Name: rs62151809
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.

rs62151809

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:103816798 (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: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.300578 (79560/264690, TOPMED)
T=0.324047 (45351/139952, GnomAD)
T=0.00471 (133/28256, 14KJPN) (+ 16 more)
T=0.37824 (7145/18890, ALFA)
T=0.00453 (76/16760, 8.3KJPN)
T=0.1899 (1216/6404, 1000G_30x)
T=0.1915 (959/5008, 1000G)
T=0.4355 (1951/4480, Estonian)
T=0.4512 (1739/3854, ALSPAC)
T=0.4609 (1709/3708, TWINSUK)
T=0.0024 (7/2922, KOREAN)
T=0.0055 (10/1832, Korea1K)
T=0.460 (459/998, GoNL)
T=0.482 (289/600, NorthernSweden)
T=0.338 (73/216, Qatari)
T=0.005 (1/214, Vietnamese)
C=0.376 (64/170, SGDP_PRJ)
T=0.38 (15/40, GENOME_DK)
C=0.46 (12/26, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105373520 : 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	18890	C=0.62176	T=0.37824	0.401059	0.157544	0.441398	19
European	Sub	14286	C=0.55033	T=0.44967	0.297214	0.196556	0.50623	2
African	Sub	2946	C=0.9039	T=0.0961	0.816022	0.008147	0.175832	0
African Others	Sub	114	C=0.930	T=0.070	0.877193	0.017544	0.105263	1
African American	Sub	2832	C=0.9029	T=0.0971	0.813559	0.007768	0.178672	0
Asian	Sub	112	C=1.000	T=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	86	C=1.00	T=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	26	C=1.00	T=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	146	C=0.671	T=0.329	0.493151	0.150685	0.356164	2
Latin American 2	Sub	610	C=0.744	T=0.256	0.57377	0.085246	0.340984	2
South Asian	Sub	98	C=0.74	T=0.26	0.571429	0.081633	0.346939	0
Other	Sub	692	C=0.698	T=0.302	0.485549	0.089595	0.424855	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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.699422	T=0.300578
gnomAD - Genomes	Global	Study-wide	139952	C=0.675953	T=0.324047
gnomAD - Genomes	European	Sub	75806	C=0.54595	T=0.45405
gnomAD - Genomes	African	Sub	41944	C=0.89708	T=0.10292
gnomAD - Genomes	American	Sub	13610	C=0.66929	T=0.33071
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.5849	T=0.4151
gnomAD - Genomes	East Asian	Sub	3130	C=0.9942	T=0.0058
gnomAD - Genomes	Other	Sub	2142	C=0.6653	T=0.3347
14KJPN	JAPANESE	Study-wide	28256	C=0.99529	T=0.00471
Allele Frequency Aggregator	Total	Global	18890	C=0.62176	T=0.37824
Allele Frequency Aggregator	European	Sub	14286	C=0.55033	T=0.44967
Allele Frequency Aggregator	African	Sub	2946	C=0.9039	T=0.0961
Allele Frequency Aggregator	Other	Sub	692	C=0.698	T=0.302
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.744	T=0.256
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.671	T=0.329
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.74	T=0.26
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99547	T=0.00453
1000Genomes_30x	Global	Study-wide	6404	C=0.8101	T=0.1899
1000Genomes_30x	African	Sub	1786	C=0.9670	T=0.0330
1000Genomes_30x	Europe	Sub	1266	C=0.4850	T=0.5150
1000Genomes_30x	South Asian	Sub	1202	C=0.7945	T=0.2055
1000Genomes_30x	East Asian	Sub	1170	C=0.9915	T=0.0085
1000Genomes_30x	American	Sub	980	C=0.747	T=0.253
1000Genomes	Global	Study-wide	5008	C=0.8085	T=0.1915
1000Genomes	African	Sub	1322	C=0.9622	T=0.0378
1000Genomes	East Asian	Sub	1008	C=0.9911	T=0.0089
1000Genomes	Europe	Sub	1006	C=0.4920	T=0.5080
1000Genomes	South Asian	Sub	978	C=0.791	T=0.209
1000Genomes	American	Sub	694	C=0.733	T=0.267
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.5645	T=0.4355
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.5488	T=0.4512
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.5391	T=0.4609
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9976	T=0.0024
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9945	T=0.0055
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.540	T=0.460
Northern Sweden	ACPOP	Study-wide	600	C=0.518	T=0.482
Qatari	Global	Study-wide	216	C=0.662	T=0.338
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.995	T=0.005
SGDP_PRJ	Global	Study-wide	170	C=0.376	T=0.624
The Danish reference pan genome	Danish	Study-wide	40	C=0.62	T=0.38
Siberian	Global	Study-wide	26	C=0.46	T=0.54

