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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 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.

rs447

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr7:84143099 (GRCh38.p13) 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
T>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.163282 (43219/264690, TOPMED)
T=0.171460 (24012/140044, GnomAD)
T=0.18733 (6323/33754, ALFA) (+ 16 more)
T=0.05442 (912/16758, 8.3KJPN)
T=0.1565 (784/5008, 1000G)
T=0.1853 (830/4480, Estonian)
T=0.2052 (791/3854, ALSPAC)
T=0.2168 (804/3708, TWINSUK)
T=0.0478 (140/2930, KOREAN)
T=0.1593 (301/1890, HapMap)
T=0.195 (195/998, GoNL)
T=0.061 (48/792, PRJEB37584)
T=0.165 (99/600, NorthernSweden)
T=0.149 (79/530, SGDP_PRJ)
T=0.259 (56/216, Qatari)
T=0.103 (22/214, Vietnamese)
T=0.05 (3/56, Siberian)
T=0.12 (6/50, Ancient Sardinia)
T=0.12 (5/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SEMA3A : Intron 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.p13 chr 7 NC_000007.14:g.84143099T>A
GRCh38.p13 chr 7 NC_000007.14:g.84143099T>C
GRCh38.p13 chr 7 NC_000007.14:g.84143099T>G
GRCh37.p13 chr 7 NC_000007.13:g.83772415T>A
GRCh37.p13 chr 7 NC_000007.13:g.83772415T>C
GRCh37.p13 chr 7 NC_000007.13:g.83772415T>G
SEMA3A RefSeqGene NG_011489.1:g.56803A>T
SEMA3A RefSeqGene NG_011489.1:g.56803A>G
SEMA3A RefSeqGene NG_011489.1:g.56803A>C
Gene: SEMA3A, semaphorin 3A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SEMA3A transcript NM_006080.3:c.113-8148A>T N/A Intron Variant
SEMA3A transcript variant X2 XM_005250110.3:c.113-8148…

XM_005250110.3:c.113-8148A>T

N/A Intron Variant
SEMA3A transcript variant X5 XM_005250111.4:c.113-8148…

XM_005250111.4:c.113-8148A>T

N/A Intron Variant
SEMA3A transcript variant X3 XM_006715839.3:c.113-8148…

XM_006715839.3:c.113-8148A>T

N/A Intron Variant
SEMA3A transcript variant X4 XM_011515734.3:c.113-8148…

XM_011515734.3:c.113-8148A>T

N/A Intron Variant
SEMA3A transcript variant X6 XM_017011673.1:c.113-8148…

XM_017011673.1:c.113-8148A>T

N/A Intron Variant
SEMA3A transcript variant X1 XM_024446633.1:c.113-8148…

XM_024446633.1:c.113-8148A>T

N/A Intron 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

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 33754 T=0.18733 C=0.81267
European Sub 24046 T=0.20540 C=0.79460
African Sub 3762 T=0.1302 C=0.8698
African Others Sub 130 T=0.077 C=0.923
African American Sub 3632 T=0.1322 C=0.8678
Asian Sub 172 T=0.105 C=0.895
East Asian Sub 114 T=0.088 C=0.912
Other Asian Sub 58 T=0.14 C=0.86
Latin American 1 Sub 314 T=0.169 C=0.831
Latin American 2 Sub 2860 T=0.1469 C=0.8531
South Asian Sub 122 T=0.254 C=0.746
Other Sub 2478 T=0.1501 C=0.8499


