Name: rs461193
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.

rs461193

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:1368882 (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=0.210106 (55613/264690, TOPMED)
G=0.212612 (34350/161562, ALFA)
G=0.207839 (29124/140128, GnomAD) (+ 17 more)
G=0.12747 (3602/28258, 14KJPN)
G=0.12625 (2116/16760, 8.3KJPN)
G=0.2150 (1377/6404, 1000G_30x)
G=0.2117 (1060/5008, 1000G)
G=0.1618 (725/4480, Estonian)
G=0.1928 (743/3854, ALSPAC)
G=0.1855 (688/3708, TWINSUK)
G=0.1742 (510/2928, KOREAN)
G=0.2481 (469/1890, HapMap)
G=0.191 (191/998, GoNL)
G=0.161 (101/626, Chileans)
G=0.207 (124/600, NorthernSweden)
G=0.343 (74/216, Qatari)
A=0.412 (75/182, SGDP_PRJ)
G=0.15 (6/40, GENOME_DK)
A=0.5 (5/10, Siberian)
G=0.5 (5/10, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC01511 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	161562	A=0.787388	G=0.212612	0.621867	0.04709	0.331043	6
European	Sub	135530	A=0.785088	G=0.214912	0.618107	0.04793	0.333963	4
African	Sub	9850	A=0.7509	G=0.2491	0.56467	0.062944	0.372386	0
African Others	Sub	334	A=0.719	G=0.281	0.520958	0.083832	0.39521	0
African American	Sub	9516	A=0.7520	G=0.2480	0.566204	0.062211	0.371585	0
Asian	Sub	706	A=0.751	G=0.249	0.572238	0.070822	0.356941	0
East Asian	Sub	544	A=0.783	G=0.217	0.621324	0.055147	0.323529	0
Other Asian	Sub	162	A=0.642	G=0.358	0.407407	0.123457	0.469136	0
Latin American 1	Sub	880	A=0.803	G=0.197	0.634091	0.027273	0.338636	2
Latin American 2	Sub	8412	A=0.8578	G=0.1422	0.736805	0.02116	0.242035	0
South Asian	Sub	198	A=0.838	G=0.162	0.69697	0.020202	0.282828	0
Other	Sub	5986	A=0.8009	G=0.1991	0.641163	0.039425	0.319412	0

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=0.789894	G=0.210106
Allele Frequency Aggregator	Total	Global	161562	A=0.787388	G=0.212612
Allele Frequency Aggregator	European	Sub	135530	A=0.785088	G=0.214912
Allele Frequency Aggregator	African	Sub	9850	A=0.7509	G=0.2491
Allele Frequency Aggregator	Latin American 2	Sub	8412	A=0.8578	G=0.1422
Allele Frequency Aggregator	Other	Sub	5986	A=0.8009	G=0.1991
Allele Frequency Aggregator	Latin American 1	Sub	880	A=0.803	G=0.197
Allele Frequency Aggregator	Asian	Sub	706	A=0.751	G=0.249
Allele Frequency Aggregator	South Asian	Sub	198	A=0.838	G=0.162
gnomAD - Genomes	Global	Study-wide	140128	A=0.792161	G=0.207839
gnomAD - Genomes	European	Sub	75890	A=0.81034	G=0.18966
gnomAD - Genomes	African	Sub	41980	A=0.75193	G=0.24807
gnomAD - Genomes	American	Sub	13660	A=0.82086	G=0.17914
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.8170	G=0.1830
gnomAD - Genomes	East Asian	Sub	3124	A=0.7474	G=0.2526
gnomAD - Genomes	Other	Sub	2152	A=0.7802	G=0.2198
14KJPN	JAPANESE	Study-wide	28258	A=0.87253	G=0.12747
8.3KJPN	JAPANESE	Study-wide	16760	A=0.87375	G=0.12625
1000Genomes_30x	Global	Study-wide	6404	A=0.7850	G=0.2150
1000Genomes_30x	African	Sub	1786	A=0.7553	G=0.2447
1000Genomes_30x	Europe	Sub	1266	A=0.7520	G=0.2480
1000Genomes_30x	South Asian	Sub	1202	A=0.8536	G=0.1464
1000Genomes_30x	East Asian	Sub	1170	A=0.7632	G=0.2368
1000Genomes_30x	American	Sub	980	A=0.823	G=0.177
1000Genomes	Global	Study-wide	5008	A=0.7883	G=0.2117
1000Genomes	African	Sub	1322	A=0.7519	G=0.2481
1000Genomes	East Asian	Sub	1008	A=0.7718	G=0.2282
1000Genomes	Europe	Sub	1006	A=0.7584	G=0.2416
1000Genomes	South Asian	Sub	978	A=0.856	G=0.144
1000Genomes	American	Sub	694	A=0.830	G=0.170
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.8382	G=0.1618
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.8072	G=0.1928
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.8145	G=0.1855
KOREAN population from KRGDB	KOREAN	Study-wide	2928	A=0.8258	G=0.1742
HapMap	Global	Study-wide	1890	A=0.7519	G=0.2481
HapMap	American	Sub	768	A=0.794	G=0.206
HapMap	African	Sub	692	A=0.676	G=0.324
HapMap	Asian	Sub	254	A=0.846	G=0.154
HapMap	Europe	Sub	176	A=0.727	G=0.273
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.809	G=0.191
Chileans	Chilean	Study-wide	626	A=0.839	G=0.161
Northern Sweden	ACPOP	Study-wide	600	A=0.793	G=0.207
Qatari	Global	Study-wide	216	A=0.657	G=0.343
SGDP_PRJ	Global	Study-wide	182	A=0.412	G=0.588
The Danish reference pan genome	Danish	Study-wide	40	A=0.85	G=0.15
Siberian	Global	Study-wide	10	A=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 5	NC_000005.10:g.1368882A>G
GRCh37.p13 chr 5	NC_000005.9:g.1368997A>G
GRCh38.p14 chr 5 alt locus HSCHR5_3_CTG1	NT_187547.1:g.145127T>C

