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dbSNP Short Genetic Variations

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 Aliases 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.

rs4299484

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:108470780 (GRCh38.p12) 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=0.21022 (52321/248882, GnomAD_exome)
T=0.19899 (24987/125568, TOPMED)
T=0.20696 (24897/120298, ExAC) (+ 9 more)
T=0.1034 (8141/78702, PAGE_STUDY)
T=0.2016 (6320/31352, GnomAD)
T=0.2211 (2717/12288, GO-ESP)
T=0.101 (505/5008, 1000G)
T=0.246 (1100/4480, Estonian)
T=0.302 (1164/3854, ALSPAC)
T=0.310 (1148/3708, TWINSUK)
T=0.00 (2/614, Vietnamese)
T=0.28 (166/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MYH15 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
Help

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.p12 chr 3 NC_000003.12:g.108470780C>T
GRCh37.p13 chr 3 NC_000003.11:g.108189627C>T
Gene: MYH15, myosin heavy chain 15 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MYH15 transcript NM_014981.2:c.1361G>A R [CGG] > Q [CAG] Coding Sequence Variant
myosin-15 precursor NP_055796.1:p.Arg454Gln R (Arg) > Q (Gln) Missense Variant
MYH15 transcript variant X1 XM_011512559.2:c.1361G>A R [CGG] > Q [CAG] Coding Sequence Variant
myosin-15 isoform X1 XP_011510861.1:p.Arg454Gln R (Arg) > Q (Gln) Missense Variant
MYH15 transcript variant X2 XM_017005922.1:c.320G>A R [CGG] > Q [CAG] Coding Sequence Variant
myosin-15 isoform X2 XP_016861411.1:p.Arg107Gln R (Arg) > Q (Gln) Missense Variant
Help

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
Help

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
gnomAD - Exomes Global Study-wide 248882 C=0.78978 T=0.21022
gnomAD - Exomes European Sub 134358 C=0.70489 T=0.29511
gnomAD - Exomes Asian Sub 48502 C=0.9385 T=0.0615
gnomAD - Exomes American Sub 34466 C=0.8684 T=0.1316
gnomAD - Exomes African Sub 15484 C=0.9494 T=0.0506
gnomAD - Exomes Ashkenazi Jewish Sub 10046 C=0.7124 T=0.2876
gnomAD - Exomes Other Sub 6026 C=0.754 T=0.246
TopMed Global Study-wide 125568 C=0.80101 T=0.19899
ExAC Global Study-wide 120298 C=0.79304 T=0.20696
ExAC Europe Sub 73090 C=0.7092 T=0.2908
ExAC Asian Sub 25032 C=0.9368 T=0.0632
ExAC American Sub 11490 C=0.8837 T=0.1163
ExAC African Sub 9796 C=0.945 T=0.055
ExAC Other Sub 890 C=0.79 T=0.21
The PAGE Study Global Study-wide 78702 C=0.8966 T=0.1034
The PAGE Study AfricanAmerican Sub 32516 C=0.9375 T=0.0625
The PAGE Study Mexican Sub 10810 C=0.8509 T=0.1491
The PAGE Study Asian Sub 8318 C=0.997 T=0.003
The PAGE Study PuertoRican Sub 7918 C=0.805 T=0.195
The PAGE Study NativeHawaiian Sub 4534 C=0.916 T=0.084
The PAGE Study Cuban Sub 4230 C=0.755 T=0.245
The PAGE Study Dominican Sub 3828 C=0.850 T=0.150
The PAGE Study CentralAmerican Sub 2450 C=0.879 T=0.121
The PAGE Study SouthAmerican Sub 1982 C=0.843 T=0.157
The PAGE Study NativeAmerican Sub 1260 C=0.786 T=0.214
The PAGE Study SouthAsian Sub 856 C=0.93 T=0.07
gnomAD - Genomes Global Study-wide 31352 C=0.7984 T=0.2016
gnomAD - Genomes European Sub 18874 C=0.7130 T=0.2870
gnomAD - Genomes African Sub 8696 C=0.947 T=0.053
gnomAD - Genomes East Asian Sub 1560 C=0.999 T=0.001
gnomAD - Genomes Other Sub 1084 C=0.771 T=0.229
gnomAD - Genomes American Sub 848 C=0.87 T=0.13
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.73 T=0.27
GO Exome Sequencing Project Global Study-wide 12288 C=0.7789 T=0.2211
GO Exome Sequencing Project European American Sub 8296 C=0.699 T=0.301
GO Exome Sequencing Project African American Sub 3992 C=0.944 T=0.056
1000Genomes Global Study-wide 5008 C=0.899 T=0.101
1000Genomes African Sub 1322 C=0.990 T=0.010
1000Genomes East Asian Sub 1008 C=1.000 T=0.000
1000Genomes Europe Sub 1006 C=0.707 T=0.293
1000Genomes South Asian Sub 978 C=0.93 T=0.07
1000Genomes American Sub 694 C=0.81 T=0.19
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.754 T=0.246
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.698 T=0.302
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.690 T=0.310
A Vietnamese Genetic Variation Database Global Study-wide 614 C=1.00 T=0.00
Northern Sweden ACPOP Study-wide 600 C=0.72 T=0.28
Help

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 Note
GRCh38.p12 chr 3 NC_000003.12:g.108470780= NC_000003.12:g.10847078...