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
TopMed Global Study-wide 264690 T=0.163282 C=0.836718
gnomAD - Genomes Global Study-wide 140044 T=0.171460 C=0.828540
gnomAD - Genomes European Sub 75884 T=0.20878 C=0.79122
gnomAD - Genomes African Sub 41952 T=0.12574 C=0.87426
gnomAD - Genomes American Sub 13604 T=0.13695 C=0.86305
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.1641 C=0.8359
gnomAD - Genomes East Asian Sub 3132 T=0.0489 C=0.9511
gnomAD - Genomes Other Sub 2150 T=0.1549 C=0.8451
Allele Frequency Aggregator Total Global 33754 T=0.18733 C=0.81267
Allele Frequency Aggregator European Sub 24046 T=0.20540 C=0.79460
Allele Frequency Aggregator African Sub 3762 T=0.1302 C=0.8698
Allele Frequency Aggregator Latin American 2 Sub 2860 T=0.1469 C=0.8531
Allele Frequency Aggregator Other Sub 2478 T=0.1501 C=0.8499
Allele Frequency Aggregator Latin American 1 Sub 314 T=0.169 C=0.831
Allele Frequency Aggregator Asian Sub 172 T=0.105 C=0.895
Allele Frequency Aggregator South Asian Sub 122 T=0.254 C=0.746
8.3KJPN JAPANESE Study-wide 16758 T=0.05442 C=0.94558
1000Genomes Global Study-wide 5008 T=0.1565 C=0.8435
1000Genomes African Sub 1322 T=0.1165 C=0.8835
1000Genomes East Asian Sub 1008 T=0.0655 C=0.9345
1000Genomes Europe Sub 1006 T=0.2227 C=0.7773
1000Genomes South Asian Sub 978 T=0.238 C=0.762
1000Genomes American Sub 694 T=0.154 C=0.846
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.1853 C=0.8147
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.2052 C=0.7948
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.2168 C=0.7832
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.0478 A=0.0000, C=0.9522, G=0.0000
HapMap Global Study-wide 1890 T=0.1593 C=0.8407
HapMap American Sub 770 T=0.153 C=0.847
HapMap African Sub 690 T=0.172 C=0.828
HapMap Asian Sub 254 T=0.071 C=0.929
HapMap Europe Sub 176 T=0.261 C=0.739
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.195 C=0.805
CNV burdens in cranial meningiomas Global Study-wide 792 T=0.061 C=0.939
CNV burdens in cranial meningiomas CRM Sub 792 T=0.061 C=0.939
Northern Sweden ACPOP Study-wide 600 T=0.165 C=0.835
SGDP_PRJ Global Study-wide 530 T=0.149 C=0.851
Qatari Global Study-wide 216 T=0.259 C=0.741
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.103 C=0.897
Siberian Global Study-wide 56 T=0.05 C=0.95
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 50 T=0.12 C=0.88
The Danish reference pan genome Danish Study-wide 40 T=0.12 C=0.88
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 T= A C G
GRCh38.p13 chr 7 NC_000007.14:g.84143099= NC_000007.14:g.84143099T>A NC_000007.14:g.84143099T>C NC_000007.14:g.84143099T>G
GRCh37.p13 chr 7 NC_000007.13:g.83772415= NC_000007.13:g.83772415T>A NC_000007.13:g.83772415T>C NC_000007.13:g.83772415T>G
SEMA3A RefSeqGene NG_011489.1:g.56803= NG_011489.1:g.56803A>T NG_011489.1:g.56803A>G NG_011489.1:g.56803A>C
SEMA3A transcript NM_006080.2:c.113-8148= NM_006080.2:c.113-8148A>T NM_006080.2:c.113-8148A>G NM_006080.2:c.113-8148A>C
SEMA3A transcript NM_006080.3:c.113-8148= NM_006080.3:c.113-8148A>T NM_006080.3:c.113-8148A>G NM_006080.3:c.113-8148A>C
SEMA3A transcript variant X1 XM_005250110.1:c.113-8148= XM_005250110.1:c.113-8148A>T XM_005250110.1:c.113-8148A>G XM_005250110.1:c.113-8148A>C
SEMA3A transcript variant X2 XM_005250110.3:c.113-8148= XM_005250110.3:c.113-8148A>T XM_005250110.3:c.113-8148A>G XM_005250110.3:c.113-8148A>C
SEMA3A transcript variant X2 XM_005250111.1:c.113-8148= XM_005250111.1:c.113-8148A>T XM_005250111.1:c.113-8148A>G XM_005250111.1:c.113-8148A>C
SEMA3A transcript variant X5 XM_005250111.4:c.113-8148= XM_005250111.4:c.113-8148A>T XM_005250111.4:c.113-8148A>G XM_005250111.4:c.113-8148A>C
SEMA3A transcript variant X3 XM_006715839.3:c.113-8148= XM_006715839.3:c.113-8148A>T XM_006715839.3:c.113-8148A>G XM_006715839.3:c.113-8148A>C
SEMA3A transcript variant X4 XM_011515734.3:c.113-8148= XM_011515734.3:c.113-8148A>T XM_011515734.3:c.113-8148A>G XM_011515734.3:c.113-8148A>C
SEMA3A transcript variant X6 XM_017011673.1:c.113-8148= XM_017011673.1:c.113-8148A>T XM_017011673.1:c.113-8148A>G XM_017011673.1:c.113-8148A>C
SEMA3A transcript variant X1 XM_024446633.1:c.113-8148= XM_024446633.1:c.113-8148A>T XM_024446633.1:c.113-8148A>G XM_024446633.1:c.113-8148A>C
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#.

