Name: rs1792080
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.

rs1792080

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:28735645 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.430046 (113829/264690, TOPMED)
C=0.451403 (63238/140092, GnomAD)
C=0.19782 (5590/28258, 14KJPN) (+ 16 more)
C=0.47655 (9002/18890, ALFA)
C=0.19988 (3350/16760, 8.3KJPN)
C=0.3755 (2405/6404, 1000G_30x)
C=0.3754 (1880/5008, 1000G)
T=0.4498 (2015/4480, Estonian)
C=0.4813 (1855/3854, ALSPAC)
C=0.4811 (1784/3708, TWINSUK)
C=0.2082 (610/2930, KOREAN)
C=0.1998 (366/1832, Korea1K)
C=0.488 (487/998, GoNL)
C=0.493 (296/600, NorthernSweden)
T=0.361 (112/310, SGDP_PRJ)
C=0.389 (84/216, Qatari)
C=0.217 (46/212, Vietnamese)
T=0.45 (18/40, GENOME_DK)
T=0.40 (12/30, 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	18890	T=0.52345	C=0.47655
European	Sub	14286	T=0.50070	C=0.49930
African	Sub	2946	T=0.5923	C=0.4077
African Others	Sub	114	T=0.658	C=0.342
African American	Sub	2832	T=0.5897	C=0.4103
Asian	Sub	112	T=0.777	C=0.223
East Asian	Sub	86	T=0.80	C=0.20
Other Asian	Sub	26	T=0.69	C=0.31
Latin American 1	Sub	146	T=0.534	C=0.466
Latin American 2	Sub	610	T=0.620	C=0.380
South Asian	Sub	98	T=0.57	C=0.43
Other	Sub	692	T=0.565	C=0.435

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	T=0.569954	C=0.430046
gnomAD - Genomes	Global	Study-wide	140092	T=0.548597	C=0.451403
gnomAD - Genomes	European	Sub	75860	T=0.50508	C=0.49492
gnomAD - Genomes	African	Sub	41976	T=0.58865	C=0.41135
gnomAD - Genomes	American	Sub	13650	T=0.61201	C=0.38799
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.5443	C=0.4557
gnomAD - Genomes	East Asian	Sub	3132	T=0.7931	C=0.2069
gnomAD - Genomes	Other	Sub	2152	T=0.5502	C=0.4498
14KJPN	JAPANESE	Study-wide	28258	T=0.80218	C=0.19782
Allele Frequency Aggregator	Total	Global	18890	T=0.52345	C=0.47655
Allele Frequency Aggregator	European	Sub	14286	T=0.50070	C=0.49930
Allele Frequency Aggregator	African	Sub	2946	T=0.5923	C=0.4077
Allele Frequency Aggregator	Other	Sub	692	T=0.565	C=0.435
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.620	C=0.380
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.534	C=0.466
Allele Frequency Aggregator	Asian	Sub	112	T=0.777	C=0.223
Allele Frequency Aggregator	South Asian	Sub	98	T=0.57	C=0.43
8.3KJPN	JAPANESE	Study-wide	16760	T=0.80012	C=0.19988
1000Genomes_30x	Global	Study-wide	6404	T=0.6245	C=0.3755
1000Genomes_30x	African	Sub	1786	T=0.5969	C=0.4031
1000Genomes_30x	Europe	Sub	1266	T=0.5237	C=0.4763
1000Genomes_30x	South Asian	Sub	1202	T=0.6165	C=0.3835
1000Genomes_30x	East Asian	Sub	1170	T=0.8068	C=0.1932
1000Genomes_30x	American	Sub	980	T=0.597	C=0.403
1000Genomes	Global	Study-wide	5008	T=0.6246	C=0.3754
1000Genomes	African	Sub	1322	T=0.5946	C=0.4054
1000Genomes	East Asian	Sub	1008	T=0.8056	C=0.1944
1000Genomes	Europe	Sub	1006	T=0.5169	C=0.4831
1000Genomes	South Asian	Sub	978	T=0.611	C=0.389
1000Genomes	American	Sub	694	T=0.594	C=0.406
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.4498	C=0.5502
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5187	C=0.4813
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5189	C=0.4811
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.7918	C=0.2082
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8002	C=0.1998
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.512	C=0.488
Northern Sweden	ACPOP	Study-wide	600	T=0.507	C=0.493
SGDP_PRJ	Global	Study-wide	310	T=0.361	C=0.639
Qatari	Global	Study-wide	216	T=0.611	C=0.389
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.783	C=0.217
The Danish reference pan genome	Danish	Study-wide	40	T=0.45	C=0.55
Siberian	Global	Study-wide	30	T=0.40	C=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 13	NC_000013.11:g.28735645T>C
GRCh37.p13 chr 13	NC_000013.10:g.29309782T>C

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	T=	C
GRCh38.p14 chr 13	NC_000013.11:g.28735645=	NC_000013.11:g.28735645T>C
GRCh37.p13 chr 13	NC_000013.10:g.29309782=	NC_000013.10:g.29309782T>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#.