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.103816798C>T
GRCh37.p13 chr 2	NC_000002.11:g.104433256C>T

Gene: LOC105373520, uncharacterized LOC105373520 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373520 transcript variant X2	XR_001739200.1:n.	N/A	Intron Variant
LOC105373520 transcript variant X1	XR_923123.1:n.	N/A	Intron Variant
LOC105373520 transcript variant X3	XR_923124.2: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	C=	T
GRCh38.p14 chr 2	NC_000002.12:g.103816798=	NC_000002.12:g.103816798C>T
GRCh37.p13 chr 2	NC_000002.11:g.104433256=	NC_000002.11:g.104433256C>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#.

55 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss91278934	Mar 24, 2008 (129)
2	ENSEMBL	ss138498883	Dec 01, 2009 (131)
3	COMPLETE_GENOMICS	ss164897143	Jul 04, 2010 (132)
4	COMPLETE_GENOMICS	ss166952706	Jul 04, 2010 (132)
5	BCM-HGSC-SUB	ss205845445	Jul 04, 2010 (132)
6	1000GENOMES	ss219410302	Jul 14, 2010 (132)
7	1000GENOMES	ss231289519	Jul 14, 2010 (132)
8	BL	ss253334078	May 09, 2011 (134)
9	GMI	ss284402492	Apr 25, 2013 (138)
10	TISHKOFF	ss555761079	Apr 25, 2013 (138)
11	EVA-GONL	ss977164381	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1069354765	Aug 21, 2014 (142)
13	1000GENOMES	ss1298563518	Aug 21, 2014 (142)
14	DDI	ss1428676454	Apr 01, 2015 (144)
15	EVA_GENOME_DK	ss1579007343	Apr 01, 2015 (144)
16	EVA_DECODE	ss1586587840	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1604180109	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1647174142	Apr 01, 2015 (144)
19	WEILL_CORNELL_DGM	ss1920409282	Feb 12, 2016 (147)
20	GENOMED	ss1968842676	Jul 19, 2016 (147)
21	JJLAB	ss2020734502	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2148789839	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2232859567	Dec 20, 2016 (150)
24	GRF	ss2703393398	Nov 08, 2017 (151)
25	GNOMAD	ss2777432260	Nov 08, 2017 (151)
26	SWEGEN	ss2990094403	Nov 08, 2017 (151)
27	BIOINF_KMB_FNS_UNIBA	ss3024129533	Nov 08, 2017 (151)
28	CSHL	ss3344383644	Nov 08, 2017 (151)
29	EGCUT_WGS	ss3657986922	Jul 13, 2019 (153)
30	EVA_DECODE	ss3704530958	Jul 13, 2019 (153)
31	ACPOP	ss3728703630	Jul 13, 2019 (153)
32	EVA	ss3757151464	Jul 13, 2019 (153)
33	PACBIO	ss3783944154	Jul 13, 2019 (153)
34	PACBIO	ss3789515510	Jul 13, 2019 (153)
35	PACBIO	ss3794388308	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3801518551	Jul 13, 2019 (153)
37	EVA	ss3827129851	Apr 25, 2020 (154)
38	EVA	ss3836975951	Apr 25, 2020 (154)
39	EVA	ss3842394482	Apr 25, 2020 (154)
40	SGDP_PRJ	ss3852988508	Apr 25, 2020 (154)
41	KRGDB	ss3898523677	Apr 25, 2020 (154)
42	KOGIC	ss3948575363	Apr 25, 2020 (154)
43	TOPMED	ss4517386515	Apr 26, 2021 (155)
44	TOMMO_GENOMICS	ss5152966689	Apr 26, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5249325876	Oct 12, 2022 (156)
46	EVA	ss5331085058	Oct 12, 2022 (156)
47	HUGCELL_USP	ss5449260662	Oct 12, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5525238624	Oct 12, 2022 (156)