87 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss451 Sep 19, 2000 (36)
2 CSHL-HAPMAP ss17150221 Feb 27, 2004 (120)
3 SSAHASNP ss22520459 Apr 05, 2004 (121)
4 SSAHASNP ss22892280 Apr 05, 2004 (121)
5 ABI ss44821765 Mar 14, 2006 (126)
6 AFFY ss76702352 Dec 08, 2007 (130)
7 HGSV ss77558841 Dec 07, 2007 (129)
8 HGSV ss80069480 Dec 14, 2007 (130)
9 HGSV ss85509676 Dec 14, 2007 (130)
10 BCMHGSC_JDW ss93718683 Mar 25, 2008 (129)
11 HUMANGENOME_JCVI ss98166519 Feb 04, 2009 (130)
12 KRIBB_YJKIM ss104807681 Feb 04, 2009 (130)
13 BGI ss105553967 Feb 04, 2009 (130)
14 1000GENOMES ss112283794 Jan 25, 2009 (130)
15 1000GENOMES ss114024732 Jan 25, 2009 (130)
16 ILLUMINA-UK ss116168822 Feb 14, 2009 (130)
17 ENSEMBL ss133757230 Dec 01, 2009 (131)
18 ENSEMBL ss142630886 Dec 01, 2009 (131)
19 GMI ss155127153 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss162491909 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss164727054 Jul 04, 2010 (132)
22 BUSHMAN ss203578777 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss208021326 Jul 04, 2010 (132)
24 1000GENOMES ss223175062 Jul 14, 2010 (132)
25 1000GENOMES ss234055498 Jul 15, 2010 (132)
26 1000GENOMES ss240994996 Jul 15, 2010 (132)
27 BL ss254481534 May 09, 2011 (134)
28 GMI ss279417314 May 04, 2012 (137)
29 GMI ss285669063 Apr 25, 2013 (138)
30 PJP ss293906618 May 09, 2011 (134)
31 ILLUMINA ss483518179 May 04, 2012 (137)
32 ILLUMINA ss485485044 May 04, 2012 (137)
33 ILLUMINA ss535726048 Sep 08, 2015 (146)
34 TISHKOFF ss560120996 Apr 25, 2013 (138)
35 SSMP ss654518982 Apr 25, 2013 (138)
36 ILLUMINA ss780307686 Aug 21, 2014 (142)
37 ILLUMINA ss782202615 Aug 21, 2014 (142)
38 ILLUMINA ss835794554 Aug 21, 2014 (142)
39 EVA-GONL ss984482971 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1074753118 Aug 21, 2014 (142)
41 1000GENOMES ss1325922264 Aug 21, 2014 (142)
42 DDI ss1431194347 Apr 01, 2015 (144)
43 EVA_GENOME_DK ss1582284409 Apr 01, 2015 (144)
44 EVA_DECODE ss1594058009 Apr 01, 2015 (144)
45 EVA_UK10K_ALSPAC ss1618582713 Apr 01, 2015 (144)
46 EVA_UK10K_TWINSUK ss1661576746 Apr 01, 2015 (144)
47 EVA_SVP ss1712967456 Apr 01, 2015 (144)
48 HAMMER_LAB ss1805088892 Sep 08, 2015 (146)
49 WEILL_CORNELL_DGM ss1927744950 Feb 12, 2016 (147)
50 GENOMED ss1970747234 Jul 19, 2016 (147)
51 JJLAB ss2024555578 Sep 14, 2016 (149)
52 ILLUMINA ss2095201292 Dec 20, 2016 (150)
53 USC_VALOUEV ss2152775996 Dec 20, 2016 (150)
54 HUMAN_LONGEVITY ss2295334581 Dec 20, 2016 (150)
