Name: rs5781943
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.

rs5781943

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:237244816-237244817 (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: dupC
Variation Type: Indel Insertion and Deletion
Frequency: CC=0.274982 (72785/264690, TOPMED)
CC=0.280295 (39225/139942, GnomAD)
CC=0.19146 (5410/28256, 14KJPN) (+ 11 more)
CC=0.29111 (6203/21308, ALFA)
CC=0.18998 (3184/16760, 8.3KJPN)
CC=0.2333 (1494/6404, 1000G_30x)
CC=0.2342 (1173/5008, 1000G)
CC=0.2951 (1322/4480, Estonian)
CC=0.3352 (1292/3854, ALSPAC)
CC=0.3247 (1204/3708, TWINSUK)
CC=0.1703 (312/1832, Korea1K)
CC=0.319 (318/998, GoNL)
CC=0.243 (146/600, NorthernSweden)
CC=0.33 (13/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RYR2 : 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	21308	CC=0.29111	CCC=0.70889
European	Sub	14236	CC=0.31750	CCC=0.68250
African	Sub	5532	CC=0.2392	CCC=0.7608
African Others	Sub	198	CC=0.293	CCC=0.707
African American	Sub	5334	CC=0.2372	CCC=0.7628
Asian	Sub	114	CC=0.158	CCC=0.842
East Asian	Sub	88	CC=0.14	CCC=0.86
Other Asian	Sub	26	CC=0.23	CCC=0.77
Latin American 1	Sub	146	CC=0.363	CCC=0.637
Latin American 2	Sub	610	CC=0.161	CCC=0.839
South Asian	Sub	100	CC=0.19	CCC=0.81
Other	Sub	570	CC=0.302	CCC=0.698

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	- No frequency provided	dupC=0.725018
gnomAD - Genomes	Global	Study-wide	139942	- No frequency provided	dupC=0.719705
gnomAD - Genomes	European	Sub	75804	- No frequency provided	dupC=0.68367
gnomAD - Genomes	African	Sub	41908	- No frequency provided	dupC=0.76267
gnomAD - Genomes	American	Sub	13628	- No frequency provided	dupC=0.75895
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	- No frequency provided	dupC=0.7163
gnomAD - Genomes	East Asian	Sub	3130	- No frequency provided	dupC=0.8636
gnomAD - Genomes	Other	Sub	2148	- No frequency provided	dupC=0.6997
14KJPN	JAPANESE	Study-wide	28256	- No frequency provided	dupC=0.80854
Allele Frequency Aggregator	Total	Global	21308	CC=0.29111	dupC=0.70889
Allele Frequency Aggregator	European	Sub	14236	CC=0.31750	dupC=0.68250
Allele Frequency Aggregator	African	Sub	5532	CC=0.2392	dupC=0.7608
Allele Frequency Aggregator	Latin American 2	Sub	610	CC=0.161	dupC=0.839
Allele Frequency Aggregator	Other	Sub	570	CC=0.302	dupC=0.698
Allele Frequency Aggregator	Latin American 1	Sub	146	CC=0.363	dupC=0.637
Allele Frequency Aggregator	Asian	Sub	114	CC=0.158	dupC=0.842
Allele Frequency Aggregator	South Asian	Sub	100	CC=0.19	dupC=0.81
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupC=0.81002
1000Genomes_30x	Global	Study-wide	6404	- No frequency provided	dupC=0.7667
1000Genomes_30x	African	Sub	1786	- No frequency provided	dupC=0.7604
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	dupC=0.6524
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	dupC=0.7812
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	dupC=0.8880
1000Genomes_30x	American	Sub	980	- No frequency provided	dupC=0.763
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupC=0.7658
1000Genomes	African	Sub	1322	- No frequency provided	dupC=0.7564
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupC=0.8810
1000Genomes	Europe	Sub	1006	- No frequency provided	dupC=0.6541
1000Genomes	South Asian	Sub	978	- No frequency provided	dupC=0.779
1000Genomes	American	Sub	694	- No frequency provided	dupC=0.759
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	dupC=0.7049
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	- No frequency provided	dupC=0.6648
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	- No frequency provided	dupC=0.6753
Korean Genome Project	KOREAN	Study-wide	1832	- No frequency provided	dupC=0.8297
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	- No frequency provided	dupC=0.681
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupC=0.757
The Danish reference pan genome	Danish	Study-wide	40	- No frequency provided	dupC=0.68

