Name: rs133900
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.

rs133900

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:25767857 (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: delT
Variation Type: Deletion
Frequency: delT=0.223235 (59088/264690, TOPMED)
delT=0.218844 (30650/140054, GnomAD)
delT=0.09502 (2685/28258, 14KJPN) (+ 12 more)
delT=0.09517 (1595/16760, 8.3KJPN)
delT=0.05770 (737/12772, ALFA)
delT=0.1877 (1202/6404, 1000G_30x)
delT=0.1893 (948/5008, 1000G)
delT=0.1632 (731/4480, Estonian)
delT=0.1943 (749/3854, ALSPAC)
delT=0.2098 (778/3708, TWINSUK)
delT=0.1299 (238/1832, Korea1K)
delT=0.203 (203/998, GoNL)
delT=0.192 (115/600, NorthernSweden)
delT=0.130 (27/208, Vietnamese)
delT=0.23 (9/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: MYO18B : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	12772	T=0.94230	=0.05770	0.892734	0.008143	0.099123	27
European	Sub	10296	T=0.92852	=0.07148	0.867133	0.010101	0.122766	16
African	Sub	1538	T=1.0000	=0.0000	1.0	0.0	0.0	N/A
African Others	Sub	52	T=1.00	=0.00	1.0	0.0	0.0	N/A
African American	Sub	1486	T=1.0000	=0.0000	1.0	0.0	0.0	N/A
Asian	Sub	90	T=1.00	=0.00	1.0	0.0	0.0	N/A
East Asian	Sub	72	T=1.00	=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	18	T=1.00	=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	68	T=1.00	=0.00	1.0	0.0	0.0	N/A
Latin American 2	Sub	424	T=1.000	=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	76	T=1.00	=0.00	1.0	0.0	0.0	N/A
Other	Sub	280	T=0.996	=0.004	0.992857	0.0	0.007143	0

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=0.776765	delT=0.223235
gnomAD - Genomes	Global	Study-wide	140054	T=0.781156	delT=0.218844
gnomAD - Genomes	European	Sub	75888	T=0.79490	delT=0.20510
gnomAD - Genomes	African	Sub	41914	T=0.73932	delT=0.26068
gnomAD - Genomes	American	Sub	13646	T=0.82405	delT=0.17595
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.7172	delT=0.2828
gnomAD - Genomes	East Asian	Sub	3134	T=0.8816	delT=0.1184
gnomAD - Genomes	Other	Sub	2152	T=0.7918	delT=0.2082
14KJPN	JAPANESE	Study-wide	28258	T=0.90498	delT=0.09502
8.3KJPN	JAPANESE	Study-wide	16760	T=0.90483	delT=0.09517
Allele Frequency Aggregator	Total	Global	12772	T=0.94230	delT=0.05770
Allele Frequency Aggregator	European	Sub	10296	T=0.92852	delT=0.07148
Allele Frequency Aggregator	African	Sub	1538	T=1.0000	delT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	424	T=1.000	delT=0.000
Allele Frequency Aggregator	Other	Sub	280	T=0.996	delT=0.004
Allele Frequency Aggregator	Asian	Sub	90	T=1.00	delT=0.00
Allele Frequency Aggregator	South Asian	Sub	76	T=1.00	delT=0.00
Allele Frequency Aggregator	Latin American 1	Sub	68	T=1.00	delT=0.00
1000Genomes_30x	Global	Study-wide	6404	T=0.8123	delT=0.1877
1000Genomes_30x	African	Sub	1786	T=0.7368	delT=0.2632
1000Genomes_30x	Europe	Sub	1266	T=0.7986	delT=0.2014
1000Genomes_30x	South Asian	Sub	1202	T=0.8968	delT=0.1032
1000Genomes_30x	East Asian	Sub	1170	T=0.8675	delT=0.1325
1000Genomes_30x	American	Sub	980	T=0.798	delT=0.202
1000Genomes	Global	Study-wide	5008	T=0.8107	delT=0.1893
1000Genomes	African	Sub	1322	T=0.7300	delT=0.2700
1000Genomes	East Asian	Sub	1008	T=0.8681	delT=0.1319
1000Genomes	Europe	Sub	1006	T=0.7962	delT=0.2038
1000Genomes	South Asian	Sub	978	T=0.889	delT=0.111
1000Genomes	American	Sub	694	T=0.793	delT=0.207
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8368	delT=0.1632
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8057	delT=0.1943
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.7902	delT=0.2098
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8701	delT=0.1299
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.797	delT=0.203
Northern Sweden	ACPOP	Study-wide	600	T=0.808	delT=0.192
A Vietnamese Genetic Variation Database	Global	Study-wide	208	T=0.870	delT=0.130
The Danish reference pan genome	Danish	Study-wide	40	T=0.78	delT=0.23