55 TOPMED ss2464690188 Dec 20, 2016 (150)
56 SYSTEMSBIOZJU ss2626769295 Nov 08, 2017 (151)
57 ILLUMINA ss2634626543 Nov 08, 2017 (151)
58 GRF ss2708479268 Nov 08, 2017 (151)
59 GNOMAD ss2855546676 Nov 08, 2017 (151)
60 SWEGEN ss3001540856 Nov 08, 2017 (151)
61 ILLUMINA ss3022752405 Nov 08, 2017 (151)
62 BIOINF_KMB_FNS_UNIBA ss3026071167 Nov 08, 2017 (151)
63 CSHL ss3347707455 Nov 08, 2017 (151)
64 TOPMED ss3536205540 Nov 08, 2017 (151)
65 ILLUMINA ss3629852412 Oct 12, 2018 (152)
66 ILLUMINA ss3632532927 Oct 12, 2018 (152)
67 ILLUMINA ss3642572940 Oct 12, 2018 (152)
68 URBANLAB ss3648688990 Oct 12, 2018 (152)
69 ILLUMINA ss3653285960 Oct 12, 2018 (152)
70 EGCUT_WGS ss3669292594 Jul 13, 2019 (153)
71 EVA_DECODE ss3720102616 Jul 13, 2019 (153)
72 ILLUMINA ss3726457774 Jul 13, 2019 (153)
73 ACPOP ss3734814583 Jul 13, 2019 (153)
74 EVA ss3766801961 Jul 13, 2019 (153)
75 PACBIO ss3785878644 Jul 13, 2019 (153)
76 PACBIO ss3791171837 Jul 13, 2019 (153)
77 PACBIO ss3796051764 Jul 13, 2019 (153)
78 KHV_HUMAN_GENOMES ss3809973074 Jul 13, 2019 (153)
79 EVA ss3830675073 Apr 26, 2020 (154)
80 EVA ss3838834501 Apr 26, 2020 (154)
81 EVA ss3844289135 Apr 26, 2020 (154)
82 SGDP_PRJ ss3867766749 Apr 26, 2020 (154)
83 KRGDB ss3915024628 Apr 26, 2020 (154)
84 EVA ss3984590940 Apr 26, 2021 (155)
85 EVA ss3985305822 Apr 26, 2021 (155)
86 TOPMED ss4752799915 Apr 26, 2021 (155)
87 TOMMO_GENOMICS ss5184182838 Apr 26, 2021 (155)
88 1000Genomes NC_000007.13 - 83772415 Oct 12, 2018 (152)
89 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 83772415 Oct 12, 2018 (152)
90 Genetic variation in the Estonian population NC_000007.13 - 83772415 Oct 12, 2018 (152)
91 The Danish reference pan genome NC_000007.13 - 83772415 Apr 26, 2020 (154)
92 gnomAD - Genomes NC_000007.14 - 84143099 Apr 26, 2021 (155)
93 Genome of the Netherlands Release 5 NC_000007.13 - 83772415 Apr 26, 2020 (154)
94 HapMap NC_000007.14 - 84143099 Apr 26, 2020 (154)
95 KOREAN population from KRGDB NC_000007.13 - 83772415 Apr 26, 2020 (154)
96 Northern Sweden NC_000007.13 - 83772415 Jul 13, 2019 (153)
97 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000007.13 - 83772415 Apr 26, 2021 (155)
98 CNV burdens in cranial meningiomas NC_000007.13 - 83772415 Apr 26, 2021 (155)
99 Qatari NC_000007.13 - 83772415 Apr 26, 2020 (154)
100 SGDP_PRJ NC_000007.13 - 83772415 Apr 26, 2020 (154)
101 Siberian NC_000007.13 - 83772415 Apr 26, 2020 (154)
102 8.3KJPN NC_000007.13 - 83772415 Apr 26, 2021 (155)