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 1	NC_000001.11:g.237244817dup
GRCh37.p13 chr 1	NC_000001.10:g.237408117dup
RYR2 RefSeqGene (LRG_402)	NG_008799.3:g.207634dup

Gene: RYR2, ryanodine receptor 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RYR2 transcript	NM_001035.3:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X1	XM_006711802.4:c.49-25680… XM_006711802.4:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X2	XM_006711803.4:c.49-25680… XM_006711803.4:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X4	XM_006711804.4:c.49-25680… XM_006711804.4:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X5	XM_006711805.4:c.49-25680… XM_006711805.4:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X7	XM_006711806.4:c.49-25680… XM_006711806.4:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X8	XM_006711807.4:c.49-25680… XM_006711807.4:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X9	XM_006711808.4:c.49-25680… XM_006711808.4:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X17	XM_006711810.4:c.49-25680… XM_006711810.4:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X3	XM_017002028.2:c.49-25680… XM_017002028.2:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X6	XM_047427317.1:c.49-25680… XM_047427317.1:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X10	XM_047427329.1:c.49-25680… XM_047427329.1:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X11	XM_047427333.1:c.49-25680… XM_047427333.1:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X12	XM_047427336.1:c.49-25680… XM_047427336.1:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X13	XM_047427337.1:c.49-25680… XM_047427337.1:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X14	XM_047427341.1:c.49-25680… XM_047427341.1:c.49-25680dup	N/A	Intron Variant
RYR2 transcript variant X16	XR_002957299.2:n.	N/A	Intron Variant
RYR2 transcript variant X15	XR_007062490.1: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	CC=	dupC
GRCh38.p14 chr 1	NC_000001.11:g.237244816_237244817=	NC_000001.11:g.237244817dup
GRCh37.p13 chr 1	NC_000001.10:g.237408116_237408117=	NC_000001.10:g.237408117dup
RYR2 RefSeqGene (LRG_402)	NG_008799.3:g.207633_207634=	NG_008799.3:g.207634dup
RYR2 transcript	NM_001035.2:c.49-25681=	NM_001035.2:c.49-25680dup
RYR2 transcript	NM_001035.3:c.49-25681=	NM_001035.3:c.49-25680dup
RYR2 transcript variant X1	XM_005273224.1:c.49-25681=	XM_005273224.1:c.49-25680dup
RYR2 transcript variant X1	XM_006711802.4:c.49-25681=	XM_006711802.4:c.49-25680dup
RYR2 transcript variant X2	XM_006711803.4:c.49-25681=	XM_006711803.4:c.49-25680dup
RYR2 transcript variant X4	XM_006711804.4:c.49-25681=	XM_006711804.4:c.49-25680dup
RYR2 transcript variant X5	XM_006711805.4:c.49-25681=	XM_006711805.4:c.49-25680dup
RYR2 transcript variant X7	XM_006711806.4:c.49-25681=	XM_006711806.4:c.49-25680dup
RYR2 transcript variant X8	XM_006711807.4:c.49-25681=	XM_006711807.4:c.49-25680dup
RYR2 transcript variant X9	XM_006711808.4:c.49-25681=	XM_006711808.4:c.49-25680dup
RYR2 transcript variant X17	XM_006711810.4:c.49-25681=	XM_006711810.4:c.49-25680dup
RYR2 transcript variant X3	XM_017002028.2:c.49-25681=	XM_017002028.2:c.49-25680dup
RYR2 transcript variant X6	XM_047427317.1:c.49-25681=	XM_047427317.1:c.49-25680dup
RYR2 transcript variant X10	XM_047427329.1:c.49-25681=	XM_047427329.1:c.49-25680dup
RYR2 transcript variant X11	XM_047427333.1:c.49-25681=	XM_047427333.1:c.49-25680dup
RYR2 transcript variant X12	XM_047427336.1:c.49-25681=	XM_047427336.1:c.49-25680dup
RYR2 transcript variant X13	XM_047427337.1:c.49-25681=	XM_047427337.1:c.49-25680dup
RYR2 transcript variant X14	XM_047427341.1:c.49-25681=	XM_047427341.1:c.49-25680dup

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#.

