Name: rs9505999
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.

rs9505999

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:28519134 (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 / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.040466 (10711/264690, TOPMED)
A=0.01971 (557/28258, 14KJPN)
A=0.00844 (165/19540, ALFA) (+ 13 more)
A=0.02029 (340/16760, 8.3KJPN)
A=0.0553 (354/6404, 1000G_30x)
A=0.0511 (256/5008, 1000G)
A=0.0003 (1/3854, ALSPAC)
A=0.0008 (3/3708, TWINSUK)
A=0.0276 (81/2930, KOREAN)
A=0.0311 (57/1832, Korea1K)
A=0.000 (0/600, NorthernSweden)
A=0.016 (9/556, SGDP_PRJ)
A=0.019 (4/216, Qatari)
A=0.056 (12/214, Vietnamese)
A=0.02 (1/56, Siberian)
A=0.03 (1/40, GENOME_DK)

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	19540	A=0.00844	G=0.99156, T=0.00000
European	Sub	17740	A=0.00023	G=0.99977, T=0.00000
African	Sub	910	A=0.160	G=0.840, T=0.000
African Others	Sub	42	A=0.29	G=0.71, T=0.00
African American	Sub	868	A=0.154	G=0.846, T=0.000
Asian	Sub	20	A=0.05	G=0.95, T=0.00
East Asian	Sub	16	A=0.00	G=1.00, T=0.00
Other Asian	Sub	4	A=0.2	G=0.8, T=0.0
Latin American 1	Sub	22	A=0.05	G=0.95, T=0.00
Latin American 2	Sub	88	A=0.01	G=0.99, T=0.00
South Asian	Sub	20	A=0.00	G=1.00, T=0.00
Other	Sub	740	A=0.016	G=0.984, T=0.000

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=0.040466	G=0.959534
14KJPN	JAPANESE	Study-wide	28258	A=0.01971	G=0.98029
Allele Frequency Aggregator	Total	Global	19540	A=0.00844	G=0.99156, T=0.00000
Allele Frequency Aggregator	European	Sub	17740	A=0.00023	G=0.99977, T=0.00000
Allele Frequency Aggregator	African	Sub	910	A=0.160	G=0.840, T=0.000
Allele Frequency Aggregator	Other	Sub	740	A=0.016	G=0.984, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	88	A=0.01	G=0.99, T=0.00
Allele Frequency Aggregator	Latin American 1	Sub	22	A=0.05	G=0.95, T=0.00
Allele Frequency Aggregator	South Asian	Sub	20	A=0.00	G=1.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	20	A=0.05	G=0.95, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	A=0.02029	G=0.97971
1000Genomes_30x	Global	Study-wide	6404	A=0.0553	G=0.9447
1000Genomes_30x	African	Sub	1786	A=0.1523	G=0.8477
1000Genomes_30x	Europe	Sub	1266	A=0.0024	G=0.9976
1000Genomes_30x	South Asian	Sub	1202	A=0.0075	G=0.9925
1000Genomes_30x	East Asian	Sub	1170	A=0.0496	G=0.9504
1000Genomes_30x	American	Sub	980	A=0.012	G=0.988
1000Genomes	Global	Study-wide	5008	A=0.0511	G=0.9489
1000Genomes	African	Sub	1322	A=0.1437	G=0.8563
1000Genomes	East Asian	Sub	1008	A=0.0466	G=0.9534
1000Genomes	Europe	Sub	1006	A=0.0040	G=0.9960
1000Genomes	South Asian	Sub	978	A=0.006	G=0.994
1000Genomes	American	Sub	694	A=0.013	G=0.987
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.0003	G=0.9997
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.0008	G=0.9992
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.0276	G=0.9724
Korean Genome Project	KOREAN	Study-wide	1832	A=0.0311	G=0.9689
Northern Sweden	ACPOP	Study-wide	600	A=0.000	G=1.000
SGDP_PRJ	Global	Study-wide	556	A=0.016	G=0.984
Qatari	Global	Study-wide	216	A=0.019	G=0.981
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.056	G=0.944
Siberian	Global	Study-wide	56	A=0.02	G=0.98
The Danish reference pan genome	Danish	Study-wide	40	A=0.03	G=0.97

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.28519134A>G
GRCh38.p14 chr 13	NC_000013.11:g.28519134A>T
GRCh37.p13 chr 13	NC_000013.10:g.29093271A>G
GRCh37.p13 chr 13	NC_000013.10:g.29093271A>T

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	T
GRCh38.p14 chr 13	NC_000013.11:g.28519134=	NC_000013.11:g.28519134A>G	NC_000013.11:g.28519134A>T
GRCh37.p13 chr 13	NC_000013.10:g.29093271=	NC_000013.10:g.29093271A>G	NC_000013.10:g.29093271A>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#.