Gene: LINC01511, long intergenic non-protein coding RNA 1511 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01511 transcript	NR_125810.1:n.	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=	G
GRCh38.p14 chr 5	NC_000005.10:g.1368882=	NC_000005.10:g.1368882A>G
GRCh37.p13 chr 5	NC_000005.9:g.1368997=	NC_000005.9:g.1368997A>G
GRCh38.p14 chr 5 alt locus HSCHR5_3_CTG1	NT_187547.1:g.145127=	NT_187547.1:g.145127T>C

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#.

97 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss623433	Jul 16, 2000 (80)
2	KWOK	ss1167060	Oct 05, 2000 (87)
3	KWOK	ss1572855	Oct 18, 2000 (87)
4	ABI	ss42556679	Mar 14, 2006 (126)
5	PERLEGEN	ss68923819	May 17, 2007 (127)
6	ILLUMINA	ss75062954	Dec 06, 2007 (129)
7	AFFY	ss76509749	Dec 06, 2007 (129)
8	1000GENOMES	ss108733524	Jan 23, 2009 (130)
9	KRIBB_YJKIM	ss119354401	Dec 01, 2009 (131)
10	ILLUMINA	ss160691143	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss161945375	Jul 04, 2010 (132)
12	ILLUMINA	ss173761210	Jul 04, 2010 (132)
13	BUSHMAN	ss199767608	Jul 04, 2010 (132)
14	1000GENOMES	ss221467040	Jul 14, 2010 (132)
15	1000GENOMES	ss232792459	Jul 14, 2010 (132)
16	1000GENOMES	ss239997135	Jul 15, 2010 (132)
17	BL	ss253149501	May 09, 2011 (134)
18	GMI	ss278133670	May 04, 2012 (137)
19	GMI	ss285102934	Apr 25, 2013 (138)
20	ILLUMINA	ss410934402	Sep 17, 2011 (135)
21	ILLUMINA	ss480980425	May 04, 2012 (137)
22	ILLUMINA	ss481000909	May 04, 2012 (137)
23	ILLUMINA	ss481978706	Sep 08, 2015 (146)
24	ILLUMINA	ss485285125	May 04, 2012 (137)
25	ILLUMINA	ss537249699	Sep 08, 2015 (146)
26	TISHKOFF	ss558146805	Apr 25, 2013 (138)
27	SSMP	ss651990719	Apr 25, 2013 (138)
28	ILLUMINA	ss778539916	Sep 08, 2015 (146)
29	ILLUMINA	ss783088472	Sep 08, 2015 (146)
30	ILLUMINA	ss784045936	Sep 08, 2015 (146)
31	ILLUMINA	ss832346917	Sep 08, 2015 (146)
32	ILLUMINA	ss833996534	Sep 08, 2015 (146)
33	EVA-GONL	ss981164554	Aug 21, 2014 (142)
34	JMKIDD_LAB	ss1072325597	Aug 21, 2014 (142)
35	1000GENOMES	ss1313602688	Aug 21, 2014 (142)
36	DDI	ss1430216642	Apr 01, 2015 (144)
37	EVA_GENOME_DK	ss1580976158	Apr 01, 2015 (144)
38	EVA_DECODE	ss1590680586	Apr 01, 2015 (144)
39	EVA_UK10K_ALSPAC	ss1612110099	Apr 01, 2015 (144)
40	EVA_UK10K_TWINSUK	ss1655104132	Apr 01, 2015 (144)
41	EVA_SVP	ss1712736913	Apr 01, 2015 (144)
42	ILLUMINA	ss1752550290	Sep 08, 2015 (146)
43	HAMMER_LAB	ss1802922735	Sep 08, 2015 (146)
44	WEILL_CORNELL_DGM	ss1924420857	Feb 12, 2016 (147)
45	JJLAB	ss2022803709	Sep 14, 2016 (149)
46	ILLUMINA	ss2094817578	Dec 20, 2016 (150)
47	ILLUMINA	ss2095152786	Dec 20, 2016 (150)
48	USC_VALOUEV	ss2150953737	Dec 20, 2016 (150)
49	HUMAN_LONGEVITY	ss2270764022	Dec 20, 2016 (150)
