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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.

rs56917645

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:86883999-86884008 (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
delA / dupA / dupAA
Variation Type
Indel Insertion and Deletion
Frequency
dupA=0.3234 (2503/7740, ALFA)
(A)10=0.4355 (1937/4448, Estonian)
(A)10=0.4574 (1763/3854, ALSPAC) (+ 4 more)
(A)10=0.4525 (1678/3708, TWINSUK)
delA=0.0853 (235/2754, 1000G)
(A)10=0.480 (287/598, NorthernSweden)
dupA=0.47 (19/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
C4orf36 : 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 7740 AAAAAAAAAA=0.6765 AAAAAAAAA=0.0000, AAAAAAAAAAA=0.3234, AAAAAAAAAAAA=0.0001 0.53864 0.185319 0.27604 32
European Sub 6038 AAAAAAAAAA=0.5861 AAAAAAAAA=0.0000, AAAAAAAAAAA=0.4137, AAAAAAAAAAAA=0.0002 0.409874 0.237243 0.352883 32
African Sub 1338 AAAAAAAAAA=1.0000 AAAAAAAAA=0.0000, AAAAAAAAAAA=0.0000, AAAAAAAAAAAA=0.0000 1.0 0.0 0.0 N/A
African Others Sub 56 AAAAAAAAAA=1.00 AAAAAAAAA=0.00, AAAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00 1.0 0.0 0.0 N/A
African American Sub 1282 AAAAAAAAAA=1.0000 AAAAAAAAA=0.0000, AAAAAAAAAAA=0.0000, AAAAAAAAAAAA=0.0000 1.0 0.0 0.0 N/A
Asian Sub 30 AAAAAAAAAA=1.00 AAAAAAAAA=0.00, AAAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00 1.0 0.0 0.0 N/A
East Asian Sub 24 AAAAAAAAAA=1.00 AAAAAAAAA=0.00, AAAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 6 AAAAAAAAAA=1.0 AAAAAAAAA=0.0, AAAAAAAAAAA=0.0, AAAAAAAAAAAA=0.0 1.0 0.0 0.0 N/A
Latin American 1 Sub 40 AAAAAAAAAA=1.00 AAAAAAAAA=0.00, AAAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00 1.0 0.0 0.0 N/A
Latin American 2 Sub 134 AAAAAAAAAA=1.000 AAAAAAAAA=0.000, AAAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000 1.0 0.0 0.0 N/A
South Asian Sub 10 AAAAAAAAAA=1.0 AAAAAAAAA=0.0, AAAAAAAAAAA=0.0, AAAAAAAAAAAA=0.0 1.0 0.0 0.0 N/A
Other Sub 150 AAAAAAAAAA=0.967 AAAAAAAAA=0.000, AAAAAAAAAAA=0.033, AAAAAAAAAAAA=0.000 0.946667 0.013333 0.04 6


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
Allele Frequency Aggregator Total Global 7740 (A)10=0.6765 delA=0.0000, dupA=0.3234, dupAA=0.0001
Allele Frequency Aggregator European Sub 6038 (A)10=0.5861 delA=0.0000, dupA=0.4137, dupAA=0.0002
Allele Frequency Aggregator African Sub 1338 (A)10=1.0000 delA=0.0000, dupA=0.0000, dupAA=0.0000
Allele Frequency Aggregator Other Sub 150 (A)10=0.967 delA=0.000, dupA=0.033, dupAA=0.000
Allele Frequency Aggregator Latin American 2 Sub 134 (A)10=1.000 delA=0.000, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator Latin American 1 Sub 40 (A)10=1.00 delA=0.00, dupA=0.00, dupAA=0.00
Allele Frequency Aggregator Asian Sub 30 (A)10=1.00 delA=0.00, dupA=0.00, dupAA=0.00
Allele Frequency Aggregator South Asian Sub 10 (A)10=1.0 delA=0.0, dupA=0.0, dupAA=0.0
Genetic variation in the Estonian population Estonian Study-wide 4448 -

