Name: rs855053
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.

rs855053

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:20262028 (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: A>C / A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.475877 (125960/264690, TOPMED)
A=0.09456 (2672/28258, 14KJPN)
A=0.09117 (1528/16760, 8.3KJPN) (+ 15 more)
C=0.36473 (5468/14992, ALFA)
A=0.4482 (2870/6404, 1000G_30x)
A=0.4411 (2209/5008, 1000G)
C=0.4618 (2069/4480, Estonian)
C=0.4761 (1835/3854, ALSPAC)
C=0.4822 (1788/3708, TWINSUK)
A=0.0844 (247/2926, KOREAN)
A=0.0862 (158/1832, Korea1K)
C=0.470 (469/998, GoNL)
A=0.493 (296/600, NorthernSweden)
A=0.259 (117/452, SGDP_PRJ)
C=0.347 (75/216, Qatari)
A=0.176 (38/216, Vietnamese)
A=0.12 (6/48, Siberian)
C=0.38 (15/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RTN4R : 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	14992	A=0.63527	C=0.36473, G=0.00000, T=0.00000
European	Sub	13336	A=0.60363	C=0.39637, G=0.00000, T=0.00000
African	Sub	1094	A=0.9561	C=0.0439, G=0.0000, T=0.0000
African Others	Sub	52	A=0.98	C=0.02, G=0.00, T=0.00
African American	Sub	1042	A=0.9549	C=0.0451, G=0.0000, T=0.0000
Asian	Sub	4	A=0.5	C=0.5, G=0.0, T=0.0
East Asian	Sub	2	A=0.5	C=0.5, G=0.0, T=0.0
Other Asian	Sub	2	A=0.5	C=0.5, G=0.0, T=0.0
Latin American 1	Sub	60	A=1.00	C=0.00, G=0.00, T=0.00
Latin American 2	Sub	102	A=1.000	C=0.000, G=0.000, T=0.000
South Asian	Sub	28	A=0.89	C=0.11, G=0.00, T=0.00
Other	Sub	368	A=0.649	C=0.351, G=0.000, T=0.000

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	A=0.524123	C=0.475877
14KJPN	JAPANESE	Study-wide	28258	A=0.09456	C=0.90544
8.3KJPN	JAPANESE	Study-wide	16760	A=0.09117	C=0.90883
Allele Frequency Aggregator	Total	Global	14992	A=0.63527	C=0.36473, G=0.00000, T=0.00000
Allele Frequency Aggregator	European	Sub	13336	A=0.60363	C=0.39637, G=0.00000, T=0.00000
Allele Frequency Aggregator	African	Sub	1094	A=0.9561	C=0.0439, G=0.0000, T=0.0000
Allele Frequency Aggregator	Other	Sub	368	A=0.649	C=0.351, G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	102	A=1.000	C=0.000, G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	60	A=1.00	C=0.00, G=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	28	A=0.89	C=0.11, G=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	4	A=0.5	C=0.5, G=0.0, T=0.0
1000Genomes_30x	Global	Study-wide	6404	A=0.4482	C=0.5518
1000Genomes_30x	African	Sub	1786	A=0.5907	C=0.4093
1000Genomes_30x	Europe	Sub	1266	A=0.5253	C=0.4747
1000Genomes_30x	South Asian	Sub	1202	A=0.4376	C=0.5624
1000Genomes_30x	East Asian	Sub	1170	A=0.1256	C=0.8744
1000Genomes_30x	American	Sub	980	A=0.487	C=0.513
1000Genomes	Global	Study-wide	5008	A=0.4411	C=0.5589
1000Genomes	African	Sub	1322	A=0.6014	C=0.3986
1000Genomes	East Asian	Sub	1008	A=0.1260	C=0.8740
1000Genomes	Europe	Sub	1006	A=0.5219	C=0.4781
1000Genomes	South Asian	Sub	978	A=0.439	C=0.561
1000Genomes	American	Sub	694	A=0.480	C=0.520
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5382	C=0.4618
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.5239	C=0.4761
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.5178	C=0.4822
KOREAN population from KRGDB	KOREAN	Study-wide	2926	A=0.0844	C=0.9156, G=0.0000, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	A=0.0862	C=0.9138
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.530	C=0.470
Northern Sweden	ACPOP	Study-wide	600	A=0.493	C=0.507
SGDP_PRJ	Global	Study-wide	452	A=0.259	C=0.741
Qatari	Global	Study-wide	216	A=0.653	C=0.347
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.176	C=0.824
Siberian	Global	Study-wide	48	A=0.12	C=0.88
The Danish reference pan genome	Danish	Study-wide	40	A=0.62	C=0.38

