Name: rs62119920
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.

rs62119920

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:2484445 (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=0.163274 (43217/264690, TOPMED)
T=0.168589 (23618/140092, GnomAD)
T=0.21196 (6388/30138, ALFA) (+ 16 more)
T=0.08341 (2357/28258, 14KJPN)
T=0.08377 (1404/16760, 8.3KJPN)
T=0.1302 (834/6404, 1000G_30x)
T=0.1298 (650/5008, 1000G)
T=0.2533 (1135/4480, Estonian)
T=0.2146 (827/3854, ALSPAC)
T=0.2136 (792/3708, TWINSUK)
T=0.0856 (250/2922, KOREAN)
T=0.0759 (139/1832, Korea1K)
T=0.205 (205/998, GoNL)
T=0.202 (121/600, NorthernSweden)
T=0.241 (52/216, Qatari)
T=0.103 (22/214, Vietnamese)
C=0.434 (66/152, SGDP_PRJ)
T=0.25 (10/40, GENOME_DK)
C=0.40 (8/20, 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	30138	C=0.78804	T=0.21196
European	Sub	24390	C=0.77040	T=0.22960
African	Sub	3114	C=0.9011	T=0.0989
African Others	Sub	124	C=0.952	T=0.048
African American	Sub	2990	C=0.8990	T=0.1010
Asian	Sub	122	C=0.934	T=0.066
East Asian	Sub	96	C=0.92	T=0.08
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	156	C=0.776	T=0.224
Latin American 2	Sub	678	C=0.858	T=0.142
South Asian	Sub	114	C=0.868	T=0.132
Other	Sub	1564	C=0.7916	T=0.2084

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=0.836726	T=0.163274
gnomAD - Genomes	Global	Study-wide	140092	C=0.831411	T=0.168589
gnomAD - Genomes	European	Sub	75880	C=0.78529	T=0.21471
gnomAD - Genomes	African	Sub	41980	C=0.90405	T=0.09595
gnomAD - Genomes	American	Sub	13626	C=0.85953	T=0.14047
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.7557	T=0.2443
gnomAD - Genomes	East Asian	Sub	3132	C=0.9377	T=0.0623
gnomAD - Genomes	Other	Sub	2154	C=0.8245	T=0.1755
Allele Frequency Aggregator	Total	Global	30138	C=0.78804	T=0.21196
Allele Frequency Aggregator	European	Sub	24390	C=0.77040	T=0.22960
Allele Frequency Aggregator	African	Sub	3114	C=0.9011	T=0.0989
Allele Frequency Aggregator	Other	Sub	1564	C=0.7916	T=0.2084
Allele Frequency Aggregator	Latin American 2	Sub	678	C=0.858	T=0.142
Allele Frequency Aggregator	Latin American 1	Sub	156	C=0.776	T=0.224
Allele Frequency Aggregator	Asian	Sub	122	C=0.934	T=0.066
Allele Frequency Aggregator	South Asian	Sub	114	C=0.868	T=0.132
14KJPN	JAPANESE	Study-wide	28258	C=0.91659	T=0.08341
8.3KJPN	JAPANESE	Study-wide	16760	C=0.91623	T=0.08377
1000Genomes_30x	Global	Study-wide	6404	C=0.8698	T=0.1302
1000Genomes_30x	African	Sub	1786	C=0.9255	T=0.0745
1000Genomes_30x	Europe	Sub	1266	C=0.7804	T=0.2196
1000Genomes_30x	South Asian	Sub	1202	C=0.8511	T=0.1489
1000Genomes_30x	East Asian	Sub	1170	C=0.9154	T=0.0846
1000Genomes_30x	American	Sub	980	C=0.852	T=0.148
1000Genomes	Global	Study-wide	5008	C=0.8702	T=0.1298
1000Genomes	African	Sub	1322	C=0.9259	T=0.0741
1000Genomes	East Asian	Sub	1008	C=0.9127	T=0.0873
1000Genomes	Europe	Sub	1006	C=0.7813	T=0.2187
1000Genomes	South Asian	Sub	978	C=0.852	T=0.148
1000Genomes	American	Sub	694	C=0.857	T=0.143
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7467	T=0.2533
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7854	T=0.2146
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7864	T=0.2136
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9144	T=0.0856
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9241	T=0.0759
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.795	T=0.205
Northern Sweden	ACPOP	Study-wide	600	C=0.798	T=0.202
Qatari	Global	Study-wide	216	C=0.759	T=0.241
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.897	T=0.103
SGDP_PRJ	Global	Study-wide	152	C=0.434	T=0.566
The Danish reference pan genome	Danish	Study-wide	40	C=0.75	T=0.25
Siberian	Global	Study-wide	20	C=0.40	T=0.60

