Name: rs17651119
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.

rs17651119

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:16812529 (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=0.033896 (8972/264690, TOPMED)
T=0.022712 (3185/140232, GnomAD)
T=0.07058 (5555/78702, PAGE_STUDY) (+ 22 more)
T=0.21590 (6101/28258, 14KJPN)
T=0.03099 (774/24976, ALFA)
T=0.21587 (3618/16760, 8.3KJPN)
T=0.0634 (406/6404, 1000G_30x)
T=0.0661 (331/5008, 1000G)
T=0.0080 (36/4480, Estonian)
T=0.0200 (77/3854, ALSPAC)
T=0.0178 (66/3708, TWINSUK)
T=0.2382 (696/2922, KOREAN)
T=0.2456 (450/1832, Korea1K)
T=0.0782 (118/1508, HapMap)
T=0.017 (17/998, GoNL)
T=0.188 (149/792, PRJEB37584)
T=0.088 (55/626, Chileans)
T=0.020 (12/600, NorthernSweden)
T=0.056 (12/216, Qatari)
T=0.145 (31/214, Vietnamese)
T=0.00 (0/80, Ancient Sardinia)
C=0.49 (34/70, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)
C=0.5 (3/6, Siberian)
T=0.5 (3/6, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MYO10 : 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	24976	C=0.96901	T=0.03099
European	Sub	15744	C=0.98596	T=0.01404
African	Sub	4078	C=0.9953	T=0.0047
African Others	Sub	126	C=0.984	T=0.016
African American	Sub	3952	C=0.9957	T=0.0043
Asian	Sub	196	C=0.776	T=0.224
East Asian	Sub	138	C=0.790	T=0.210
Other Asian	Sub	58	C=0.74	T=0.26
Latin American 1	Sub	300	C=0.933	T=0.067
Latin American 2	Sub	2734	C=0.8621	T=0.1379
South Asian	Sub	116	C=0.983	T=0.017
Other	Sub	1808	C=0.9497	T=0.0503