NC_000003.12:g.108470780C>T

GRCh37.p13 chr 3 NC_000003.11:g.108189627= NC_000003.11:g.10818962...

NC_000003.11:g.108189627C>T

MYH15 transcript variant X1 XM_011512559.2:c.1361= XM_011512559.2:c.1361G>A
MYH15 transcript NM_014981.1:c.1361= NM_014981.1:c.1361G>A
MYH15 transcript NM_014981.2:c.1361= NM_014981.2:c.1361G>A
MYH15 transcript variant X2 XM_017005922.1:c.320= XM_017005922.1:c.320G>A
myosin-15 isoform X1 XP_011510861.1:p.Arg454= XP_011510861.1:p.Arg454Gln
myosin-15 precursor NP_055796.1:p.Arg454= NP_055796.1:p.Arg454Gln
myosin-15 isoform X2 XP_016861411.1:p.Arg107= XP_016861411.1:p.Arg107Gln
Help

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#.

120 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss5695316 Feb 20, 2003 (111)
2 PERLEGEN ss24367589 Sep 20, 2004 (123)
3 ABI ss44468197 Mar 15, 2006 (126)
4 ILLUMINA ss66683016 Nov 30, 2006 (127)
5 ILLUMINA ss67324939 Nov 30, 2006 (127)
6 ILLUMINA ss67727359 Nov 30, 2006 (127)
7 CSHL-HAPMAP ss68364660 Jan 12, 2007 (127)
8 PERLEGEN ss68871216 May 17, 2007 (127)
9 ILLUMINA ss70798951 May 23, 2008 (130)
10 ILLUMINA ss71377508 May 17, 2007 (127)
11 AFFY ss74815495 Aug 16, 2007 (128)
12 ILLUMINA ss75580977 Dec 07, 2007 (129)
13 ILLUMINA ss79178730 Dec 14, 2007 (130)
14 KRIBB_YJKIM ss84246644 Dec 14, 2007 (130)
15 CORNELL ss86261309 Mar 23, 2008 (129)
16 1000GENOMES ss112316356 Jan 25, 2009 (130)
17 ILLUMINA ss120036777 Dec 01, 2009 (131)
18 ILLUMINA ss122290811 Dec 01, 2009 (131)
19 ILLUMINA ss154288880 Dec 01, 2009 (131)
20 ILLUMINA ss159465842 Dec 01, 2009 (131)
21 ILLUMINA ss160671015 Dec 01, 2009 (131)
22 ILLUMINA ss171769347 Jul 04, 2010 (132)
23 ILLUMINA ss173711294 Jul 04, 2010 (132)
24 1000GENOMES ss231970071 Jul 14, 2010 (132)
25 BL ss253378389 May 09, 2011 (134)
26 ILLUMINA ss480919457 May 04, 2012 (137)
27 ILLUMINA ss480938658 May 04, 2012 (137)
28 ILLUMINA ss481898667 Sep 08, 2015 (146)
29 ILLUMINA ss485254707 May 04, 2012 (137)
30 1000GENOMES ss489891375 May 04, 2012 (137)
31 EXOME_CHIP ss491343623 May 04, 2012 (137)
32 CLINSEQ_SNP ss491839023 May 04, 2012 (137)
33 ILLUMINA ss537225574 Sep 08, 2015 (146)
34 SSMP ss650553977 Apr 25, 2013 (138)
35 NHLBI-ESP ss712536984 Apr 25, 2013 (138)
36 ILLUMINA ss778533303 Sep 08, 2015 (146)
37 ILLUMINA ss780819830 Sep 08, 2015 (146)
38 ILLUMINA ss783073310 Sep 08, 2015 (146)
39 ILLUMINA ss783502211 Sep 08, 2015 (146)
40 ILLUMINA ss784031087 Sep 08, 2015 (146)
41 ILLUMINA ss825509248 Apr 01, 2015 (144)
42 ILLUMINA ss832331478 Sep 08, 2015 (146)
43 ILLUMINA ss832977333 Jul 13, 2019 (153)
44 ILLUMINA ss833989854 Sep 08, 2015 (146)
45 JMKIDD_LAB ss974449067 Aug 21, 2014 (142)
46 EVA-GONL ss978996185 Aug 21, 2014 (142)
47 JMKIDD_LAB ss1067453425 Aug 21, 2014 (142)
48 JMKIDD_LAB ss1070710316 Aug 21, 2014 (142)
49 1000GENOMES ss1305529582 Aug 21, 2014 (142)
50 HAMMER_LAB ss1397347835 Sep 08, 2015 (146)
51 DDI ss1429536290 Apr 01, 2015 (144)
52 EVA_GENOME_DK ss1580115826 Apr 01, 2015 (144)
53 EVA_FINRISK ss1584029190 Apr 01, 2015 (144)
54 EVA_DECODE ss1588474349 Apr 01, 2015 (144)
55 EVA_UK10K_ALSPAC ss1607878524 Apr 01, 2015 (144)
56 EVA_UK10K_TWINSUK ss1650872557 Apr 01, 2015 (144)
57 EVA_EXAC ss1687129325 Apr 01, 2015 (144)
58 EVA_MGP ss1711027372 Apr 01, 2015 (144)
59 EVA_SVP ss1712600816 Apr 01, 2015 (144)
60 ILLUMINA ss1752430597 Sep 08, 2015 (146)
61 ILLUMINA ss1752430598 Sep 08, 2015 (146)
62 ILLUMINA ss1917770388 Feb 12, 2016 (147)