70 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss2657982	Nov 09, 2000 (89)
2	SC_SNP	ss13302770	Dec 05, 2003 (119)
3	SSAHASNP	ss21149988	Apr 05, 2004 (121)
4	ABI	ss43485469	Mar 15, 2006 (126)
5	BCMHGSC_JDW	ss89559377	Mar 24, 2008 (129)
6	HUMANGENOME_JCVI	ss96954814	Feb 04, 2009 (130)
7	BGI	ss103106570	Dec 01, 2009 (131)
8	ENSEMBL	ss133504865	Dec 01, 2009 (131)
9	ENSEMBL	ss137273718	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss167792953	Jul 04, 2010 (132)
11	COMPLETE_GENOMICS	ss169073229	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss170933091	Jul 04, 2010 (132)
13	BUSHMAN	ss199014328	Jul 04, 2010 (132)
14	1000GENOMES	ss211380187	Jul 14, 2010 (132)
15	1000GENOMES	ss226099763	Jul 14, 2010 (132)
16	1000GENOMES	ss236190813	Jul 15, 2010 (132)
17	1000GENOMES	ss242698285	Jul 15, 2010 (132)
18	BL	ss254885928	May 09, 2011 (134)
19	GMI	ss281653352	May 04, 2012 (137)
20	GMI	ss286675452	Apr 25, 2013 (138)
21	PJP	ss291565041	May 09, 2011 (134)
22	TISHKOFF	ss563572150	Apr 25, 2013 (138)
23	SSMP	ss659167875	Apr 25, 2013 (138)
24	EVA-GONL	ss990229260	Aug 21, 2014 (142)
25	JMKIDD_LAB	ss1078964359	Aug 21, 2014 (142)
26	1000GENOMES	ss1347622896	Aug 21, 2014 (142)
27	DDI	ss1427140773	Apr 01, 2015 (144)
28	EVA_GENOME_DK	ss1576695576	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1629958866	Apr 01, 2015 (144)
30	EVA_DECODE	ss1642333737	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1672952899	Apr 01, 2015 (144)
32	HAMMER_LAB	ss1807542241	Sep 08, 2015 (146)
33	WEILL_CORNELL_DGM	ss1933598225	Feb 12, 2016 (147)
34	GENOMED	ss1967743568	Jul 19, 2016 (147)
35	JJLAB	ss2027554844	Sep 14, 2016 (149)
36	USC_VALOUEV	ss2155919490	Dec 20, 2016 (150)
37	HUMAN_LONGEVITY	ss2195108884	Dec 20, 2016 (150)
38	SYSTEMSBIOZJU	ss2628265524	Nov 08, 2017 (151)
39	GRF	ss2700291660	Nov 08, 2017 (151)
40	GNOMAD	ss2917952809	Nov 08, 2017 (151)
41	SWEGEN	ss3010775483	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3027592922	Nov 08, 2017 (151)
43	CSHL	ss3350382300	Nov 08, 2017 (151)
44	URBANLAB	ss3649996688	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3678036244	Jul 13, 2019 (153)
46	EVA_DECODE	ss3694993078	Jul 13, 2019 (153)
47	ACPOP	ss3739613153	Jul 13, 2019 (153)
48	EVA	ss3751276738	Jul 13, 2019 (153)
49	PACBIO	ss3787414510	Jul 13, 2019 (153)
50	PACBIO	ss3792487147	Jul 13, 2019 (153)
51	PACBIO	ss3797370863	Jul 13, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3816607971	Jul 13, 2019 (153)
53	EVA	ss3833467410	Apr 27, 2020 (154)
54	SGDP_PRJ	ss3879662391	Apr 27, 2020 (154)
55	KRGDB	ss3928483925	Apr 27, 2020 (154)
56	KOGIC	ss3973269736	Apr 27, 2020 (154)
57	TOPMED	ss4941024217	Apr 26, 2021 (155)
58	TOMMO_GENOMICS	ss5209320063	Apr 26, 2021 (155)
59	1000G_HIGH_COVERAGE	ss5293211275	Oct 16, 2022 (156)
60	EVA	ss5409810542	Oct 16, 2022 (156)
61	HUGCELL_USP	ss5487627228	Oct 16, 2022 (156)
62	EVA	ss5510919201	Oct 16, 2022 (156)
63	1000G_HIGH_COVERAGE	ss5591897117	Oct 16, 2022 (156)
64	SANFORD_IMAGENETICS	ss5654468201	Oct 16, 2022 (156)
65	TOMMO_GENOMICS	ss5761002572	Oct 16, 2022 (156)
66	YY_MCH	ss5813979524	Oct 16, 2022 (156)