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=0.966104	T=0.033896
gnomAD - Genomes	Global	Study-wide	140232	C=0.977288	T=0.022712
gnomAD - Genomes	European	Sub	75958	C=0.98602	T=0.01398
gnomAD - Genomes	African	Sub	42030	C=0.99291	T=0.00709
gnomAD - Genomes	American	Sub	13652	C=0.92536	T=0.07464
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9708	T=0.0292
gnomAD - Genomes	East Asian	Sub	3120	C=0.8032	T=0.1968
gnomAD - Genomes	Other	Sub	2152	C=0.9559	T=0.0441
The PAGE Study	Global	Study-wide	78702	C=0.92942	T=0.07058
The PAGE Study	AfricanAmerican	Sub	32516	C=0.99268	T=0.00732
The PAGE Study	Mexican	Sub	10810	C=0.85726	T=0.14274
The PAGE Study	Asian	Sub	8318	C=0.7843	T=0.2157
The PAGE Study	PuertoRican	Sub	7918	C=0.9581	T=0.0419
The PAGE Study	NativeHawaiian	Sub	4534	C=0.8275	T=0.1725
The PAGE Study	Cuban	Sub	4230	C=0.9723	T=0.0277
The PAGE Study	Dominican	Sub	3828	C=0.9611	T=0.0389
The PAGE Study	CentralAmerican	Sub	2450	C=0.8959	T=0.1041
The PAGE Study	SouthAmerican	Sub	1982	C=0.8819	T=0.1181
The PAGE Study	NativeAmerican	Sub	1260	C=0.9341	T=0.0659
The PAGE Study	SouthAsian	Sub	856	C=0.967	T=0.033
14KJPN	JAPANESE	Study-wide	28258	C=0.78410	T=0.21590
Allele Frequency Aggregator	Total	Global	24976	C=0.96901	T=0.03099
Allele Frequency Aggregator	European	Sub	15744	C=0.98596	T=0.01404
Allele Frequency Aggregator	African	Sub	4078	C=0.9953	T=0.0047
Allele Frequency Aggregator	Latin American 2	Sub	2734	C=0.8621	T=0.1379
Allele Frequency Aggregator	Other	Sub	1808	C=0.9497	T=0.0503
Allele Frequency Aggregator	Latin American 1	Sub	300	C=0.933	T=0.067
Allele Frequency Aggregator	Asian	Sub	196	C=0.776	T=0.224
Allele Frequency Aggregator	South Asian	Sub	116	C=0.983	T=0.017
8.3KJPN	JAPANESE	Study-wide	16760	C=0.78413	T=0.21587
1000Genomes_30x	Global	Study-wide	6404	C=0.9366	T=0.0634
1000Genomes_30x	African	Sub	1786	C=0.9989	T=0.0011
1000Genomes_30x	Europe	Sub	1266	C=0.9858	T=0.0142
1000Genomes_30x	South Asian	Sub	1202	C=0.9676	T=0.0324
1000Genomes_30x	East Asian	Sub	1170	C=0.7915	T=0.2085
1000Genomes_30x	American	Sub	980	C=0.895	T=0.105
1000Genomes	Global	Study-wide	5008	C=0.9339	T=0.0661
1000Genomes	African	Sub	1322	C=0.9985	T=0.0015
1000Genomes	East Asian	Sub	1008	C=0.7897	T=0.2103
1000Genomes	Europe	Sub	1006	C=0.9851	T=0.0149
1000Genomes	South Asian	Sub	978	C=0.967	T=0.033
1000Genomes	American	Sub	694	C=0.899	T=0.101
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9920	T=0.0080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9800	T=0.0200
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9822	T=0.0178
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.7618	T=0.2382
Korean Genome Project	KOREAN	Study-wide	1832	C=0.7544	T=0.2456
HapMap	Global	Study-wide	1508	C=0.9218	T=0.0782
HapMap	American	Sub	672	C=0.915	T=0.085
HapMap	African	Sub	406	C=0.998	T=0.002
HapMap	Asian	Sub	254	C=0.772	T=0.228
HapMap	Europe	Sub	176	C=0.989	T=0.011
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.983	T=0.017
CNV burdens in cranial meningiomas	Global	Study-wide	792	C=0.812	T=0.188
CNV burdens in cranial meningiomas	CRM	Sub	792	C=0.812	T=0.188
Chileans	Chilean	Study-wide	626	C=0.912	T=0.088
Northern Sweden	ACPOP	Study-wide	600	C=0.980	T=0.020
Qatari	Global	Study-wide	216	C=0.944	T=0.056
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.855	T=0.145
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	80	C=1.00	T=0.00
SGDP_PRJ	Global	Study-wide	70	C=0.49	T=0.51
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	T=0.03
Siberian	Global	Study-wide	6	C=0.5	T=0.5

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 5	NC_000005.10:g.16812529C>T
GRCh37.p13 chr 5	NC_000005.9:g.16812638C>T

Gene: MYO10, myosin X (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MYO10 transcript	NM_012334.3:c.279+5480G>A	N/A	Intron Variant
MYO10 transcript variant X1	XM_006714475.4:c.279+5480… XM_006714475.4:c.279+5480G>A	N/A	Intron Variant
MYO10 transcript variant X2	XM_005248306.5:c.	N/A	Genic Upstream Transcript Variant
MYO10 transcript variant X4	XM_005248307.3:c.	N/A	Genic Upstream Transcript Variant
MYO10 transcript variant X3	XM_011514046.3: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.

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 5	NC_000005.10:g.16812529=	NC_000005.10:g.16812529C>T
GRCh37.p13 chr 5	NC_000005.9:g.16812638=	NC_000005.9:g.16812638C>T
MYO10 transcript	NM_012334.2:c.279+5480=	NM_012334.2:c.279+5480G>A
MYO10 transcript	NM_012334.3:c.279+5480=	NM_012334.3:c.279+5480G>A
MYO10 transcript variant X1	XM_006714475.4:c.279+5480=	XM_006714475.4:c.279+5480G>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#.

