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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.

rs28994672

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:30786635-30786638 (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
delTT / delT / dupT
Variation Type
Indel Insertion and Deletion
Frequency
dupT=0.381159 (100889/264690, TOPMED)
(T)4=0.33559 (9483/28258, 14KJPN)
(T)4=0.33562 (5625/16760, 8.3KJPN) (+ 8 more)
dupT=0.1384 (1338/9666, ALFA)
dupT=0.4694 (3006/6404, 1000G_30x)
dupT=0.4736 (2372/5008, 1000G)
dupT=0.3004 (1345/4478, Estonian)
dupT=0.2548 (982/3854, ALSPAC)
dupT=0.2683 (995/3708, TWINSUK)
dupT=0.302 (181/600, NorthernSweden)
dupT=0.35 (14/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HCG20 : 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 9666 TTTT=0.8616 TT=0.0000, TTTTT=0.1384 0.764742 0.041589 0.193669 32
European Sub 8064 TTTT=0.8344 TT=0.0000, TTTTT=0.1656 0.71875 0.049851 0.231399 32
African Sub 1194 TTTT=1.0000 TT=0.0000, TTTTT=0.0000 1.0 0.0 0.0 N/A
African Others Sub 54 TTTT=1.00 TT=0.00, TTTTT=0.00 1.0 0.0 0.0 N/A
African American Sub 1140 TTTT=1.0000 TT=0.0000, TTTTT=0.0000 1.0 0.0 0.0 N/A
Asian Sub 30 TTTT=1.00 TT=0.00, TTTTT=0.00 1.0 0.0 0.0 N/A
East Asian Sub 22 TTTT=1.00 TT=0.00, TTTTT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 8 TTTT=1.0 TT=0.0, TTTTT=0.0 1.0 0.0 0.0 N/A
Latin American 1 Sub 50 TTTT=1.00 TT=0.00, TTTTT=0.00 1.0 0.0 0.0 N/A
Latin American 2 Sub 106 TTTT=1.000 TT=0.000, TTTTT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 8 TTTT=1.0 TT=0.0, TTTTT=0.0 1.0 0.0 0.0 N/A
Other Sub 214 TTTT=0.986 TT=0.000, TTTTT=0.014 0.971963 0.0 0.028037 0


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 -

No frequency provided

dupT=0.381159
14KJPN JAPANESE Study-wide 28258 -

No frequency provided

dupT=0.66441
8.3KJPN JAPANESE Study-wide 16760 -

No frequency provided

dupT=0.66438
Allele Frequency Aggregator Total Global 9666 (T)4=0.8616 delTT=0.0000, dupT=0.1384
Allele Frequency Aggregator European Sub 8064 (T)4=0.8344 delTT=0.0000, dupT=0.1656
Allele Frequency Aggregator African Sub 1194 (T)4=1.0000 delTT=0.0000, dupT=0.0000
Allele Frequency Aggregator Other Sub 214 (T)4=0.986 delTT=0.000, dupT=0.014
Allele Frequency Aggregator Latin American 2 Sub 106 (T)4=1.000 delTT=0.000, dupT=0.000
Allele Frequency Aggregator Latin American 1 Sub 50 (T)4=1.00 delTT=0.00, dupT=0.00
Allele Frequency Aggregator Asian Sub 30 (T)4=1.00 delTT=0.00, dupT=0.00
Allele Frequency Aggregator South Asian Sub 8 (T)4=1.0 delTT=0.0, dupT=0.0
1000Genomes_30x Global Study-wide 6404 -

No frequency provided

dupT=0.4694
1000Genomes_30x African Sub 1786 -

No frequency provided

dupT=0.3595
1000Genomes_30x Europe Sub 1266 -

No frequency provided

dupT=0.3341
1000Genomes_30x South Asian Sub 1202 -

No frequency provided

dupT=0.6963
1000Genomes_30x East Asian Sub 1170 -

No frequency provided

dupT=0.4889
1000Genomes_30x American Sub 980 -

No frequency provided

dupT=0.543
1000Genomes Global Study-wide 5008 -

No frequency provided

dupT=0.4736
1000Genomes African Sub 1322 -

No frequency provided

dupT=0.3601
1000Genomes East Asian Sub 1008 -

No frequency provided

dupT=0.4970
1000Genomes Europe Sub 1006 -

No frequency provided

dupT=0.3380
1000Genomes South Asian Sub 978 -

No frequency provided

dupT=0.690
1000Genomes American Sub 694 -

No frequency provided

dupT=0.548
Genetic variation in the Estonian population Estonian Study-wide 4478 -

