project	NC_000013.11 - 87086209	Apr 27, 2020 (154)
53	Northern Sweden	NC_000013.10 - 87738464	Jul 13, 2019 (153)
54	The PAGE Study	NC_000013.11 - 87086209	Jul 13, 2019 (153)
55	Qatari	NC_000013.10 - 87738464	Apr 27, 2020 (154)
56	SGDP_PRJ	NC_000013.10 - 87738464	Apr 27, 2020 (154)
57	Siberian	NC_000013.10 - 87738464	Apr 27, 2020 (154)
58	8.3KJPN	NC_000013.10 - 87738464	Apr 26, 2021 (155)
59	14KJPN	NC_000013.11 - 87086209	Oct 16, 2022 (156)
60	TopMed	NC_000013.11 - 87086209	Apr 26, 2021 (155)
61	A Vietnamese Genetic Variation Database	NC_000013.10 - 87738464	Jul 13, 2019 (153)
62	ALFA	NC_000013.11 - 87086209	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
ss291499172	NC_000013.9:86536464:T:G	NC_000013.11:87086208:T:G	(self)
62154787, 24463876, 3411777, 36603966, 13265730, 16075927, 32531794, 8671969, 69126926, 7675058, ss236362262, ss659454285, ss990674546, ss1349241888, ss1427273616, ss1576956627, ss1934033997, ss1959518068, ss1967851943, ss2027790024, ss2156155615, ss2700547319, ss2922582952, ss3011444881, ss3021527326, ss3350583860, ss3651916144, ss3678725628, ss3739980865, ss3751780351, ss3833683373, ss3880514814, ss3929426572, ss5211157619, ss5412402177, ss5511086573, ss5655296735, ss5839834466, ss5946730978	NC_000013.10:87738463:T:G	NC_000013.11:87086208:T:G	(self)
81627008, 438320840, 30423380, 981048, 97188483, 171105665, 9521103625, ss2198487095, ss3027714730, ss3695801447, ss3771759579, ss3817110470, ss3974045379, ss4955560007, ss5294628243, ss5488902544, ss5594101073, ss5763351379, ss5814342498, ss5850841569, ss5926129197	NC_000013.11:87086208:T:G	NC_000013.11:87086208:T:G	(self)
ss13179301	NT_009952.13:828138:T:G	NC_000013.11:87086208:T: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 rs9516430

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

rs9516430