61 SubSNP, 24 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss24183126	Sep 20, 2004 (123)
2	AFFY	ss76589543	Dec 08, 2007 (130)
3	KRIBB_YJKIM	ss105103361	Feb 04, 2009 (130)
4	1000GENOMES	ss240039115	Jul 15, 2010 (132)
5	GMI	ss278184856	May 04, 2012 (137)
6	ILLUMINA	ss536294875	Sep 08, 2015 (146)
7	SSMP	ss652078814	Apr 25, 2013 (138)
8	EVA-GONL	ss981294169	Aug 21, 2014 (142)
9	JMKIDD_LAB	ss1072426917	Aug 21, 2014 (142)
10	1000GENOMES	ss1314081709	Aug 21, 2014 (142)
11	EVA_GENOME_DK	ss1581030460	Apr 01, 2015 (144)
12	EVA_DECODE	ss1590812999	Apr 01, 2015 (144)
13	EVA_UK10K_ALSPAC	ss1612373185	Apr 01, 2015 (144)
14	EVA_UK10K_TWINSUK	ss1655367218	Apr 01, 2015 (144)
15	EVA_SVP	ss1712747632	Apr 01, 2015 (144)
16	WEILL_CORNELL_DGM	ss1924555271	Feb 12, 2016 (147)
17	ILLUMINA	ss1958770199	Feb 12, 2016 (147)
18	GENOMED	ss1970024339	Jul 19, 2016 (147)
19	JJLAB	ss2022875754	Sep 14, 2016 (149)
20	USC_VALOUEV	ss2151024868	Dec 20, 2016 (150)
21	HUMAN_LONGEVITY	ss2271747772	Dec 20, 2016 (150)
22	SYSTEMSBIOZJU	ss2625936855	Nov 08, 2017 (151)
23	ILLUMINA	ss2634251416	Nov 08, 2017 (151)
24	GRF	ss2706553010	Nov 08, 2017 (151)
25	GNOMAD	ss2821642878	Nov 08, 2017 (151)
26	AFFY	ss2985947364	Nov 08, 2017 (151)
27	SWEGEN	ss2996506194	Nov 08, 2017 (151)
28	ILLUMINA	ss3022470048	Nov 08, 2017 (151)
29	ILLUMINA	ss3629187521	Oct 12, 2018 (152)
30	ILLUMINA	ss3652963104	Oct 12, 2018 (152)
31	EGCUT_WGS	ss3664402833	Jul 13, 2019 (153)
32	EVA_DECODE	ss3714190931	Jul 13, 2019 (153)
33	ILLUMINA	ss3726216741	Jul 13, 2019 (153)
34	ACPOP	ss3732128049	Jul 13, 2019 (153)
35	EVA	ss3763122330	Jul 13, 2019 (153)
36	PAGE_CC	ss3771189374	Jul 13, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3806288575	Jul 13, 2019 (153)
38	EVA	ss3829116733	Apr 26, 2020 (154)
39	SGDP_PRJ	ss3861309046	Apr 26, 2020 (154)
40	KRGDB	ss3907755976	Apr 26, 2020 (154)
41	KOGIC	ss3956173789	Apr 26, 2020 (154)
42	EVA	ss3984543657	Apr 26, 2021 (155)
43	EVA	ss3985128199	Apr 26, 2021 (155)
44	TOPMED	ss4651109354	Apr 26, 2021 (155)
45	TOMMO_GENOMICS	ss5170573257	Apr 26, 2021 (155)
46	EVA	ss5237367566	Apr 26, 2021 (155)
47	1000G_HIGH_COVERAGE	ss5263030822	Oct 13, 2022 (156)
48	EVA	ss5355944056	Oct 13, 2022 (156)
49	HUGCELL_USP	ss5461363602	Oct 13, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5546160671	Oct 13, 2022 (156)
51	SANFORD_IMAGENETICS	ss5624583587	Oct 13, 2022 (156)
52	SANFORD_IMAGENETICS	ss5637274050	Oct 13, 2022 (156)
53	TOMMO_GENOMICS	ss5706300780	Oct 13, 2022 (156)
54	YY_MCH	ss5806058561	Oct 13, 2022 (156)
55	EVA	ss5834580200	Oct 13, 2022 (156)
56	EVA	ss5847262471	Oct 13, 2022 (156)
57	EVA	ss5848042816	Oct 13, 2022 (156)
58	EVA	ss5854703378	Oct 13, 2022 (156)
59	EVA	ss5893174924	Oct 13, 2022 (156)
60	EVA	ss5965692288	Oct 13, 2022 (156)
61	EVA	ss5979732871	Oct 13, 2022 (156)
62	1000Genomes	NC_000005.9 - 16812638	Oct 12, 2018 (152)
63	1000Genomes_30x	NC_000005.10 - 16812529	Oct 13, 2022 (156)
64	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 16812638	Oct 12, 2018 (152)
65	Chileans	NC_000005.9 - 16812638	Apr 26, 2020 (154)
66	Genetic variation in the Estonian population	NC_000005.9 - 16812638	Oct 12, 2018 (152)
67	The Danish reference pan genome	NC_000005.9 - 16812638	Apr 26, 2020 (154)
68	gnomAD - Genomes	NC_000005.10 - 16812529	Apr 26, 2021 (155)
69	Genome of the Netherlands Release 5	NC_000005.9 - 16812638	Apr 26, 2020 (154)
70	HapMap	NC_000005.10 - 16812529	Apr 26, 2020 (154)
71	KOREAN population from KRGDB	NC_000005.9 - 16812638	Apr 26, 2020 (154)
72	Korean Genome Project	NC_000005.10 - 16812529	Apr 26, 2020 (154)
73	Northern Sweden	NC_000005.9 - 16812638	Jul 13, 2019 (153)
74	The PAGE Study	NC_000005.10 - 16812529	Jul 13, 2019 (153)
75	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000005.9 - 16812638	Apr 26, 2021 (155)
76	CNV burdens in cranial meningiomas	NC_000005.9 - 16812638	Apr 26, 2021 (155)
77	Qatari	NC_000005.9 - 16812638	Apr 26, 2020 (154)
78	SGDP_PRJ	NC_000005.9 - 16812638	Apr 26, 2020 (154)
79	Siberian	NC_000005.9 - 16812638	Apr 26, 2020 (154)
80	8.3KJPN	NC_000005.9 - 16812638	Apr 26, 2021 (155)
81	14KJPN	NC_000005.10 - 16812529	Oct 13, 2022 (156)
82	TopMed	NC_000005.10 - 16812529	Apr 26, 2021 (155)
83	UK 10K study - Twins	NC_000005.9 - 16812638	Oct 12, 2018 (152)
84	A Vietnamese Genetic Variation Database	NC_000005.9 - 16812638	Jul 13, 2019 (153)
85	ALFA	NC_000005.10 - 16812529	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).