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 19	NC_000019.10:g.2484445C>T
GRCh37.p13 chr 19	NC_000019.9:g.2484443C>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	C=	T
GRCh38.p14 chr 19	NC_000019.10:g.2484445=	NC_000019.10:g.2484445C>T
GRCh37.p13 chr 19	NC_000019.9:g.2484443=	NC_000019.9:g.2484443C>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#.

66 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss90882338	Mar 24, 2008 (129)
2	ENSEMBL	ss137517126	Dec 01, 2009 (131)
3	COMPLETE_GENOMICS	ss167666429	Jul 04, 2010 (132)
4	BUSHMAN	ss203593606	Jul 04, 2010 (132)
5	1000GENOMES	ss228010728	Jul 14, 2010 (132)
6	1000GENOMES	ss237579819	Jul 15, 2010 (132)
7	1000GENOMES	ss243806847	Jul 15, 2010 (132)
8	BL	ss255436410	May 09, 2011 (134)
9	GMI	ss283099365	May 04, 2012 (137)
10	ILLUMINA	ss483782598	May 04, 2012 (137)
11	ILLUMINA	ss483808227	May 04, 2012 (137)
12	ILLUMINA	ss535981064	Sep 08, 2015 (146)
13	TISHKOFF	ss565811579	Apr 25, 2013 (138)
14	SSMP	ss661664204	Apr 25, 2013 (138)
15	ILLUMINA	ss780406557	Sep 08, 2015 (146)
16	ILLUMINA	ss782334826	Sep 08, 2015 (146)
17	ILLUMINA	ss835895512	Sep 08, 2015 (146)
18	EVA-GONL	ss994018221	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1081714504	Aug 21, 2014 (142)
20	1000GENOMES	ss1362089001	Aug 21, 2014 (142)
21	DDI	ss1428313311	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1578527815	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1637441812	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1680435845	Apr 01, 2015 (144)
25	EVA_DECODE	ss1698080963	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1809175508	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1937495552	Feb 12, 2016 (147)
28	GENOMED	ss1968593477	Jul 19, 2016 (147)
29	JJLAB	ss2029522852	Sep 14, 2016 (149)
30	USC_VALOUEV	ss2158036082	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2223758172	Dec 20, 2016 (150)
32	ILLUMINA	ss2633509656	Nov 08, 2017 (151)
33	GRF	ss2702639604	Nov 08, 2017 (151)
34	GNOMAD	ss2959680937	Nov 08, 2017 (151)
35	SWEGEN	ss3016972956	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3028593779	Nov 08, 2017 (151)
37	CSHL	ss3352163282	Nov 08, 2017 (151)
38	ILLUMINA	ss3627872779	Oct 12, 2018 (152)
39	ILLUMINA	ss3631483861	Oct 12, 2018 (152)
40	ILLUMINA	ss3642046230	Oct 12, 2018 (152)
41	EGCUT_WGS	ss3683821132	Jul 13, 2019 (153)
42	EVA_DECODE	ss3702200025	Jul 13, 2019 (153)
43	ACPOP	ss3742792718	Jul 13, 2019 (153)
44	EVA	ss3755730403	Jul 13, 2019 (153)
45	PACBIO	ss3788447906	Jul 13, 2019 (153)
46	PACBIO	ss3793371105	Jul 13, 2019 (153)
47	PACBIO	ss3798257651	Jul 13, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3820983819	Jul 13, 2019 (153)
49	EVA	ss3835313635	Apr 27, 2020 (154)
50	SGDP_PRJ	ss3887608372	Apr 27, 2020 (154)
51	KRGDB	ss3937540638	Apr 27, 2020 (154)
52	KOGIC	ss3980665944	Apr 27, 2020 (154)
53	TOPMED	ss5065826216	Apr 26, 2021 (155)
54	TOMMO_GENOMICS	ss5226394762	Apr 26, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5306238521	Oct 16, 2022 (156)
56	EVA	ss5315956458	Oct 16, 2022 (156)
57	EVA	ss5433142181	Oct 16, 2022 (156)