79 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss13157383	Dec 05, 2003 (119)
2	CSHL-HAPMAP	ss16617544	Feb 27, 2004 (120)
3	SSAHASNP	ss21040147	Apr 05, 2004 (121)
4	HGSV	ss78080361	Dec 06, 2007 (129)
5	HGSV	ss84451126	Dec 14, 2007 (130)
6	BCMHGSC_JDW	ss89558039	Mar 24, 2008 (129)
7	HUMANGENOME_JCVI	ss96954606	Feb 03, 2009 (130)
8	1000GENOMES	ss112646496	Jan 25, 2009 (130)
9	1000GENOMES	ss114465559	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss118401288	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss167788930	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss169069024	Jul 04, 2010 (132)
13	BUSHMAN	ss199011988	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss208465978	Jul 04, 2010 (132)
15	1000GENOMES	ss226098680	Jul 14, 2010 (132)
16	1000GENOMES	ss236190155	Jul 15, 2010 (132)
17	1000GENOMES	ss242697743	Jul 15, 2010 (132)
18	BL	ss254884279	May 09, 2011 (134)
19	GMI	ss281652681	May 04, 2012 (137)
20	GMI	ss286675086	Apr 25, 2013 (138)
21	PJP	ss291564621	May 09, 2011 (134)
22	ILLUMINA	ss479709185	May 04, 2012 (142)
23	ILLUMINA	ss483173818	May 04, 2012 (142)
24	ILLUMINA	ss533214295	Sep 08, 2015 (146)
25	TISHKOFF	ss563571002	Apr 25, 2013 (138)
26	SSMP	ss659166818	Apr 25, 2013 (138)
27	ILLUMINA	ss779637188	Sep 08, 2015 (146)
28	ILLUMINA	ss781048957	Sep 08, 2015 (146)
29	ILLUMINA	ss835109931	Sep 08, 2015 (146)
30	JMKIDD_LAB	ss1078962983	Aug 21, 2014 (142)
31	1000GENOMES	ss1347616521	Aug 21, 2014 (142)
32	DDI	ss1427140157	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1576694392	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1629955377	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1672949410	Apr 01, 2015 (144)
36	HAMMER_LAB	ss1807541314	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1933596435	Feb 12, 2016 (147)
38	GENOMED	ss1967743092	Jul 19, 2016 (147)
39	JJLAB	ss2027553812	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2155918531	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2195096154	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2628265032	Nov 08, 2017 (151)
43	ILLUMINA	ss2633043708	Nov 08, 2017 (151)
44	GRF	ss2700290706	Nov 08, 2017 (151)
45	GNOMAD	ss2917935502	Nov 08, 2017 (151)
46	SWEGEN	ss3010773045	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3027592428	Nov 08, 2017 (151)
48	CSHL	ss3350381511	Nov 08, 2017 (151)
49	ILLUMINA	ss3627029454	Oct 12, 2018 (152)
50	ILLUMINA	ss3631047959	Oct 12, 2018 (152)
51	ILLUMINA	ss3641829920	Oct 12, 2018 (152)
52	URBANLAB	ss3649996235	Oct 12, 2018 (152)
53	EVA_DECODE	ss3694990103	Jul 13, 2019 (153)
54	ACPOP	ss3739611668	Jul 13, 2019 (153)
55	EVA	ss3751274787	Jul 13, 2019 (153)
56	PACBIO	ss3787414040	Jul 13, 2019 (153)
57	PACBIO	ss3792486726	Jul 13, 2019 (153)
58	PACBIO	ss3797370443	Jul 13, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3816605812	Jul 13, 2019 (153)
60	EVA	ss3833466471	Apr 27, 2020 (154)
61	EVA	ss3840310345	Apr 27, 2020 (154)
62	EVA	ss3845795077	Apr 27, 2020 (154)
63	SGDP_PRJ	ss3879659112	Apr 27, 2020 (154)
64	KRGDB	ss3928480481	Apr 27, 2020 (154)
65	KOGIC	ss3973266608	Apr 27, 2020 (154)
66	TOPMED	ss4940971566	Apr 26, 2021 (155)
67	TOMMO_GENOMICS	ss5209313182	Apr 26, 2021 (155)
68	1000G_HIGH_COVERAGE	ss5293205668	Oct 16, 2022 (156)
69	EVA	ss5315671453	Oct 16, 2022 (156)
70	EVA	ss5409800442	Oct 16, 2022 (156)
71	HUGCELL_USP	ss5487621844	Oct 16, 2022 (156)
72	1000G_HIGH_COVERAGE	ss5591889090	Oct 16, 2022 (156)
73	SANFORD_IMAGENETICS	ss5654464937	Oct 16, 2022 (156)
74	TOMMO_GENOMICS	ss5760993833	Oct 16, 2022 (156)
75	YY_MCH	ss5813978157	Oct 16, 2022 (156)
76	EVA	ss5839265656	Oct 16, 2022 (156)
77	EVA	ss5850661571	Oct 16, 2022 (156)
78	EVA	ss5924494026	Oct 16, 2022 (156)
79	EVA	ss5945871159	Oct 16, 2022 (156)
80	1000Genomes	NC_000013.10 - 29093271	Oct 12, 2018 (152)
81	1000Genomes_30x	NC_000013.11 - 28519134	Oct 16, 2022 (156)
82	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 29093271	Oct 12, 2018 (152)
83	The Danish reference pan genome	NC_000013.10 - 29093271	Apr 27, 2020 (154)
84	gnomAD - Genomes Submission ignored due to conflicting rows: Row 426362582 (NC_000013.11:28519133:A:G 134855/140154) Row 426362583 (NC_000013.11:28519133:A:T 1/140160)	-	Apr 26, 2021 (155)
85	gnomAD - Genomes Submission ignored due to conflicting rows: Row 426362582 (NC_000013.11:28519133:A:G 134855/140154) Row 426362583 (NC_000013.11:28519133:A:T 1/140160)	-	Apr 26, 2021 (155)
86	KOREAN population from KRGDB	NC_000013.10 - 29093271	Apr 27, 2020 (154)
87	Korean Genome Project	NC_000013.11 - 28519134	Apr 27, 2020 (154)
88	Northern Sweden	NC_000013.10 - 29093271	Jul 13, 2019 (153)
89	Qatari	NC_000013.10 - 29093271	Apr 27, 2020 (154)
90	SGDP_PRJ	NC_000013.10 - 29093271	Apr 27, 2020 (154)
91	Siberian	NC_000013.10 - 29093271	Apr 27, 2020 (154)
92	8.3KJPN	NC_000013.10 - 29093271	Apr 26, 2021 (155)
93	14KJPN	NC_000013.11 - 28519134	Oct 16, 2022 (156)
94	TopMed	NC_000013.11 - 28519134	Apr 26, 2021 (155)
95	UK 10K study - Twins	NC_000013.10 - 29093271	Oct 12, 2018 (152)
96	A Vietnamese Genetic Variation Database	NC_000013.10 - 29093271	Jul 13, 2019 (153)
97	ALFA	NC_000013.11 - 28519134	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).