103 TopMed NC_000007.14 - 84143099 Apr 26, 2021 (155)
104 UK 10K study - Twins NC_000007.13 - 83772415 Oct 12, 2018 (152)
105 A Vietnamese Genetic Variation Database NC_000007.13 - 83772415 Jul 13, 2019 (153)
106 ALFA NC_000007.14 - 84143099 Apr 26, 2021 (155)
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)
rs56594673 May 23, 2008 (130)
rs57635779 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
22202022, ss3915024628 NC_000007.13:83772414:T:A NC_000007.14:84143098:T:A (self)
ss77558841, ss80069480, ss85509676 NC_000007.11:83417065:T:C NC_000007.14:84143098:T:C (self)
ss93718683, ss112283794, ss114024732, ss116168822, ss162491909, ss164727054, ss203578777, ss208021326, ss254481534, ss279417314, ss285669063, ss293906618, ss485485044, ss1594058009, ss1712967456 NC_000007.12:83610350:T:C NC_000007.14:84143098:T:C (self)
37920647, 21102110, 15030842, 8449348, 9422861, 22202022, 8099448, 531749, 140365, 9786880, 19783729, 5292350, 42152145, 21102110, 4706120, ss223175062, ss234055498, ss240994996, ss483518179, ss535726048, ss560120996, ss654518982, ss780307686, ss782202615, ss835794554, ss984482971, ss1074753118, ss1325922264, ss1431194347, ss1582284409, ss1618582713, ss1661576746, ss1805088892, ss1927744950, ss1970747234, ss2024555578, ss2095201292, ss2152775996, ss2464690188, ss2626769295, ss2634626543, ss2708479268, ss2855546676, ss3001540856, ss3022752405, ss3347707455, ss3629852412, ss3632532927, ss3642572940, ss3653285960, ss3669292594, ss3734814583, ss3766801961, ss3785878644, ss3791171837, ss3796051764, ss3830675073, ss3838834501, ss3867766749, ss3915024628, ss3984590940, ss3985305822, ss5184182838 NC_000007.13:83772414:T:C NC_000007.14:84143098:T:C (self)
267510879, 3433958, 590177474, 1640556682, ss2295334581, ss3026071167, ss3536205540, ss3648688990, ss3720102616, ss3726457774, ss3809973074, ss3844289135, ss4752799915 NC_000007.14:84143098:T:C NC_000007.14:84143098:T:C (self)
ss17150221, ss22520459, ss22892280 NT_007933.13:9006652:T:C NC_000007.14:84143098:T:C (self)
ss451, ss44821765, ss76702352, ss98166519, ss104807681, ss105553967, ss133757230, ss142630886, ss155127153 NT_007933.15:21805257:T:C NC_000007.14:84143098:T:C (self)
22202022, ss3915024628 NC_000007.13:83772414:T:G NC_000007.14:84143098:T:G (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 rs447

Help

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.

Software version is: 2.0.1.post596+ae089ad