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 22	NC_000022.11:g.20262028A>C
GRCh38.p14 chr 22	NC_000022.11:g.20262028A>G
GRCh38.p14 chr 22	NC_000022.11:g.20262028A>T
GRCh37.p13 chr 22	NC_000022.10:g.20249551A>C
GRCh37.p13 chr 22	NC_000022.10:g.20249551A>G
GRCh37.p13 chr 22	NC_000022.10:g.20249551A>T
RTN4R RefSeqGene	NG_012176.2:g.11266T>G
RTN4R RefSeqGene	NG_012176.2:g.11266T>C
RTN4R RefSeqGene	NG_012176.2:g.11266T>A

Gene: RTN4R, reticulon 4 receptor (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RTN4R transcript	NM_023004.6:c.22+6043T>G	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	A=	C	G	T
GRCh38.p14 chr 22	NC_000022.11:g.20262028=	NC_000022.11:g.20262028A>C	NC_000022.11:g.20262028A>G	NC_000022.11:g.20262028A>T
GRCh37.p13 chr 22	NC_000022.10:g.20249551=	NC_000022.10:g.20249551A>C	NC_000022.10:g.20249551A>G	NC_000022.10:g.20249551A>T
RTN4R RefSeqGene	NG_012176.2:g.11266=	NG_012176.2:g.11266T>G	NG_012176.2:g.11266T>C	NG_012176.2:g.11266T>A
RTN4R transcript	NM_023004.5:c.22+6043=	NM_023004.5:c.22+6043T>G	NM_023004.5:c.22+6043T>C	NM_023004.5:c.22+6043T>A
RTN4R transcript	NM_023004.6:c.22+6043=	NM_023004.6:c.22+6043T>G	NM_023004.6:c.22+6043T>C	NM_023004.6:c.22+6043T>A

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#.