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.25767857del
GRCh37.p13 chr 22	NC_000022.10:g.26163824del
MYO18B RefSeqGene	NG_046772.1:g.30714del

Gene: MYO18B, myosin XVIIIB (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MYO18B transcript variant 1	NM_001318245.2:c.199-258d… NM_001318245.2:c.199-258del	N/A	Intron Variant
MYO18B transcript variant 2	NM_032608.7:c.199-258del	N/A	Intron Variant
MYO18B transcript variant X1	XM_011530458.3:c.325-258d… XM_011530458.3:c.325-258del	N/A	Intron Variant
MYO18B transcript variant X3	XM_011530459.3:c.325-258d… XM_011530459.3:c.325-258del	N/A	Intron Variant
MYO18B transcript variant X5	XM_011530460.3:c.325-258d… XM_011530460.3:c.325-258del	N/A	Intron Variant
MYO18B transcript variant X2	XM_011530461.3:c.325-258d… XM_011530461.3:c.325-258del	N/A	Intron Variant
MYO18B transcript variant X6	XM_011530464.3:c.325-258d… XM_011530464.3:c.325-258del	N/A	Intron Variant
MYO18B transcript variant X10	XM_011530465.3:c.-159-258… XM_011530465.3:c.-159-258del	N/A	Intron Variant
MYO18B transcript variant X11	XM_011530466.3:c.325-258d… XM_011530466.3:c.325-258del	N/A	Intron Variant
MYO18B transcript variant X4	XM_017029013.2:c.325-258d… XM_017029013.2:c.325-258del	N/A	Intron Variant
MYO18B transcript variant X7	XM_017029014.2:c.325-258d… XM_017029014.2:c.325-258del	N/A	Intron Variant
MYO18B transcript variant X9	XM_017029015.2:c.199-258d… XM_017029015.2:c.199-258del	N/A	Intron Variant
MYO18B transcript variant X8	XM_047441551.1:c.325-258d… XM_047441551.1:c.325-258del	N/A	Intron Variant
MYO18B transcript variant X12	XM_017029016.2:c.	N/A	Genic Upstream 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.

Allele: delT (allele ID: 1221887 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001616683.3	not provided	Benign