50	SYSTEMSBIOZJU	ss2625900326	Nov 08, 2017 (151)
51	ILLUMINA	ss2634234058	Nov 08, 2017 (151)
52	GRF	ss2706475107	Nov 08, 2017 (151)
53	ILLUMINA	ss2711026449	Nov 08, 2017 (151)
54	SWEGEN	ss2996315117	Nov 08, 2017 (151)
55	BIOINF_KMB_FNS_UNIBA	ss3025184605	Nov 08, 2017 (151)
56	CSHL	ss3346200532	Nov 08, 2017 (151)
57	ILLUMINA	ss3629159397	Oct 12, 2018 (152)
58	ILLUMINA	ss3632163474	Oct 12, 2018 (152)
59	ILLUMINA	ss3633362279	Oct 12, 2018 (152)
60	ILLUMINA	ss3634082328	Oct 12, 2018 (152)
61	ILLUMINA	ss3634987432	Oct 12, 2018 (152)
62	ILLUMINA	ss3635764631	Oct 12, 2018 (152)
63	ILLUMINA	ss3636696091	Oct 12, 2018 (152)
64	ILLUMINA	ss3637517227	Oct 12, 2018 (152)
65	ILLUMINA	ss3638533803	Oct 12, 2018 (152)
66	ILLUMINA	ss3640694725	Oct 12, 2018 (152)
67	ILLUMINA	ss3643481343	Oct 12, 2018 (152)
68	ILLUMINA	ss3652951076	Oct 12, 2018 (152)
69	EGCUT_WGS	ss3664203855	Jul 13, 2019 (153)
70	EVA_DECODE	ss3713953534	Jul 13, 2019 (153)
71	ACPOP	ss3732017244	Jul 13, 2019 (153)
72	ILLUMINA	ss3745287606	Jul 13, 2019 (153)
73	EVA	ss3762966558	Jul 13, 2019 (153)
74	ILLUMINA	ss3772781986	Jul 13, 2019 (153)
75	KHV_HUMAN_GENOMES	ss3806135736	Jul 13, 2019 (153)
76	EVA	ss3829052207	Apr 26, 2020 (154)
77	EVA	ss3837985596	Apr 26, 2020 (154)
78	EVA	ss3843428042	Apr 26, 2020 (154)
79	SGDP_PRJ	ss3861043369	Apr 26, 2020 (154)
80	KRGDB	ss3907480614	Apr 26, 2020 (154)
81	EVA	ss4017188667	Apr 26, 2021 (155)
82	VINODS	ss4024243196	Apr 26, 2021 (155)
83	TOPMED	ss4647147168	Apr 26, 2021 (155)
84	TOMMO_GENOMICS	ss5170047669	Apr 26, 2021 (155)
85	1000G_HIGH_COVERAGE	ss5262610350	Oct 13, 2022 (156)
86	EVA	ss5315024803	Oct 13, 2022 (156)
87	EVA	ss5355161940	Oct 13, 2022 (156)
88	HUGCELL_USP	ss5460982732	Oct 13, 2022 (156)
89	1000G_HIGH_COVERAGE	ss5545528702	Oct 13, 2022 (156)
90	SANFORD_IMAGENETICS	ss5637026571	Oct 13, 2022 (156)
91	TOMMO_GENOMICS	ss5705628768	Oct 13, 2022 (156)
92	EVA	ss5799638486	Oct 13, 2022 (156)
93	YY_MCH	ss5805951709	Oct 13, 2022 (156)
94	EVA	ss5834409889	Oct 13, 2022 (156)
95	EVA	ss5854645201	Oct 13, 2022 (156)
96	EVA	ss5892684182	Oct 13, 2022 (156)
97	EVA	ss5965433879	Oct 13, 2022 (156)
98	1000Genomes	NC_000005.9 - 1368997	Oct 12, 2018 (152)
99	1000Genomes_30x	NC_000005.10 - 1368882	Oct 13, 2022 (156)
100	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 1368997	Oct 12, 2018 (152)
101	Chileans	NC_000005.9 - 1368997	Apr 26, 2020 (154)
102	Genetic variation in the Estonian population	NC_000005.9 - 1368997	Oct 12, 2018 (152)
103	The Danish reference pan genome	NC_000005.9 - 1368997	Apr 26, 2020 (154)
104	gnomAD - Genomes	NC_000005.10 - 1368882	Apr 26, 2021 (155)
105	Genome of the Netherlands Release 5	NC_000005.9 - 1368997	Apr 26, 2020 (154)