67	EVA	ss5839267835	Oct 16, 2022 (156)
68	EVA	ss5850662205	Oct 16, 2022 (156)
69	EVA	ss5924500548	Oct 16, 2022 (156)
70	EVA	ss5945874670	Oct 16, 2022 (156)
71	1000Genomes	NC_000013.10 - 29309782	Oct 12, 2018 (152)
72	1000Genomes_30x	NC_000013.11 - 28735645	Oct 16, 2022 (156)
73	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 29309782	Oct 12, 2018 (152)
74	Genetic variation in the Estonian population	NC_000013.10 - 29309782	Oct 12, 2018 (152)
75	The Danish reference pan genome	NC_000013.10 - 29309782	Apr 27, 2020 (154)
76	gnomAD - Genomes	NC_000013.11 - 28735645	Apr 26, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000013.10 - 29309782	Apr 27, 2020 (154)
78	KOREAN population from KRGDB	NC_000013.10 - 29309782	Apr 27, 2020 (154)
79	Korean Genome Project	NC_000013.11 - 28735645	Apr 27, 2020 (154)
80	Northern Sweden	NC_000013.10 - 29309782	Jul 13, 2019 (153)
81	Qatari	NC_000013.10 - 29309782	Apr 27, 2020 (154)
82	SGDP_PRJ	NC_000013.10 - 29309782	Apr 27, 2020 (154)
83	Siberian	NC_000013.10 - 29309782	Apr 27, 2020 (154)
84	8.3KJPN	NC_000013.10 - 29309782	Apr 26, 2021 (155)
85	14KJPN	NC_000013.11 - 28735645	Oct 16, 2022 (156)
86	TopMed	NC_000013.11 - 28735645	Apr 26, 2021 (155)
87	UK 10K study - Twins	NC_000013.10 - 29309782	Oct 12, 2018 (152)
88	A Vietnamese Genetic Variation Database	NC_000013.10 - 29309782	Jul 13, 2019 (153)
89	ALFA	NC_000013.11 - 28735645	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
ss89559377, ss167792953, ss169073229, ss170933091, ss199014328, ss211380187, ss254885928, ss281653352, ss286675452, ss291565041, ss1642333737	NC_000013.9:28207781:T:C	NC_000013.11:28735644:T:C	(self)
60471460, 33585886, 23774492, 3234769, 14985719, 35661319, 12898018, 15640155, 31679371, 8435844, 67289370, 33585886, 7449973, ss226099763, ss236190813, ss242698285, ss563572150, ss659167875, ss990229260, ss1078964359, ss1347622896, ss1427140773, ss1576695576, ss1629958866, ss1672952899, ss1807542241, ss1933598225, ss1967743568, ss2027554844, ss2155919490, ss2628265524, ss2700291660, ss2917952809, ss3010775483, ss3350382300, ss3678036244, ss3739613153, ss3751276738, ss3787414510, ss3792487147, ss3797370863, ss3833467410, ss3879662391, ss3928483925, ss5209320063, ss5409810542, ss5510919201, ss5654468201, ss5839267835, ss5945874670	NC_000013.10:29309781:T:C	NC_000013.11:28735644:T:C	(self)
79423052, 426407968, 29647737, 94839676, 156569875, 208655840, ss2195108884, ss3027592922, ss3649996688, ss3694993078, ss3816607971, ss3973269736, ss4941024217, ss5293211275, ss5487627228, ss5591897117, ss5761002572, ss5813979524, ss5850662205, ss5924500548	NC_000013.11:28735644:T:C	NC_000013.11:28735644:T:C	(self)
ss13302770	NT_009799.12:10289781:T:C	NC_000013.11:28735644:T:C	(self)
ss21149988	NT_024524.13:10289781:T:C	NC_000013.11:28735644:T:C	(self)
ss2657982, ss43485469, ss96954814, ss103106570, ss133504865, ss137273718	NT_024524.14:10289781:T:C	NC_000013.11:28735644:T:C	(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 rs1792080

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

rs1792080