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=	delT
GRCh38.p14 chr 22	NC_000022.11:g.25767857=	NC_000022.11:g.25767857del
GRCh37.p13 chr 22	NC_000022.10:g.26163824=	NC_000022.10:g.26163824del
MYO18B RefSeqGene	NG_046772.1:g.30714=	NG_046772.1:g.30714del
MYO18B transcript variant 1	NM_001318245.2:c.199-258=	NM_001318245.2:c.199-258del
MYO18B transcript	NM_032608.5:c.199-258=	NM_032608.5:c.199-258del
MYO18B transcript variant 2	NM_032608.7:c.199-258=	NM_032608.7:c.199-258del
MYO18B transcript variant X1	XM_005261786.1:c.199-258=	XM_005261786.1:c.199-258del
MYO18B transcript variant X2	XM_005261787.1:c.199-258=	XM_005261787.1:c.199-258del
MYO18B transcript variant X3	XM_005261788.1:c.199-258=	XM_005261788.1:c.199-258del
MYO18B transcript variant X1	XM_011530458.3:c.325-258=	XM_011530458.3:c.325-258del
MYO18B transcript variant X3	XM_011530459.3:c.325-258=	XM_011530459.3:c.325-258del
MYO18B transcript variant X5	XM_011530460.3:c.325-258=	XM_011530460.3:c.325-258del
MYO18B transcript variant X2	XM_011530461.3:c.325-258=	XM_011530461.3:c.325-258del
MYO18B transcript variant X6	XM_011530464.3:c.325-258=	XM_011530464.3:c.325-258del
MYO18B transcript variant X10	XM_011530465.3:c.-159-258=	XM_011530465.3:c.-159-258del
MYO18B transcript variant X11	XM_011530466.3:c.325-258=	XM_011530466.3:c.325-258del
MYO18B transcript variant X4	XM_017029013.2:c.325-258=	XM_017029013.2:c.325-258del
MYO18B transcript variant X7	XM_017029014.2:c.325-258=	XM_017029014.2:c.325-258del
MYO18B transcript variant X9	XM_017029015.2:c.199-258=	XM_017029015.2:c.199-258del
MYO18B transcript variant X8	XM_047441551.1:c.325-258=	XM_047441551.1:c.325-258del

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#.

52 SubSNP, 15 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	SC	ss141761	Jun 24, 2000 (78)
2	HGSV	ss83627841	Dec 14, 2007 (130)
3	GMI	ss155838366	Dec 01, 2009 (131)
4	BUSHMAN	ss193642622	Jul 04, 2010 (132)
5	GMI	ss288553811	May 09, 2011 (134)
6	GMI	ss289443692	May 04, 2012 (137)
7	1000GENOMES	ss328002164	May 09, 2011 (137)
8	1000GENOMES	ss328102908	May 09, 2011 (137)
9	1000GENOMES	ss328324049	May 09, 2011 (137)
10	1000GENOMES	ss499848584	May 04, 2012 (137)
11	LUNTER	ss552713409	Apr 25, 2013 (138)
12	LUNTER	ss553136367	Apr 25, 2013 (138)
13	LUNTER	ss553701030	Apr 25, 2013 (138)
14	TISHKOFF	ss555031397	Apr 25, 2013 (138)
15	SSMP	ss664520014	Apr 01, 2015 (144)
16	BILGI_BIOE	ss666768027	Apr 25, 2013 (138)
17	EVA-GONL	ss995269010	Aug 21, 2014 (142)
18	1000GENOMES	ss1378957250	Aug 21, 2014 (142)
19	EVA_GENOME_DK	ss1575817896	Apr 01, 2015 (144)
20	EVA_DECODE	ss1699337331	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1709558132	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1709558244	Apr 01, 2015 (144)
23	HAMMER_LAB	ss1809754886	Sep 08, 2015 (146)
24	GENOMED	ss1969256071	Jul 19, 2016 (147)
25	JJLAB	ss2031463774	Sep 14, 2016 (149)
26	GNOMAD	ss2973527479	Nov 08, 2017 (151)
27	SWEGEN	ss3019177484	Nov 08, 2017 (151)
28	MCHAISSO	ss3064024551	Nov 08, 2017 (151)
29	MCHAISSO	ss3065851525	Nov 08, 2017 (151)
30	BIOINF_KMB_FNS_UNIBA	ss3645679890	Oct 12, 2018 (152)
31	EGCUT_WGS	ss3685672929	Jul 13, 2019 (153)
32	EVA_DECODE	ss3708042489	Jul 13, 2019 (153)
33	ACPOP	ss3743863691	Jul 13, 2019 (153)
34	PACBIO	ss3788807023	Jul 13, 2019 (153)
35	PACBIO	ss3793676159	Jul 13, 2019 (153)
36	PACBIO	ss3798562559	Jul 13, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3822453428	Jul 13, 2019 (153)
38	EVA	ss3835950085	Apr 27, 2020 (154)
39	KOGIC	ss3983482149	Apr 27, 2020 (154)
40	TOPMED	ss5106544309	Apr 27, 2021 (155)
41	TOMMO_GENOMICS	ss5232274035	Apr 27, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5310832107	Oct 16, 2022 (156)
43	HUGCELL_USP	ss5502697939	Oct 16, 2022 (156)
44	1000G_HIGH_COVERAGE	ss5618264546	Oct 16, 2022 (156)
45	SANFORD_IMAGENETICS	ss5664345157	Oct 16, 2022 (156)
46	TOMMO_GENOMICS	ss5793284115	Oct 16, 2022 (156)
47	YY_MCH	ss5818644423	Oct 16, 2022 (156)
48	EVA	ss5821965123	Oct 16, 2022 (156)
49	EVA	ss5853364348	Oct 16, 2022 (156)
50	EVA	ss5881515028	Oct 16, 2022 (156)
51	EVA	ss5959193480	Oct 16, 2022 (156)
52	EVA	ss5981129121	Oct 16, 2022 (156)
53	1000Genomes	NC_000022.10 - 26163824	Oct 12, 2018 (152)
54	1000Genomes_30x	NC_000022.11 - 25767857	Oct 16, 2022 (156)
55	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 26163824	Oct 12, 2018 (152)
56	Genetic variation in the Estonian population	NC_000022.10 - 26163824	Oct 12, 2018 (152)
57	The Danish reference pan genome	NC_000022.10 - 26163824	Apr 27, 2020 (154)
58	gnomAD - Genomes	NC_000022.11 - 25767857	Apr 27, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000022.10 - 26163824	Apr 27, 2020 (154)
60	Korean Genome Project	NC_000022.11 - 25767857	Apr 27, 2020 (154)
61	Northern Sweden	NC_000022.10 - 26163824	Jul 13, 2019 (153)
62	8.3KJPN	NC_000022.10 - 26163824	Apr 27, 2021 (155)
63	14KJPN	NC_000022.11 - 25767857	Oct 16, 2022 (156)
64	TopMed	NC_000022.11 - 25767857	Apr 27, 2021 (155)
65	UK 10K study - Twins	NC_000022.10 - 26163824	Oct 12, 2018 (152)
66	A Vietnamese Genetic Variation Database	NC_000022.10 - 26163824	Jul 13, 2019 (153)
67	ALFA	NC_000022.11 - 25767857	Apr 27, 2021 (155)
68	ClinVar	RCV001616683.3	Oct 16, 2022 (156)