64 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ABI	ss41264015	Mar 14, 2006 (126)
2	HUMANGENOME_JCVI	ss95259023	Feb 06, 2009 (138)
3	BGI	ss104672770	Feb 13, 2009 (138)
4	BGI	ss105449572	Feb 13, 2009 (138)
5	GMI	ss154616654	Oct 11, 2018 (152)
6	BUSHMAN	ss193158679	Jul 04, 2010 (132)
7	BL	ss255977131	May 09, 2011 (135)
8	GMI	ss287690590	May 09, 2011 (134)
9	GMI	ss288109368	May 04, 2012 (137)
10	PJP	ss294632621	May 09, 2011 (138)
11	PJP	ss294632622	May 09, 2011 (138)
12	1000GENOMES	ss326149684	May 09, 2011 (135)
13	1000GENOMES	ss326155046	May 09, 2011 (135)
14	1000GENOMES	ss326202523	May 09, 2011 (135)
15	1000GENOMES	ss499165172	May 04, 2012 (137)
16	LUNTER	ss551033624	Apr 25, 2013 (138)
17	LUNTER	ss551067916	Apr 25, 2013 (138)
18	LUNTER	ss552855678	Apr 25, 2013 (138)
19	TISHKOFF	ss554866206	Apr 25, 2013 (138)
20	SSMP	ss663169707	Apr 01, 2015 (144)
21	BILGI_BIOE	ss666132116	Apr 25, 2013 (138)
22	EVA-GONL	ss976298969	Aug 21, 2014 (142)
23	1000GENOMES	ss1368051454	Aug 21, 2014 (142)
24	DDI	ss1536270513	Apr 01, 2015 (144)
25	EVA_GENOME_DK	ss1574114000	Apr 01, 2015 (144)
26	EVA_DECODE	ss1585700989	Apr 01, 2015 (144)
27	EVA_UK10K_ALSPAC	ss1701969621	Apr 01, 2015 (144)
28	EVA_UK10K_TWINSUK	ss1701969624	Apr 01, 2015 (144)
29	HAMMER_LAB	ss1795949346	Sep 08, 2015 (146)
30	GENOMED	ss1967009723	Jul 19, 2016 (147)
31	JJLAB	ss2030384666	Sep 14, 2016 (149)
32	SYSTEMSBIOZJU	ss2624656635	Nov 08, 2017 (151)
33	GNOMAD	ss2767837316	Nov 08, 2017 (151)
34	SWEGEN	ss2988689733	Nov 08, 2017 (151)
35	MCHAISSO	ss3063632140	Nov 08, 2017 (151)
36	MCHAISSO	ss3064450717	Nov 08, 2017 (151)
37	MCHAISSO	ss3065357389	Nov 08, 2017 (151)
38	BEROUKHIMLAB	ss3644081667	Oct 11, 2018 (152)
39	BIOINF_KMB_FNS_UNIBA	ss3645106266	Oct 11, 2018 (152)
40	URBANLAB	ss3646919128	Oct 11, 2018 (152)
41	EGCUT_WGS	ss3656648495	Jul 12, 2019 (153)
42	EVA_DECODE	ss3688916963	Jul 12, 2019 (153)
43	ACPOP	ss3727990699	Jul 12, 2019 (153)
44	PACBIO	ss3783728250	Jul 12, 2019 (153)
45	PACBIO	ss3789334097	Jul 12, 2019 (153)
46	PACBIO	ss3794206525	Jul 12, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3800520180	Jul 12, 2019 (153)
48	EVA	ss3826721270	Apr 25, 2020 (154)
49	EVA	ss3836763290	Apr 25, 2020 (154)
50	EVA	ss3842176056	Apr 25, 2020 (154)
51	KOGIC	ss3946792258	Apr 25, 2020 (154)
52	TOPMED	ss4488556322	Apr 25, 2021 (155)
53	TOMMO_GENOMICS	ss5149093387	Apr 25, 2021 (155)
54	1000G_HIGH_COVERAGE	ss5246300319	Oct 17, 2022 (156)
55	HUGCELL_USP	ss5446687416	Oct 17, 2022 (156)
56	1000G_HIGH_COVERAGE	ss5520644529	Oct 17, 2022 (156)
57	SANFORD_IMAGENETICS	ss5627733623	Oct 17, 2022 (156)
58	TOMMO_GENOMICS	ss5677046600	Oct 17, 2022 (156)
59	YY_MCH	ss5801769205	Oct 17, 2022 (156)
60	EVA	ss5833467473	Oct 17, 2022 (156)
61	EVA	ss5849351829	Oct 17, 2022 (156)
62	EVA	ss5912554030	Oct 17, 2022 (156)
63	EVA	ss5939584841	Oct 17, 2022 (156)
64	EVA	ss5980024917	Oct 17, 2022 (156)
65	1000Genomes	NC_000001.10 - 237408116	Oct 11, 2018 (152)
66	1000Genomes_30x	NC_000001.11 - 237244816	Oct 17, 2022 (156)