No frequency provided

dupT=0.3004
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 -

No frequency provided

dupT=0.2548
UK 10K study - Twins TWIN COHORT Study-wide 3708 -

No frequency provided

dupT=0.2683
Northern Sweden ACPOP Study-wide 600 -

No frequency provided

dupT=0.302
The Danish reference pan genome Danish Study-wide 40 -

No frequency provided

dupT=0.35
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 6 NC_000006.12:g.30786637_30786638del
GRCh38.p14 chr 6 NC_000006.12:g.30786638del
GRCh38.p14 chr 6 NC_000006.12:g.30786638dup
GRCh37.p13 chr 6 NC_000006.11:g.30754414_30754415del
GRCh37.p13 chr 6 NC_000006.11:g.30754415del
GRCh37.p13 chr 6 NC_000006.11:g.30754415dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2266349_2266350del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2266350del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2266350dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2266455_2266456del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2266456del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2266456dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2041720_2041721del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2041721del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2041721dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2047316_2047317del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2047317del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2047317dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.2042613_2042614del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.2042614del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.2042614dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2048198_2048199del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2048199del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2048199dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2096879_2096880del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2096880del
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2096880dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2102499_2102500del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2102500del
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2102500dup
Gene: HCG20, HLA complex group 20 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
HCG20 transcript NR_138037.1:n. 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
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)4= delTT delT dupT
GRCh38.p14 chr 6 NC_000006.12:g.30786635_30786638= NC_000006.12:g.30786637_30786638del NC_000006.12:g.30786638del NC_000006.12:g.30786638dup
GRCh37.p13 chr 6 NC_000006.11:g.30754412_30754415= NC_000006.11:g.30754414_30754415del NC_000006.11:g.30754415del NC_000006.11:g.30754415dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2266347_2266350= NT_113891.3:g.2266349_2266350del NT_113891.3:g.2266350del NT_113891.3:g.2266350dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2266453_2266456= NT_113891.2:g.2266455_2266456del NT_113891.2:g.2266456del NT_113891.2:g.2266456dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2041718_2041721= NT_167248.2:g.2041720_2041721del NT_167248.2:g.2041721del NT_167248.2:g.2041721dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2047314_2047317= NT_167248.1:g.2047316_2047317del NT_167248.1:g.2047317del NT_167248.1:g.2047317dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.2042610_2042614= NT_167245.2:g.2042613_2042614del NT_167245.2:g.2042614del NT_167245.2:g.2042614dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2048195_2048199= NT_167245.1:g.2048198_2048199del NT_167245.1:g.2048199del NT_167245.1:g.2048199dup
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2096877_2096880= NT_167246.2:g.2096879_2096880del NT_167246.2:g.2096880del NT_167246.2:g.2096880dup
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2102497_2102500= NT_167246.1:g.2102499_2102500del NT_167246.1:g.2102500del NT_167246.1:g.2102500dup
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#.