49	SANFORD_IMAGENETICS	ss5629408474	Oct 12, 2022 (156)
50	TOMMO_GENOMICS	ss5682828162	Oct 12, 2022 (156)
51	YY_MCH	ss5802553360	Oct 12, 2022 (156)
52	EVA	ss5820539385	Oct 12, 2022 (156)
53	EVA	ss5852642744	Oct 12, 2022 (156)
54	EVA	ss5931641979	Oct 12, 2022 (156)
55	EVA	ss5955625849	Oct 12, 2022 (156)
56	1000Genomes	NC_000002.11 - 104433256	Oct 11, 2018 (152)
57	1000Genomes_30x	NC_000002.12 - 103816798	Oct 12, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 104433256	Oct 11, 2018 (152)
59	Genetic variation in the Estonian population	NC_000002.11 - 104433256	Oct 11, 2018 (152)
60	The Danish reference pan genome	NC_000002.11 - 104433256	Apr 25, 2020 (154)
61	gnomAD - Genomes	NC_000002.12 - 103816798	Apr 26, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000002.11 - 104433256	Apr 25, 2020 (154)
63	KOREAN population from KRGDB	NC_000002.11 - 104433256	Apr 25, 2020 (154)
64	Korean Genome Project	NC_000002.12 - 103816798	Apr 25, 2020 (154)
65	Northern Sweden	NC_000002.11 - 104433256	Jul 13, 2019 (153)
66	Qatari	NC_000002.11 - 104433256	Apr 25, 2020 (154)
67	SGDP_PRJ	NC_000002.11 - 104433256	Apr 25, 2020 (154)
68	Siberian	NC_000002.11 - 104433256	Apr 25, 2020 (154)
69	8.3KJPN	NC_000002.11 - 104433256	Apr 26, 2021 (155)
70	14KJPN	NC_000002.12 - 103816798	Oct 12, 2022 (156)
71	TopMed	NC_000002.12 - 103816798	Apr 26, 2021 (155)
72	UK 10K study - Twins	NC_000002.11 - 104433256	Oct 11, 2018 (152)
73	A Vietnamese Genetic Variation Database	NC_000002.11 - 104433256	Jul 13, 2019 (153)
74	ALFA	NC_000002.12 - 103816798	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
ss91278934, ss164897143, ss166952706, ss205845445, ss253334078, ss284402492, ss1586587840	NC_000002.10:103799687:C:T	NC_000002.12:103816797:C:T	(self)
9553216, 5274338, 3725170, 5174840, 2317750, 5701071, 1988495, 2451212, 5005488, 1306193, 10935996, 5274338, 1144327, ss219410302, ss231289519, ss555761079, ss977164381, ss1069354765, ss1298563518, ss1428676454, ss1579007343, ss1604180109, ss1647174142, ss1920409282, ss1968842676, ss2020734502, ss2148789839, ss2703393398, ss2777432260, ss2990094403, ss3344383644, ss3657986922, ss3728703630, ss3757151464, ss3783944154, ss3789515510, ss3794388308, ss3827129851, ss3836975951, ss3852988508, ss3898523677, ss5152966689, ss5331085058, ss5629408474, ss5820539385, ss5955625849	NC_000002.11:104433255:C:T	NC_000002.12:103816797:C:T	(self)
12764559, 68219824, 4953364, 16665266, 321209394, 1119050897, ss2232859567, ss3024129533, ss3704530958, ss3801518551, ss3842394482, ss3948575363, ss4517386515, ss5249325876, ss5449260662, ss5525238624, ss5682828162, ss5802553360, ss5852642744, ss5931641979	NC_000002.12:103816797:C:T	NC_000002.12:103816797:C:T	(self)
ss138498883	NT_022171.15:9107084:C:T	NC_000002.12:103816797:C: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 rs62151809

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

rs62151809