67	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 237408116	Oct 11, 2018 (152)
68	Genetic variation in the Estonian population	NC_000001.10 - 237408116	Oct 11, 2018 (152)
69	The Danish reference pan genome	NC_000001.10 - 237408116	Apr 25, 2020 (154)
70	gnomAD - Genomes	NC_000001.11 - 237244816	Apr 25, 2021 (155)
71	Genome of the Netherlands Release 5	NC_000001.10 - 237408116	Apr 25, 2020 (154)
72	Korean Genome Project	NC_000001.11 - 237244816	Apr 25, 2020 (154)
73	Northern Sweden	NC_000001.10 - 237408116	Jul 12, 2019 (153)
74	8.3KJPN	NC_000001.10 - 237408116	Apr 25, 2021 (155)
75	14KJPN	NC_000001.11 - 237244816	Oct 17, 2022 (156)
76	TopMed	NC_000001.11 - 237244816	Apr 25, 2021 (155)
77	UK 10K study - Twins	NC_000001.10 - 237408116	Oct 11, 2018 (152)
78	ALFA	NC_000001.11 - 237244816	Apr 25, 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)
rs5781944	May 15, 2013 (138)
rs33954668	May 11, 2012 (137)
rs66575230	May 11, 2012 (137)
rs66575231	Feb 26, 2009 (130)
rs66575232	Feb 26, 2009 (130)
rs138686302	Sep 17, 2011 (135)
rs142880142	Sep 17, 2011 (135)
rs151055931	Sep 17, 2011 (135)
rs370171450	May 15, 2013 (138)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss255977131, ss288109368, ss326149684, ss326155046, ss326202523, ss551033624, ss551067916, ss552855678, ss1585700989	NC_000001.9:235474738::C	NC_000001.11:237244815:CC:CCC	(self)
ss294632621	NC_000001.9:235474739::C	NC_000001.11:237244815:CC:CCC	(self)
ss294632622	NC_000001.9:235474740::C	NC_000001.11:237244815:CC:CCC	(self)
6100481, 3378269, 2386743, 208989, 1477895, 1275564, 7062694, 3378269, ss499165172, ss663169707, ss666132116, ss976298969, ss1368051454, ss1536270513, ss1574114000, ss1701969621, ss1701969624, ss1795949346, ss1967009723, ss2030384666, ss2624656635, ss2767837316, ss2988689733, ss3644081667, ss3656648495, ss3727990699, ss3783728250, ss3789334097, ss3794206525, ss3826721270, ss3836763290, ss5149093387, ss5627733623, ss5833467473, ss5939584841, ss5980024917	NC_000001.10:237408115::C	NC_000001.11:237244815:CC:CCC	(self)
ss554866206	NC_000001.10:237408117::C	NC_000001.11:237244815:CC:CCC	(self)
8170464, 43700209, 3170259, 10883704, 52162657, ss3063632140, ss3064450717, ss3065357389, ss3645106266, ss3646919128, ss3688916963, ss3800520180, ss3842176056, ss3946792258, ss4488556322, ss5246300319, ss5446687416, ss5520644529, ss5677046600, ss5801769205, ss5849351829, ss5912554030	NC_000001.11:237244815::C	NC_000001.11:237244815:CC:CCC	(self)
12983186560	NC_000001.11:237244815:CC:CCC	NC_000001.11:237244815:CC:CCC	(self)
ss41264015, ss287690590	NT_167186.1:30925894::C	NC_000001.11:237244815:CC:CCC	(self)
ss104672770, ss105449572	NT_167186.1:30925895::C	NC_000001.11:237244815:CC:CCC	(self)
ss95259023, ss154616654	NT_167186.1:30925896::C	NC_000001.11:237244815:CC:CCC	(self)
ss193158679	NT_167186.2:13635880::C	NC_000001.11:237244815:CC:CCC	(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 rs5781943

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

rs5781943