Name: rs2050082
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.

rs2050082

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:7710812 (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=0.293974 (77812/264690, TOPMED)
T=0.294683 (41265/140032, GnomAD)
C=0.35615 (10064/28258, 14KJPN) (+ 15 more)
T=0.31255 (5904/18890, ALFA)
C=0.35609 (5968/16760, 8.3KJPN)
T=0.3762 (2409/6404, 1000G_30x)
T=0.3862 (1934/5008, 1000G)
T=0.3326 (1490/4480, Estonian)
T=0.3511 (1353/3854, ALSPAC)
T=0.3403 (1262/3708, TWINSUK)
C=0.3259 (955/2930, KOREAN)
T=0.312 (311/998, GoNL)
T=0.322 (193/600, NorthernSweden)
C=0.311 (105/338, SGDP_PRJ)
T=0.222 (48/216, Qatari)
C=0.198 (42/212, Vietnamese)
T=0.33 (13/40, GENOME_DK)
C=0.38 (12/32, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105372518 : 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	C=0.68745	T=0.31255
European	Sub	14286	C=0.66520	T=0.33480
African	Sub	2946	C=0.8136	T=0.1864
African Others	Sub	114	C=0.816	T=0.184
African American	Sub	2832	C=0.8136	T=0.1864
Asian	Sub	112	C=0.312	T=0.688
East Asian	Sub	86	C=0.30	T=0.70
Other Asian	Sub	26	C=0.35	T=0.65
Latin American 1	Sub	146	C=0.726	T=0.274
Latin American 2	Sub	610	C=0.700	T=0.300
South Asian	Sub	98	C=0.61	T=0.39
Other	Sub	692	C=0.662	T=0.338

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	C=0.706026	T=0.293974
gnomAD - Genomes	Global	Study-wide	140032	C=0.705317	T=0.294683
gnomAD - Genomes	European	Sub	75838	C=0.65894	T=0.34106
gnomAD - Genomes	African	Sub	41984	C=0.81193	T=0.18807
gnomAD - Genomes	American	Sub	13620	C=0.73282	T=0.26718
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.7091	T=0.2909
gnomAD - Genomes	East Asian	Sub	3122	C=0.2761	T=0.7239
gnomAD - Genomes	Other	Sub	2144	C=0.7024	T=0.2976
14KJPN	JAPANESE	Study-wide	28258	C=0.35615	T=0.64385
Allele Frequency Aggregator	Total	Global	18890	C=0.68745	T=0.31255
Allele Frequency Aggregator	European	Sub	14286	C=0.66520	T=0.33480
Allele Frequency Aggregator	African	Sub	2946	C=0.8136	T=0.1864
Allele Frequency Aggregator	Other	Sub	692	C=0.662	T=0.338
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.700	T=0.300
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.726	T=0.274
Allele Frequency Aggregator	Asian	Sub	112	C=0.312	T=0.688
Allele Frequency Aggregator	South Asian	Sub	98	C=0.61	T=0.39
8.3KJPN	JAPANESE	Study-wide	16760	C=0.35609	T=0.64391
1000Genomes_30x	Global	Study-wide	6404	C=0.6238	T=0.3762
1000Genomes_30x	African	Sub	1786	C=0.8494	T=0.1506
1000Genomes_30x	Europe	Sub	1266	C=0.6485	T=0.3515
1000Genomes_30x	South Asian	Sub	1202	C=0.5083	T=0.4917
1000Genomes_30x	East Asian	Sub	1170	C=0.2632	T=0.7368
1000Genomes_30x	American	Sub	980	C=0.753	T=0.247
1000Genomes	Global	Study-wide	5008	C=0.6138	T=0.3862
1000Genomes	African	Sub	1322	C=0.8487	T=0.1513
1000Genomes	East Asian	Sub	1008	C=0.2639	T=0.7361
1000Genomes	Europe	Sub	1006	C=0.6581	T=0.3419
1000Genomes	South Asian	Sub	978	C=0.516	T=0.484
1000Genomes	American	Sub	694	C=0.748	T=0.252
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6674	T=0.3326
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6489	T=0.3511
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6597	T=0.3403
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.3259	T=0.6741
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.688	T=0.312
Northern Sweden	ACPOP	Study-wide	600	C=0.678	T=0.322
SGDP_PRJ	Global	Study-wide	338	C=0.311	T=0.689
Qatari	Global	Study-wide	216	C=0.778	T=0.222
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.198	T=0.802
The Danish reference pan genome	Danish	Study-wide	40	C=0.68	T=0.33
Siberian	Global	Study-wide	32	C=0.38	T=0.62