106	HapMap	NC_000005.10 - 1368882	Apr 26, 2020 (154)
107	KOREAN population from KRGDB	NC_000005.9 - 1368997	Apr 26, 2020 (154)
108	Northern Sweden	NC_000005.9 - 1368997	Jul 13, 2019 (153)
109	Qatari	NC_000005.9 - 1368997	Apr 26, 2020 (154)
110	SGDP_PRJ	NC_000005.9 - 1368997	Apr 26, 2020 (154)
111	Siberian	NC_000005.9 - 1368997	Apr 26, 2020 (154)
112	8.3KJPN	NC_000005.9 - 1368997	Apr 26, 2021 (155)
113	14KJPN	NC_000005.10 - 1368882	Oct 13, 2022 (156)
114	TopMed	NC_000005.10 - 1368882	Apr 26, 2021 (155)
115	UK 10K study - Twins	NC_000005.9 - 1368997	Oct 12, 2018 (152)
116	ALFA	NC_000005.10 - 1368882	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)
rs837256	Oct 23, 2000 (87)
rs386594021	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss76509749, ss108733524, ss160691143, ss161945375, ss199767608, ss253149501, ss278133670, ss285102934, ss480980425, ss1590680586, ss1712736913, ss3643481343	NC_000005.8:1421996:A:G	NC_000005.10:1368881:A:G	(self)
25147075, 13985675, 336709, 9942103, 7141097, 6208060, 14658008, 5302109, 6462787, 13060349, 3470091, 28016976, 13985675, ss221467040, ss232792459, ss239997135, ss481000909, ss481978706, ss485285125, ss537249699, ss558146805, ss651990719, ss778539916, ss783088472, ss784045936, ss832346917, ss833996534, ss981164554, ss1072325597, ss1313602688, ss1430216642, ss1580976158, ss1612110099, ss1655104132, ss1752550290, ss1802922735, ss1924420857, ss2022803709, ss2094817578, ss2095152786, ss2150953737, ss2625900326, ss2634234058, ss2706475107, ss2711026449, ss2996315117, ss3346200532, ss3629159397, ss3632163474, ss3633362279, ss3634082328, ss3634987432, ss3635764631, ss3636696091, ss3637517227, ss3638533803, ss3640694725, ss3652951076, ss3664203855, ss3732017244, ss3745287606, ss3762966558, ss3772781986, ss3829052207, ss3837985596, ss3861043369, ss3907480614, ss4017188667, ss5170047669, ss5315024803, ss5355161940, ss5637026571, ss5799638486, ss5834409889, ss5965433879	NC_000005.9:1368996:A:G	NC_000005.10:1368881:A:G	(self)
33054637, 177847964, 2789998, 39465872, 484524725, 980051700, ss2270764022, ss3025184605, ss3713953534, ss3806135736, ss3843428042, ss4647147168, ss5262610350, ss5460982732, ss5545528702, ss5705628768, ss5805951709, ss5854645201, ss5892684182	NC_000005.10:1368881:A:G	NC_000005.10:1368881:A:G	(self)
ss623433, ss1167060, ss1572855, ss42556679, ss68923819, ss75062954, ss119354401, ss173761210, ss410934402	NT_006576.16:1358996:A:G	NC_000005.10:1368881:A:G	(self)
ss4024243196	NT_187547.1:145126:T:C	NC_000005.10:1368881: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 rs461193

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

rs461193