Associated ID	History Updated (Build)
rs56881716	May 23, 2008 (130)
rs199743379	Aug 21, 2014 (142)
rs201515492	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78080361, ss84451126, ss89558039, ss112646496, ss114465559, ss118401288, ss167788930, ss169069024, ss199011988, ss208465978, ss254884279, ss281652681, ss286675086, ss291564621, ss483173818	NC_000013.9:27991270:A:G	NC_000013.11:28519133:A:G	(self)
60464818, 33582024, 3234029, 35657875, 12896533, 15638365, 31676092, 8434885, 67282489, 33582024, 7449155, ss226098680, ss236190155, ss242697743, ss479709185, ss533214295, ss563571002, ss659166818, ss779637188, ss781048957, ss835109931, ss1078962983, ss1347616521, ss1427140157, ss1576694392, ss1629955377, ss1672949410, ss1807541314, ss1933596435, ss1967743092, ss2027553812, ss2155918531, ss2628265032, ss2633043708, ss2700290706, ss2917935502, ss3010773045, ss3350381511, ss3627029454, ss3631047959, ss3641829920, ss3739611668, ss3751274787, ss3787414040, ss3792486726, ss3797370443, ss3833466471, ss3840310345, ss3879659112, ss3928480481, ss5209313182, ss5315671453, ss5409800442, ss5654464937, ss5839265656, ss5945871159	NC_000013.10:29093270:A:G	NC_000013.11:28519133:A:G	(self)
79415025, 29644609, 94830937, 156517224, 1084001190, ss2195096154, ss3027592428, ss3649996235, ss3694990103, ss3816605812, ss3845795077, ss3973266608, ss4940971566, ss5293205668, ss5487621844, ss5591889090, ss5760993833, ss5813978157, ss5850661571, ss5924494026	NC_000013.11:28519133:A:G	NC_000013.11:28519133:A:G	(self)
ss13157383	NT_009799.12:10073270:A:G	NC_000013.11:28519133:A:G	(self)
ss16617544, ss21040147	NT_024524.13:10073270:A:G	NC_000013.11:28519133:A:G	(self)
ss96954606	NT_024524.14:10073270:A:G	NC_000013.11:28519133:A:G	(self)
1084001190	NC_000013.11:28519133:A:T	NC_000013.11:28519133: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 rs9505999

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

rs9505999