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 20	NC_000020.11:g.7710812C>T
GRCh37.p13 chr 20	NC_000020.10:g.7691459C>T

Gene: LOC105372518, uncharacterized LOC105372518 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105372518 transcript variant X3	XR_937232.1:n.	N/A	Intron Variant
LOC105372518 transcript variant X4	XR_937233.1:n.	N/A	Intron Variant
LOC105372518 transcript variant X2	XR_937230.2:n.	N/A	Genic Downstream Transcript Variant
LOC105372518 transcript variant X1	XR_937231.1:n.	N/A	Genic Downstream Transcript 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 20	NC_000020.11:g.7710812=	NC_000020.11:g.7710812C>T
GRCh37.p13 chr 20	NC_000020.10:g.7691459=	NC_000020.10:g.7691459C>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#.

65 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2960334	Apr 12, 2001 (94)
2	SC_SNP	ss8347235	Apr 21, 2003 (114)
3	SSAHASNP	ss21787655	Apr 05, 2004 (121)
4	PERLEGEN	ss24537533	Sep 20, 2004 (123)
5	ABI	ss41410260	Mar 15, 2006 (126)
6	BCMHGSC_JDW	ss91632073	Mar 24, 2008 (129)
7	HUMANGENOME_JCVI	ss96184338	Feb 06, 2009 (130)
8	ILLUMINA-UK	ss117475906	Feb 14, 2009 (130)
9	ENSEMBL	ss135671528	Dec 01, 2009 (131)
10	ENSEMBL	ss138207034	Dec 01, 2009 (131)
11	1000GENOMES	ss228245403	Jul 14, 2010 (132)
12	1000GENOMES	ss237754793	Jul 15, 2010 (132)
13	1000GENOMES	ss243942946	Jul 15, 2010 (132)
14	BL	ss255468634	May 09, 2011 (134)
15	GMI	ss283292523	May 04, 2012 (137)
16	PJP	ss292605768	May 09, 2011 (134)
17	TISHKOFF	ss566123340	Apr 25, 2013 (138)
18	SSMP	ss661994363	Apr 25, 2013 (138)
19	EVA-GONL	ss994518991	Aug 21, 2014 (142)
20	JMKIDD_LAB	ss1082056976	Aug 21, 2014 (142)
21	1000GENOMES	ss1363991353	Aug 21, 2014 (142)
22	DDI	ss1428989894	Apr 01, 2015 (144)
23	EVA_GENOME_DK	ss1579428799	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1638371828	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1681365861	Apr 01, 2015 (144)
26	EVA_DECODE	ss1698574352	Apr 01, 2015 (144)
27	HAMMER_LAB	ss1809414185	Sep 08, 2015 (146)
28	WEILL_CORNELL_DGM	ss1938029479	Feb 12, 2016 (147)
29	GENOMED	ss1969086076	Jul 19, 2016 (147)
30	JJLAB	ss2029793053	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2158347401	Dec 20, 2016 (150)
32	HUMAN_LONGEVITY	ss2241172347	Dec 20, 2016 (150)
33	SYSTEMSBIOZJU	ss2629393826	Nov 08, 2017 (151)
34	GRF	ss2704020155	Nov 08, 2017 (151)
35	GNOMAD	ss2965229728	Nov 08, 2017 (151)
36	SWEGEN	ss3017839321	Nov 08, 2017 (151)
37	BIOINF_KMB_FNS_UNIBA	ss3028729273	Nov 08, 2017 (151)
38	CSHL	ss3352410284	Nov 08, 2017 (151)
39	URBANLAB	ss3650967133	Oct 12, 2018 (152)
40	EGCUT_WGS	ss3684553935	Jul 13, 2019 (153)
41	EVA_DECODE	ss3706523253	Jul 13, 2019 (153)
42	ACPOP	ss3743232759	Jul 13, 2019 (153)
43	EVA	ss3758398872	Jul 13, 2019 (153)
44	PACBIO	ss3788594667	Jul 13, 2019 (153)
45	PACBIO	ss3793495644	Jul 13, 2019 (153)
46	PACBIO	ss3798382774	Jul 13, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3821572407	Jul 13, 2019 (153)
48	EVA	ss3835578300	Apr 27, 2020 (154)
49	EVA	ss3841413745	Apr 27, 2020 (154)
50	EVA	ss3846921370	Apr 27, 2020 (154)
51	SGDP_PRJ	ss3888693548	Apr 27, 2020 (154)
52	KRGDB	ss3938881256	Apr 27, 2020 (154)
53	TOPMED	ss5081619408	Apr 27, 2021 (155)