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)
rs56848674	May 23, 2008 (130)
rs139740021	May 04, 2012 (137)
rs377717775	May 13, 2013 (138)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss83627841	NC_000022.8:24488377:T:	NC_000022.11:25767856:T:	(self)
ss289443692, ss328002164, ss328102908, ss328324049, ss552713409, ss553136367, ss553701030, ss1699337331	NC_000022.9:24493823:T:	NC_000022.11:25767856:T:	(self)
80403442, 44468876, 31411177, 790772, 19816378, 17148556, 90243342, 44468876, 9812537, ss499848584, ss555031397, ss664520014, ss666768027, ss995269010, ss1378957250, ss1575817896, ss1709558132, ss1709558244, ss1809754886, ss1969256071, ss2031463774, ss2973527479, ss3019177484, ss3685672929, ss3743863691, ss3788807023, ss3793676159, ss3798562559, ss3835950085, ss5232274035, ss5664345157, ss5821965123, ss5959193480, ss5981129121	NC_000022.10:26163823:T:	NC_000022.11:25767856:T:	(self)
RCV001616683.3, 105790481, 567780704, 39860150, 127121219, 381653256, 11021465681, ss3064024551, ss3065851525, ss3645679890, ss3708042489, ss3822453428, ss3983482149, ss5106544309, ss5310832107, ss5502697939, ss5618264546, ss5793284115, ss5818644423, ss5853364348, ss5881515028	NC_000022.11:25767856:T:	NC_000022.11:25767856:T:	(self)
ss141761, ss155838366, ss288553811	NT_011520.12:5554392:T:	NC_000022.11:25767856:T:	(self)
ss193642622	NT_011520.13:7058292:T:	NC_000022.11:25767856: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 rs133900

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

rs133900