No frequency provided

dupA=0.5645
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 -

No frequency provided

dupA=0.5426
UK 10K study - Twins TWIN COHORT Study-wide 3708 -

No frequency provided

dupA=0.5475
1000Genomes Global Study-wide 2754 (A)10=0.9147 delA=0.0853
1000Genomes African Sub 1127 (A)10=0.8030 delA=0.1970
1000Genomes Europe Sub 473 (A)10=0.998 delA=0.002
1000Genomes East Asian Sub 461 (A)10=0.991 delA=0.009
1000Genomes South Asian Sub 350 (A)10=0.997 delA=0.003
1000Genomes American Sub 343 (A)10=0.980 delA=0.020
Northern Sweden ACPOP Study-wide 598 -

No frequency provided

dupA=0.520
The Danish reference pan genome Danish Study-wide 40 -

No frequency provided

dupA=0.47
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.p14 chr 4 NC_000004.12:g.86884008del
GRCh38.p14 chr 4 NC_000004.12:g.86884008dup
GRCh38.p14 chr 4 NC_000004.12:g.86884007_86884008dup
GRCh37.p13 chr 4 NC_000004.11:g.87805161del
GRCh37.p13 chr 4 NC_000004.11:g.87805161dup
GRCh37.p13 chr 4 NC_000004.11:g.87805160_87805161dup
Gene: C4orf36, chromosome 4 open reading frame 36 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
C4orf36 transcript variant 1 NM_144645.4:c.*2+3759del N/A Intron Variant
C4orf36 transcript variant 2 NM_001369888.1:c. N/A Genic Downstream Transcript Variant
C4orf36 transcript variant 3 NM_001369889.1:c. N/A Genic Downstream Transcript Variant
C4orf36 transcript variant X1 XM_011531612.4:c. N/A Genic Downstream Transcript Variant
C4orf36 transcript variant X3 XM_011531613.4:c. N/A Genic Downstream Transcript Variant
C4orf36 transcript variant X4 XM_011531615.4:c. N/A Genic Downstream Transcript Variant
C4orf36 transcript variant X2 XM_017007746.3:c. N/A Genic Downstream Transcript 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

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)10= delA dupA dupAA
GRCh38.p14 chr 4 NC_000004.12:g.86883999_86884008= NC_000004.12:g.86884008del NC_000004.12:g.86884008dup NC_000004.12:g.86884007_86884008dup
GRCh37.p13 chr 4 NC_000004.11:g.87805152_87805161= NC_000004.11:g.87805161del NC_000004.11:g.87805161dup NC_000004.11:g.87805160_87805161dup
C4orf36 transcript NM_144645.3:c.*2+3759= NM_144645.3:c.*2+3759del NM_144645.3:c.*2+3759dup NM_144645.3:c.*2+3758_*2+3759dup
C4orf36 transcript variant 1 NM_144645.4:c.*2+3759= NM_144645.4:c.*2+3759del NM_144645.4:c.*2+3759dup NM_144645.4:c.*2+3758_*2+3759dup
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#.