54	TOMMO_GENOMICS	ss5228761825	Apr 27, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5308023186	Oct 13, 2022 (156)
56	HUGCELL_USP	ss5500428753	Oct 13, 2022 (156)
57	EVA	ss5512148974	Oct 13, 2022 (156)
58	1000G_HIGH_COVERAGE	ss5614070150	Oct 13, 2022 (156)
59	SANFORD_IMAGENETICS	ss5662828037	Oct 13, 2022 (156)
60	TOMMO_GENOMICS	ss5787728243	Oct 13, 2022 (156)
61	YY_MCH	ss5817800535	Oct 13, 2022 (156)
62	EVA	ss5845419065	Oct 13, 2022 (156)
63	EVA	ss5853060473	Oct 13, 2022 (156)
64	EVA	ss5922600489	Oct 13, 2022 (156)
65	EVA	ss5957727870	Oct 13, 2022 (156)
66	1000Genomes	NC_000020.10 - 7691459	Oct 12, 2018 (152)
67	1000Genomes_30x	NC_000020.11 - 7710812	Oct 13, 2022 (156)
68	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 7691459	Oct 12, 2018 (152)
69	Genetic variation in the Estonian population	NC_000020.10 - 7691459	Oct 12, 2018 (152)
70	The Danish reference pan genome	NC_000020.10 - 7691459	Apr 27, 2020 (154)
71	gnomAD - Genomes	NC_000020.11 - 7710812	Apr 27, 2021 (155)
72	Genome of the Netherlands Release 5	NC_000020.10 - 7691459	Apr 27, 2020 (154)
73	KOREAN population from KRGDB	NC_000020.10 - 7691459	Apr 27, 2020 (154)
74	Northern Sweden	NC_000020.10 - 7691459	Jul 13, 2019 (153)
75	Qatari	NC_000020.10 - 7691459	Apr 27, 2020 (154)
76	SGDP_PRJ	NC_000020.10 - 7691459	Apr 27, 2020 (154)
77	Siberian	NC_000020.10 - 7691459	Apr 27, 2020 (154)
78	8.3KJPN	NC_000020.10 - 7691459	Apr 27, 2021 (155)
79	14KJPN	NC_000020.11 - 7710812	Oct 13, 2022 (156)
80	TopMed	NC_000020.11 - 7710812	Apr 27, 2021 (155)
81	UK 10K study - Twins	NC_000020.10 - 7691459	Oct 12, 2018 (152)
82	A Vietnamese Genetic Variation Database	NC_000020.10 - 7691459	Jul 13, 2019 (153)
83	ALFA	NC_000020.11 - 7710812	Apr 27, 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)
rs17405085	Oct 07, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss91632073, ss117475906, ss255468634, ss283292523, ss292605768, ss1698574352	NC_000020.9:7639458:C:T	NC_000020.11:7710811:C:T	(self)
77428361, 42860760, 30292183, 5593738, 19097507, 46058650, 16517624, 20071401, 40710528, 10863755, 86731132, 42860760, 9462077, ss228245403, ss237754793, ss243942946, ss566123340, ss661994363, ss994518991, ss1082056976, ss1363991353, ss1428989894, ss1579428799, ss1638371828, ss1681365861, ss1809414185, ss1938029479, ss1969086076, ss2029793053, ss2158347401, ss2629393826, ss2704020155, ss2965229728, ss3017839321, ss3352410284, ss3684553935, ss3743232759, ss3758398872, ss3788594667, ss3793495644, ss3798382774, ss3835578300, ss3841413745, ss3888693548, ss3938881256, ss5228761825, ss5512148974, ss5662828037, ss5845419065, ss5957727870	NC_000020.10:7691458:C:T	NC_000020.11:7710811:C:T	(self)
101596085, 545961753, 121565347, 356728353, 407961180, ss2241172347, ss3028729273, ss3650967133, ss3706523253, ss3821572407, ss3846921370, ss5081619408, ss5308023186, ss5500428753, ss5614070150, ss5787728243, ss5817800535, ss5853060473, ss5922600489	NC_000020.11:7710811:C:T	NC_000020.11:7710811:C:T	(self)
ss2960334, ss8347235, ss21787655, ss24537533, ss41410260, ss96184338, ss135671528, ss138207034	NT_011387.8:7631458:C:T	NC_000020.11:7710811: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 rs2050082

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

rs2050082