63 WEILL_CORNELL_DGM ss1922224280 Feb 12, 2016 (147)
64 ILLUMINA ss1946091102 Feb 12, 2016 (147)
65 ILLUMINA ss1946091103 Feb 12, 2016 (147)
66 ILLUMINA ss1958591997 Feb 12, 2016 (147)
67 ILLUMINA ss1958591998 Feb 12, 2016 (147)
68 JJLAB ss2021675981 Sep 14, 2016 (149)
69 ILLUMINA ss2095135980 Dec 20, 2016 (150)
70 USC_VALOUEV ss2149767506 Dec 20, 2016 (150)
71 HUMAN_LONGEVITY ss2254558296 Dec 20, 2016 (150)
72 TOPMED ss2421882964 Dec 20, 2016 (150)
73 ILLUMINA ss2633992367 Nov 08, 2017 (151)
74 ILLUMINA ss2710662684 Nov 08, 2017 (151)
75 GNOMAD ss2733945931 Nov 08, 2017 (151)
76 GNOMAD ss2747064483 Nov 08, 2017 (151)
77 GNOMAD ss2797339275 Nov 08, 2017 (151)
78 AFFY ss2985265285 Nov 08, 2017 (151)
79 SWEGEN ss2992941662 Nov 08, 2017 (151)
80 ILLUMINA ss3022271526 Nov 08, 2017 (151)
81 ILLUMINA ss3022271527 Nov 08, 2017 (151)
82 BIOINF_KMB_FNS_UNIBA ss3024604463 Nov 08, 2017 (151)
83 CSHL ss3345191696 Nov 08, 2017 (151)
84 TOPMED ss3401430118 Nov 08, 2017 (151)
85 ILLUMINA ss3625822628 Oct 12, 2018 (152)
86 ILLUMINA ss3628739706 Oct 12, 2018 (152)
87 ILLUMINA ss3628739707 Oct 12, 2018 (152)
88 ILLUMINA ss3631936241 Oct 12, 2018 (152)
89 ILLUMINA ss3633303358 Oct 12, 2018 (152)
90 ILLUMINA ss3634020822 Oct 12, 2018 (152)
91 ILLUMINA ss3634909433 Oct 12, 2018 (152)
92 ILLUMINA ss3634909434 Oct 12, 2018 (152)
93 ILLUMINA ss3635704527 Oct 12, 2018 (152)
94 ILLUMINA ss3636605870 Oct 12, 2018 (152)
95 ILLUMINA ss3637456917 Oct 12, 2018 (152)
96 ILLUMINA ss3638433025 Oct 12, 2018 (152)
97 ILLUMINA ss3639219720 Oct 12, 2018 (152)
98 ILLUMINA ss3639628430 Oct 12, 2018 (152)
99 ILLUMINA ss3640616733 Oct 12, 2018 (152)
100 ILLUMINA ss3640616734 Oct 12, 2018 (152)
101 ILLUMINA ss3643388653 Oct 12, 2018 (152)
102 ILLUMINA ss3644823732 Oct 12, 2018 (152)
103 ILLUMINA ss3644823733 Oct 12, 2018 (152)
104 OMUKHERJEE_ADBS ss3646290500 Oct 12, 2018 (152)
105 ILLUMINA ss3652748697 Oct 12, 2018 (152)
106 ILLUMINA ss3652748698 Oct 12, 2018 (152)
107 ILLUMINA ss3654034122 Oct 12, 2018 (152)
108 EGCUT_WGS ss3660860908 Jul 13, 2019 (153)
109 EVA_DECODE ss3709981808 Jul 13, 2019 (153)
110 ILLUMINA ss3726043357 Jul 13, 2019 (153)
111 ACPOP ss3730212674 Jul 13, 2019 (153)
112 ILLUMINA ss3744219730 Jul 13, 2019 (153)
113 ILLUMINA ss3744513677 Jul 13, 2019 (153)
114 ILLUMINA ss3745209402 Jul 13, 2019 (153)
115 ILLUMINA ss3745209403 Jul 13, 2019 (153)
116 EVA ss3760496131 Jul 13, 2019 (153)
117 PAGE_CC ss3771053185 Jul 13, 2019 (153)
118 ILLUMINA ss3772704733 Jul 13, 2019 (153)
119 ILLUMINA ss3772704734 Jul 13, 2019 (153)
120 KHV_HUMAN_GENOMES ss3803632554 Jul 13, 2019 (153)
121 1000Genomes NC_000003.11 - 108189627 Oct 12, 2018 (152)
122 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 108189627 Oct 12, 2018 (152)
123 Genetic variation in the Estonian population NC_000003.11 - 108189627 Oct 12, 2018 (152)
124 ExAC NC_000003.11 - 108189627 Oct 12, 2018 (152)
125 gnomAD - Genomes NC_000003.11 - 108189627 Jul 13, 2019 (153)
126 gnomAD - Exomes NC_000003.11 - 108189627 Jul 13, 2019 (153)
127 GO Exome Sequencing Project NC_000003.11 - 108189627 Oct 12, 2018 (152)
128 Northern Sweden NC_000003.11 - 108189627 Jul 13, 2019 (153)
129 The PAGE Study NC_000003.12 - 108470780 Jul 13, 2019 (153)
130 TopMed NC_000003.12 - 108470780 Oct 12, 2018 (152)
131 UK 10K study - Twins NC_000003.11 - 108189627 Oct 12, 2018 (152)
132 A Vietnamese Genetic Variation Database NC_000003.11 - 108189627 Jul 13, 2019 (153)
Help