78 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1241728	Oct 05, 2000 (86)
2	SC_JCM	ss2459975	Nov 09, 2000 (92)
3	TSC-CSHL	ss3126868	Jun 15, 2001 (96)
4	SC_SNP	ss7994713	Apr 21, 2003 (114)
5	CSHL-HAPMAP	ss19501047	Feb 27, 2004 (120)
6	SSAHASNP	ss21858095	Apr 05, 2004 (121)
7	ABI	ss44326699	Mar 15, 2006 (126)
8	KRIBB_YJKIM	ss65826380	Nov 29, 2006 (127)
9	HGSV	ss81981044	Dec 14, 2007 (130)
10	BCMHGSC_JDW	ss91878467	Mar 24, 2008 (129)
11	HUMANGENOME_JCVI	ss96092907	Feb 04, 2009 (130)
12	1000GENOMES	ss114038994	Jan 25, 2009 (130)
13	ILLUMINA-UK	ss117362994	Feb 14, 2009 (130)
14	ENSEMBL	ss133832038	Dec 01, 2009 (131)
15	ENSEMBL	ss138335630	Dec 01, 2009 (131)
16	GMI	ss157037167	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss167690322	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss168897471	Jul 04, 2010 (132)
19	1000GENOMES	ss228619355	Jul 14, 2010 (132)
20	1000GENOMES	ss238023419	Jul 15, 2010 (132)
21	1000GENOMES	ss244152514	Jul 15, 2010 (132)
22	GMI	ss283588055	May 04, 2012 (137)
23	PJP	ss292736820	May 09, 2011 (134)
24	ILLUMINA	ss480313067	May 04, 2012 (137)
25	ILLUMINA	ss484289751	May 04, 2012 (137)
26	TISHKOFF	ss566562358	Apr 25, 2013 (138)
27	SSMP	ss662485525	Apr 25, 2013 (138)
28	ILLUMINA	ss781199984	Aug 21, 2014 (142)
29	EVA-GONL	ss995225313	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1082572006	Aug 21, 2014 (142)
31	1000GENOMES	ss1366692886	Aug 21, 2014 (142)
32	DDI	ss1429220670	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1579705223	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1639758842	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1682752875	Apr 01, 2015 (144)
36	EVA_DECODE	ss1699294482	Apr 01, 2015 (144)
37	HAMMER_LAB	ss1809734993	Sep 08, 2015 (146)
38	WEILL_CORNELL_DGM	ss1938786942	Feb 12, 2016 (147)
39	GENOMED	ss1969247393	Jul 19, 2016 (147)
40	JJLAB	ss2030166665	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2158777169	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2246476010	Dec 20, 2016 (150)
43	SYSTEMSBIOZJU	ss2629581606	Nov 08, 2017 (151)
44	ILLUMINA	ss2633863168	Nov 08, 2017 (151)
45	GRF	ss2704519899	Nov 08, 2017 (151)
46	GNOMAD	ss2973014375	Nov 08, 2017 (151)
47	SWEGEN	ss3019090489	Nov 08, 2017 (151)
48	BIOINF_KMB_FNS_UNIBA	ss3028921119	Nov 08, 2017 (151)
49	CSHL	ss3352777696	Nov 08, 2017 (151)
50	ILLUMINA	ss3642211349	Oct 12, 2018 (152)
51	URBANLAB	ss3651152359	Oct 12, 2018 (152)
52	EGCUT_WGS	ss3685622612	Jul 13, 2019 (153)
53	EVA_DECODE	ss3707960222	Jul 13, 2019 (153)
54	ACPOP	ss3743825507	Jul 13, 2019 (153)
55	EVA	ss3759234365	Jul 13, 2019 (153)
56	PACBIO	ss3788794164	Jul 13, 2019 (153)
57	PACBIO	ss3793665220	Jul 13, 2019 (153)
58	PACBIO	ss3798551564	Jul 13, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3822401668	Jul 13, 2019 (153)
60	EVA	ss3835929120	Apr 27, 2020 (154)
61	SGDP_PRJ	ss3890262476	Apr 27, 2020 (154)
62	KRGDB	ss3940647540	Apr 27, 2020 (154)
63	KOGIC	ss3983395731	Apr 27, 2020 (154)
64	TOPMED	ss5105192424	Apr 27, 2021 (155)
65	TOMMO_GENOMICS	ss5232052126	Apr 27, 2021 (155)
66	1000G_HIGH_COVERAGE	ss5310666493	Oct 16, 2022 (156)
67	EVA	ss5316047257	Oct 16, 2022 (156)
68	EVA	ss5440541097	Oct 16, 2022 (156)
69	HUGCELL_USP	ss5502576749	Oct 16, 2022 (156)
70	EVA	ss5512348981	Oct 16, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5618029650	Oct 16, 2022 (156)
72	SANFORD_IMAGENETICS	ss5664241392	Oct 16, 2022 (156)
73	TOMMO_GENOMICS	ss5793006933	Oct 16, 2022 (156)
74	YY_MCH	ss5818598126	Oct 16, 2022 (156)
75	EVA	ss5821903866	Oct 16, 2022 (156)
76	EVA	ss5853347429	Oct 16, 2022 (156)
77	EVA	ss5881358341	Oct 16, 2022 (156)
78	EVA	ss5959112881	Oct 16, 2022 (156)
79	1000Genomes	NC_000022.10 - 20249551	Oct 12, 2018 (152)
80	1000Genomes_30x	NC_000022.11 - 20262028	Oct 16, 2022 (156)
81	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 20249551	Oct 12, 2018 (152)