57 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss80931011 Dec 04, 2013 (138)
2 BGI ss104751662 Dec 06, 2013 (138)
3 GMI ss288551902 May 04, 2012 (137)
4 1000GENOMES ss326543686 May 09, 2011 (138)
5 1000GENOMES ss326576021 May 09, 2011 (138)
6 1000GENOMES ss326746351 Jan 10, 2018 (151)
7 LUNTER ss551385305 Apr 25, 2013 (138)
8 LUNTER ss551509754 Apr 25, 2013 (138)
9 LUNTER ss553143441 Apr 25, 2013 (138)
10 SSMP ss663535696 Apr 01, 2015 (144)
11 BILGI_BIOE ss666267579 Apr 25, 2013 (138)
12 1000GENOMES ss1372431882 Aug 21, 2014 (142)
13 1000GENOMES ss1372431885 Aug 21, 2014 (142)
14 DDI ss1536416498 Apr 01, 2015 (144)
15 EVA_GENOME_DK ss1576280651 Apr 01, 2015 (144)
16 EVA_DECODE ss1589855179 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1704244524 Apr 01, 2015 (144)
18 EVA_UK10K_TWINSUK ss1704244745 Apr 01, 2015 (144)
19 HAMMER_LAB ss1801788834 Sep 08, 2015 (146)
20 JJLAB ss2030612022 Sep 14, 2016 (149)
21 SWEGEN ss2995067194 Jan 10, 2018 (151)
22 MCHAISSO ss3064111425 Jan 10, 2018 (151)
23 MCHAISSO ss3064978741 Jan 10, 2018 (151)
24 BEROUKHIMLAB ss3644159316 Oct 12, 2018 (152)
25 BIOINF_KMB_FNS_UNIBA ss3645809240 Oct 12, 2018 (152)
26 EGCUT_WGS ss3662953624 Jul 13, 2019 (153)
27 EVA_DECODE ss3712485857 Jul 13, 2019 (153)
28 EVA_DECODE ss3712485858 Jul 13, 2019 (153)
29 EVA_DECODE ss3712485859 Jul 13, 2019 (153)
30 ACPOP ss3731345564 Jul 13, 2019 (153)
31 PACBIO ss3784780000 Jul 13, 2019 (153)
32 PACBIO ss3790228339 Jul 13, 2019 (153)
33 PACBIO ss3795103701 Jul 13, 2019 (153)
34 KHV_HUMAN_GENOMES ss3805211723 Jul 13, 2019 (153)
35 KHV_HUMAN_GENOMES ss3805211724 Jul 13, 2019 (153)
36 KHV_HUMAN_GENOMES ss3805211725 Jul 13, 2019 (153)
37 EVA ss3828658625 Apr 26, 2020 (154)
38 EVA ss3837771047 Apr 26, 2020 (154)
39 EVA ss3843208964 Apr 26, 2020 (154)
40 KOGIC ss3954587234 Apr 26, 2020 (154)
41 KOGIC ss3954587235 Apr 26, 2020 (154)
42 GNOMAD ss4115186283 Apr 26, 2021 (155)
43 GNOMAD ss4115186284 Apr 26, 2021 (155)
44 TOMMO_GENOMICS ss5166698361 Apr 26, 2021 (155)
45 TOMMO_GENOMICS ss5166698362 Apr 26, 2021 (155)
46 1000G_HIGH_COVERAGE ss5259982679 Oct 17, 2022 (156)
47 1000G_HIGH_COVERAGE ss5259982680 Oct 17, 2022 (156)
48 HUGCELL_USP ss5458657802 Oct 17, 2022 (156)
49 HUGCELL_USP ss5458657803 Oct 17, 2022 (156)
50 HUGCELL_USP ss5458657804 Oct 17, 2022 (156)
51 TOMMO_GENOMICS ss5701320881 Oct 17, 2022 (156)
52 TOMMO_GENOMICS ss5701320882 Oct 17, 2022 (156)
53 TOMMO_GENOMICS ss5701320883 Oct 17, 2022 (156)
54 YY_MCH ss5805280329 Oct 17, 2022 (156)
55 EVA ss5844301828 Oct 17, 2022 (156)
56 EVA ss5854319715 Oct 17, 2022 (156)
57 EVA ss5963873183 Oct 17, 2022 (156)
58 1000Genomes NC_000004.11 - 87805152 Oct 12, 2018 (152)
59 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 87805152 Oct 12, 2018 (152)
60 Genetic variation in the Estonian population NC_000004.11 - 87805152 Oct 12, 2018 (152)
61 The Danish reference pan genome NC_000004.11 - 87805152 Apr 26, 2020 (154)
62 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 156262408 (NC_000004.12:86883998::A 59574/138068)
Row 156262409 (NC_000004.12:86883998::AA 7/138172)
Row 156262410 (NC_000004.12:86883998:A: 5526/138158)

- Apr 26, 2021 (155)
63 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 156262408 (NC_000004.12:86883998::A 59574/138068)
Row 156262409 (NC_000004.12:86883998::AA 7/138172)
Row 156262410 (NC_000004.12:86883998:A: 5526/138158)

- Apr 26, 2021 (155)
64 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 156262408 (NC_000004.12:86883998::A 59574/138068)
Row 156262409 (NC_000004.12:86883998::AA 7/138172)
Row 156262410 (NC_000004.12:86883998:A: 5526/138158)

- Apr 26, 2021 (155)
65 Korean Genome Project

Submission ignored due to conflicting rows:
Row 10965235 (NC_000004.12:86883998::A 1212/1832)
Row 10965236 (NC_000004.12:86883998::AA 8/1832)