Associated ID	History Updated (Build)
rs56641363	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss76589543, ss278184856, ss1590812999, ss1712747632	NC_000005.8:16865637:C:T	NC_000005.10:16812528:C:T	(self)
25643298, 14273619, 340677, 10141081, 7195399, 6334609, 14933370, 5412914, 354126, 93022, 6597201, 13326026, 3541222, 28542564, 14273619, 3166580, ss240039115, ss536294875, ss652078814, ss981294169, ss1072426917, ss1314081709, ss1581030460, ss1612373185, ss1655367218, ss1924555271, ss1958770199, ss1970024339, ss2022875754, ss2151024868, ss2625936855, ss2634251416, ss2706553010, ss2821642878, ss2985947364, ss2996506194, ss3022470048, ss3629187521, ss3652963104, ss3664402833, ss3732128049, ss3763122330, ss3829116733, ss3861309046, ss3907755976, ss3984543657, ss3985128199, ss5170573257, ss5237367566, ss5355944056, ss5624583587, ss5637274050, ss5834580200, ss5847262471, ss5848042816, ss5965692288, ss5979732871	NC_000005.9:16812637:C:T	NC_000005.10:16812528:C:T	(self)
33686606, 181175241, 2818453, 12551790, 410843, 40137884, 488486911, 5829577332, ss2271747772, ss3714190931, ss3726216741, ss3771189374, ss3806288575, ss3956173789, ss4651109354, ss5263030822, ss5461363602, ss5546160671, ss5706300780, ss5806058561, ss5854703378, ss5893174924	NC_000005.10:16812528:C:T	NC_000005.10:16812528:C:T	(self)
ss24183126, ss105103361	NT_006576.16:16802637:C:T	NC_000005.10:16812528: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 rs17651119

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

rs17651119