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)
rs17538845 Oct 07, 2004 (123)
rs52826675 Sep 21, 2007 (128)
rs56656800 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3639219720, ss3639628430 NC_000003.9:109672316:C:T NC_000003.12:108470779:C:T (self)
ss112316356, ss253378389, ss480919457, ss491839023, ss825509248, ss1397347835, ss1588474349, ss1712600816, ss2710662684, ss3643388653 NC_000003.10:109672316:C:T NC_000003.12:108470779:C:T (self)
16769728, 9333014, 6599156, 7062781, 45878395, 3029372, 397539, 3497539, 9333014, 2032377, ss231970071, ss480938658, ss481898667, ss485254707, ss489891375, ss491343623, ss537225574, ss650553977, ss712536984, ss778533303, ss780819830, ss783073310, ss783502211, ss784031087, ss832331478, ss832977333, ss833989854, ss974449067, ss978996185, ss1067453425, ss1070710316, ss1305529582, ss1429536290, ss1580115826, ss1584029190, ss1607878524, ss1650872557, ss1687129325, ss1711027372, ss1752430597, ss1752430598, ss1917770388, ss1922224280, ss1946091102, ss1946091103, ss1958591997, ss1958591998, ss2021675981, ss2095135980, ss2149767506, ss2421882964, ss2633992367, ss2733945931, ss2747064483, ss2797339275, ss2985265285, ss2992941662, ss3022271526, ss3022271527, ss3345191696, ss3625822628, ss3628739706, ss3628739707, ss3631936241, ss3633303358, ss3634020822, ss3634909433, ss3634909434, ss3635704527, ss3636605870, ss3637456917, ss3638433025, ss3640616733, ss3640616734, ss3644823732, ss3644823733, ss3646290500, ss3652748697, ss3652748698, ss3654034122, ss3660860908, ss3730212674, ss3744219730, ss3744513677, ss3745209402, ss3745209403, ss3760496131, ss3772704733, ss3772704734 NC_000003.11:108189626:C:T NC_000003.12:108470779:C:T (self)
274654, 259697413, ss2254558296, ss3024604463, ss3401430118, ss3709981808, ss3726043357, ss3771053185, ss3803632554 NC_000003.12:108470779:C:T NC_000003.12:108470779:C:T (self)
ss5695316, ss24367589, ss44468197, ss66683016, ss67324939, ss67727359, ss68364660, ss68871216, ss70798951, ss71377508, ss74815495, ss75580977, ss79178730, ss84246644, ss86261309, ss120036777, ss122290811, ss154288880, ss159465842, ss160671015, ss171769347, ss173711294 NT_005612.16:14684772:C:T NC_000003.12:108470779:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs4299484

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.

Software version is: 2.0.1.post308+0fe9b3b