- Apr 26, 2020 (154)
66 Korean Genome Project

Submission ignored due to conflicting rows:
Row 10965235 (NC_000004.12:86883998::A 1212/1832)
Row 10965236 (NC_000004.12:86883998::AA 8/1832)

- Apr 26, 2020 (154)
67 Northern Sweden NC_000004.11 - 87805152 Jul 13, 2019 (153)
68 8.3KJPN

Submission ignored due to conflicting rows:
Row 24667668 (NC_000004.11:87805151::A 9944/16760)
Row 24667669 (NC_000004.11:87805151:A: 2/16760)

- Apr 26, 2021 (155)
69 8.3KJPN

Submission ignored due to conflicting rows:
Row 24667668 (NC_000004.11:87805151::A 9944/16760)
Row 24667669 (NC_000004.11:87805151:A: 2/16760)

- Apr 26, 2021 (155)
70 14KJPN

Submission ignored due to conflicting rows:
Row 35157985 (NC_000004.12:86883998::A 16850/28258)
Row 35157986 (NC_000004.12:86883998::AA 1/28258)
Row 35157987 (NC_000004.12:86883998:A: 2/28258)

- Oct 17, 2022 (156)
71 14KJPN

Submission ignored due to conflicting rows:
Row 35157985 (NC_000004.12:86883998::A 16850/28258)
Row 35157986 (NC_000004.12:86883998::AA 1/28258)
Row 35157987 (NC_000004.12:86883998:A: 2/28258)

- Oct 17, 2022 (156)
72 14KJPN

Submission ignored due to conflicting rows:
Row 35157985 (NC_000004.12:86883998::A 16850/28258)
Row 35157986 (NC_000004.12:86883998::AA 1/28258)
Row 35157987 (NC_000004.12:86883998:A: 2/28258)

- Oct 17, 2022 (156)
73 UK 10K study - Twins NC_000004.11 - 87805152 Oct 12, 2018 (152)
74 ALFA NC_000004.12 - 86883999 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)
rs75088748 May 11, 2012 (137)
rs146572067 May 15, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss326746351, ss551509754 NC_000004.10:88024175:A: NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAA

(self)
22061350, ss1372431882, ss1801788834, ss5166698362 NC_000004.11:87805151:A: NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAA

(self)
ss3712485859, ss3805211725, ss5259982680, ss5458657804, ss5701320883 NC_000004.12:86883998:A: NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAA

(self)
8297610978 NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAA

NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAA

(self)
ss326543686, ss326576021, ss551385305, ss553143441, ss1589855179 NC_000004.10:88024175::A NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAA

(self)
ss288551902 NC_000004.10:88024185::A NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAA

(self)
12270366, 8691872, 924579, 4630429, 12270366, ss663535696, ss666267579, ss1536416498, ss1576280651, ss1704244524, ss1704244745, ss2030612022, ss2995067194, ss3644159316, ss3662953624, ss3731345564, ss3784780000, ss3790228339, ss3795103701, ss3828658625, ss3837771047, ss5166698361, ss5844301828, ss5963873183 NC_000004.11:87805151::A NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAA

(self)
ss1372431885 NC_000004.11:87805152::A NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAA

(self)
ss3064111425, ss3064978741, ss3645809240, ss3805211723, ss3843208964, ss3954587234, ss4115186283, ss5259982679, ss5458657802, ss5701320881, ss5805280329, ss5854319715 NC_000004.12:86883998::A NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAA

(self)
8297610978 NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAA

NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAA

(self)
ss3712485858, ss3805211724 NC_000004.12:86883999::A NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAA

(self)
ss104751662 NT_016354.19:12352881::A NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAA

(self)
ss80931011 NT_016354.19:12352882::A NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAA

(self)
ss3954587235, ss4115186284, ss5458657803, ss5701320882 NC_000004.12:86883998::AA NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAAA

(self)
8297610978 NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAAA

NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAAA

(self)
ss3712485857 NC_000004.12:86883999::AA NC_000004.12:86883998:AAAAAAAAAA:A…

NC_000004.12:86883998:AAAAAAAAAA:AAAAAAAAAAAA

(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 rs56917645

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.post820+afb47a3d