82	Genetic variation in the Estonian population	NC_000022.10 - 20249551	Oct 12, 2018 (152)
83	The Danish reference pan genome	NC_000022.10 - 20249551	Apr 27, 2020 (154)
84	gnomAD - Genomes Submission ignored due to conflicting rows: Row 566612541 (NC_000022.11:20262027:A:C 65917/140122) Row 566612542 (NC_000022.11:20262027:A:G 3/140144) Row 566612543 (NC_000022.11:20262027:A:T 1/140144)	-	Apr 27, 2021 (155)
85	gnomAD - Genomes Submission ignored due to conflicting rows: Row 566612541 (NC_000022.11:20262027:A:C 65917/140122) Row 566612542 (NC_000022.11:20262027:A:G 3/140144) Row 566612543 (NC_000022.11:20262027:A:T 1/140144)	-	Apr 27, 2021 (155)
86	gnomAD - Genomes Submission ignored due to conflicting rows: Row 566612541 (NC_000022.11:20262027:A:C 65917/140122) Row 566612542 (NC_000022.11:20262027:A:G 3/140144) Row 566612543 (NC_000022.11:20262027:A:T 1/140144)	-	Apr 27, 2021 (155)
87	Genome of the Netherlands Release 5	NC_000022.10 - 20249551	Apr 27, 2020 (154)
88	KOREAN population from KRGDB	NC_000022.10 - 20249551	Apr 27, 2020 (154)
89	Korean Genome Project	NC_000022.11 - 20262028	Apr 27, 2020 (154)
90	Northern Sweden	NC_000022.10 - 20249551	Jul 13, 2019 (153)
91	Qatari	NC_000022.10 - 20249551	Apr 27, 2020 (154)
92	SGDP_PRJ	NC_000022.10 - 20249551	Apr 27, 2020 (154)
93	Siberian	NC_000022.10 - 20249551	Apr 27, 2020 (154)
94	8.3KJPN	NC_000022.10 - 20249551	Apr 27, 2021 (155)
95	14KJPN	NC_000022.11 - 20262028	Oct 16, 2022 (156)
96	TopMed	NC_000022.11 - 20262028	Apr 27, 2021 (155)
97	UK 10K study - Twins	NC_000022.10 - 20249551	Oct 12, 2018 (152)
98	A Vietnamese Genetic Variation Database	NC_000022.10 - 20249551	Jul 13, 2019 (153)
99	ALFA	NC_000022.11 - 20262028	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)
rs1640374	Jan 18, 2001 (92)
rs57898658	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss81981044	NC_000022.8:18624104:A:C	NC_000022.11:20262027:A:C	(self)
ss91878467, ss114038994, ss117362994, ss167690322, ss168897471, ss283588055, ss292736820, ss484289751, ss1699294482	NC_000022.9:18629550:A:C	NC_000022.11:20262027:A:C	(self)
80227580, 44387277, 31360860, 5870162, 19776190, 47824934, 17110372, 20828864, 42279456, 11293523, 90021433, 44387277, 9793862, ss228619355, ss238023419, ss244152514, ss480313067, ss566562358, ss662485525, ss781199984, ss995225313, ss1082572006, ss1366692886, ss1429220670, ss1579705223, ss1639758842, ss1682752875, ss1809734993, ss1938786942, ss1969247393, ss2030166665, ss2158777169, ss2629581606, ss2633863168, ss2704519899, ss2973014375, ss3019090489, ss3352777696, ss3642211349, ss3685622612, ss3743825507, ss3759234365, ss3788794164, ss3793665220, ss3798551564, ss3835929120, ss3890262476, ss3940647540, ss5232052126, ss5316047257, ss5440541097, ss5512348981, ss5664241392, ss5821903866, ss5959112881	NC_000022.10:20249550:A:C	NC_000022.11:20262027:A:C	(self)
105555585, 39773732, 126844037, 380301371, 12283524441, ss2246476010, ss3028921119, ss3651152359, ss3707960222, ss3822401668, ss3983395731, ss5105192424, ss5310666493, ss5502576749, ss5618029650, ss5793006933, ss5818598126, ss5853347429, ss5881358341	NC_000022.11:20262027:A:C	NC_000022.11:20262027:A:C	(self)
ss1241728, ss2459975, ss3126868, ss7994713, ss19501047, ss21858095, ss44326699, ss65826380, ss96092907, ss133832038, ss138335630, ss157037167	NT_011519.10:3401700:A:C	NC_000022.11:20262027:A:C	(self)
47824934, ss3940647540	NC_000022.10:20249550:A:G	NC_000022.11:20262027:A:G	(self)
12283524441	NC_000022.11:20262027:A:G	NC_000022.11:20262027:A:G	(self)
47824934, ss2973014375, ss3940647540	NC_000022.10:20249550:A:T	NC_000022.11:20262027:A:T	(self)
12283524441	NC_000022.11:20262027:A:T	NC_000022.11:20262027:A: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 rs855053

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

rs855053