58	HUGCELL_USP	ss5498905754	Oct 16, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5611541527	Oct 16, 2022 (156)
60	SANFORD_IMAGENETICS	ss5661838822	Oct 16, 2022 (156)
61	TOMMO_GENOMICS	ss5784551406	Oct 16, 2022 (156)
62	YY_MCH	ss5817344082	Oct 16, 2022 (156)
63	EVA	ss5840157297	Oct 16, 2022 (156)
64	EVA	ss5852176743	Oct 16, 2022 (156)
65	EVA	ss5927035555	Oct 16, 2022 (156)
66	EVA	ss5953269166	Oct 16, 2022 (156)
67	1000Genomes	NC_000019.9 - 2484443	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000019.10 - 2484445	Oct 16, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 2484443	Oct 12, 2018 (152)
70	Genetic variation in the Estonian population	NC_000019.9 - 2484443	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000019.9 - 2484443	Apr 27, 2020 (154)
72	gnomAD - Genomes	NC_000019.10 - 2484445	Apr 26, 2021 (155)
73	Genome of the Netherlands Release 5	NC_000019.9 - 2484443	Apr 27, 2020 (154)
74	KOREAN population from KRGDB	NC_000019.9 - 2484443	Apr 27, 2020 (154)
75	Korean Genome Project	NC_000019.10 - 2484445	Apr 27, 2020 (154)
76	Northern Sweden	NC_000019.9 - 2484443	Jul 13, 2019 (153)
77	Qatari	NC_000019.9 - 2484443	Apr 27, 2020 (154)
78	SGDP_PRJ	NC_000019.9 - 2484443	Apr 27, 2020 (154)
79	Siberian	NC_000019.9 - 2484443	Apr 27, 2020 (154)
80	8.3KJPN	NC_000019.9 - 2484443	Apr 26, 2021 (155)
81	14KJPN	NC_000019.10 - 2484445	Oct 16, 2022 (156)
82	TopMed	NC_000019.10 - 2484445	Apr 26, 2021 (155)
83	UK 10K study - Twins	NC_000019.9 - 2484443	Oct 12, 2018 (152)
84	A Vietnamese Genetic Variation Database	NC_000019.9 - 2484443	Jul 13, 2019 (153)
85	ALFA	NC_000019.10 - 2484445	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
ss90882338, ss167666429, ss203593606, ss255436410, ss283099365, ss483808227, ss1698080963	NC_000019.8:2435442:C:T	NC_000019.10:2484444:C:T	(self)
75456029, 41821896, 29559380, 4714894, 18632590, 44718032, 16077583, 19537474, 39625352, 10552436, 84364069, 41821896, 9248574, ss228010728, ss237579819, ss243806847, ss483782598, ss535981064, ss565811579, ss661664204, ss780406557, ss782334826, ss835895512, ss994018221, ss1081714504, ss1362089001, ss1428313311, ss1578527815, ss1637441812, ss1680435845, ss1809175508, ss1937495552, ss1968593477, ss2029522852, ss2158036082, ss2633509656, ss2702639604, ss2959680937, ss3016972956, ss3352163282, ss3627872779, ss3631483861, ss3642046230, ss3683821132, ss3742792718, ss3755730403, ss3788447906, ss3793371105, ss3798257651, ss3835313635, ss3887608372, ss3937540638, ss5226394762, ss5315956458, ss5433142181, ss5661838822, ss5840157297, ss5953269166	NC_000019.9:2484442:C:T	NC_000019.10:2484444:C:T	(self)
99067462, 532134092, 37043945, 118388510, 281371880, 3229110674, ss2223758172, ss3028593779, ss3702200025, ss3820983819, ss3980665944, ss5065826216, ss5306238521, ss5498905754, ss5611541527, ss5784551406, ss5817344082, ss5852176743, ss5927035555	NC_000019.10:2484444:C:T	NC_000019.10:2484444:C:T	(self)
ss137517126	NT_011255.14:2424442:C:T	NC_000019.10:2484444: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 rs62119920

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

rs62119920