59 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 SI_MHC_SNP ss35527282 May 25, 2005 (125)
2 HUMANGENOME_JCVI ss95424066 Feb 05, 2009 (130)
3 GMI ss155041594 Dec 01, 2009 (131)
4 BUSHMAN ss193853837 Jul 04, 2010 (132)
5 GMI ss288693152 May 04, 2012 (137)
6 PJP ss295272690 May 09, 2011 (137)
7 1000GENOMES ss326783645 May 09, 2011 (137)
8 1000GENOMES ss326831364 May 09, 2011 (137)
9 1000GENOMES ss327075137 May 09, 2011 (137)
10 1000GENOMES ss499444041 May 04, 2012 (137)
11 LUNTER ss551599285 Apr 25, 2013 (138)
12 LUNTER ss551780207 Apr 25, 2013 (138)
13 LUNTER ss553240483 Apr 25, 2013 (138)
14 TISHKOFF ss558328223 Apr 25, 2013 (138)
15 SSMP ss663686960 Apr 01, 2015 (144)
16 BILGI_BIOE ss666348858 Apr 25, 2013 (138)
17 1000GENOMES ss1375318388 Aug 21, 2014 (142)
18 EVA_GENOME_DK ss1576716353 Apr 01, 2015 (144)
19 EVA_UK10K_ALSPAC ss1705102402 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1705103590 Apr 01, 2015 (144)
21 HAMMER_LAB ss1804350274 Sep 08, 2015 (146)
22 GENOMED ss1970351697 Jul 19, 2016 (147)
23 JJLAB ss2030751603 Sep 14, 2016 (149)
24 SYSTEMSBIOZJU ss2626301346 Nov 08, 2017 (151)
25 SWEGEN ss2998774749 Nov 08, 2017 (151)
26 MCHAISSO ss3064198309 Nov 08, 2017 (151)
27 MCHAISSO ss3065076115 Nov 08, 2017 (151)
28 MCHAISSO ss3066072564 Nov 08, 2017 (151)
29 BEROUKHIMLAB ss3644207587 Oct 12, 2018 (152)
30 BIOINF_KMB_FNS_UNIBA ss3645942712 Oct 12, 2018 (152)
31 URBANLAB ss3648305561 Oct 12, 2018 (152)
32 EGCUT_WGS ss3666697076 Jul 13, 2019 (153)
33 EVA_DECODE ss3716886319 Jul 13, 2019 (153)
34 ACPOP ss3733345770 Jul 13, 2019 (153)
35 PACBIO ss3785418176 Jul 13, 2019 (153)
36 PACBIO ss3790777811 Jul 13, 2019 (153)
37 PACBIO ss3795655179 Jul 13, 2019 (153)
38 KHV_HUMAN_GENOMES ss3807960661 Jul 13, 2019 (153)
39 EVA ss3829820797 Apr 26, 2020 (154)
40 EVA ss3838387455 Apr 26, 2020 (154)
41 EVA ss3843828813 Apr 26, 2020 (154)
42 VINODS ss4025181914 Apr 26, 2021 (155)
43 VINODS ss4025223934 Apr 26, 2021 (155)
44 VINODS ss4025261241 Apr 26, 2021 (155)
45 GNOMAD ss4139284306 Apr 26, 2021 (155)
46 GNOMAD ss4139284307 Apr 26, 2021 (155)
47 TOPMED ss4698234506 Apr 26, 2021 (155)
48 TOMMO_GENOMICS ss5176801555 Apr 26, 2021 (155)
49 1000G_HIGH_COVERAGE ss5267908759 Oct 13, 2022 (156)
50 HUGCELL_USP ss5465648284 Oct 13, 2022 (156)
51 EVA ss5508417277 Oct 13, 2022 (156)
52 1000G_HIGH_COVERAGE ss5553558423 Oct 13, 2022 (156)
53 SANFORD_IMAGENETICS ss5640067566 Oct 13, 2022 (156)
54 TOMMO_GENOMICS ss5714647270 Oct 13, 2022 (156)
55 YY_MCH ss5807291269 Oct 13, 2022 (156)
56 EVA ss5842008338 Oct 13, 2022 (156)
57 EVA ss5855274300 Oct 13, 2022 (156)
58 EVA ss5883216853 Oct 13, 2022 (156)
59 EVA ss5968571163 Oct 13, 2022 (156)
60 1000Genomes NC_000006.11 - 30754412 Oct 12, 2018 (152)
61 1000Genomes_30x NC_000006.12 - 30786635 Oct 13, 2022 (156)
62 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 30754412 Oct 12, 2018 (152)
63 Genetic variation in the Estonian population NC_000006.11 - 30754412 Oct 12, 2018 (152)
64 The Danish reference pan genome NC_000006.11 - 30754412 Apr 26, 2020 (154)
65 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 221066113 (NC_000006.12:30786634::T 48372/139814)
Row 221066114 (NC_000006.12:30786634:TT: 2/139910)

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

Submission ignored due to conflicting rows:
Row 221066113 (NC_000006.12:30786634::T 48372/139814)
Row 221066114 (NC_000006.12:30786634:TT: 2/139910)

- Apr 26, 2021 (155)
67 Northern Sweden NC_000006.11 - 30754412 Jul 13, 2019 (153)
68 8.3KJPN NC_000006.11 - 30754412 Apr 26, 2021 (155)
69 14KJPN NC_000006.12 - 30786635 Oct 13, 2022 (156)
70 TopMed NC_000006.12 - 30786635 Apr 26, 2021 (155)
71 UK 10K study - Twins NC_000006.11 - 30754412 Oct 12, 2018 (152)
72 ALFA NC_000006.12 - 30786635 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)
rs148727733 May 04, 2012 (137)
rs142520579 May 04, 2012 (137)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss4139284307 NC_000006.12:30786634:TT: NC_000006.12:30786634:TTTT:TT (self)
7990057809 NC_000006.12:30786634:TTTT:TT NC_000006.12:30786634:TTTT:TT (self)
ss5508417277 NC_000006.11:30754411:T: NC_000006.12:30786634:TTTT:TTT
ss288693152, ss326783645, ss326831364, ss327075137, ss551599285, ss551780207, ss553240483 NC_000006.10:30862390::T NC_000006.12:30786634:TTTT:TTTTT (self)
ss295272690 NC_000006.10:30862394::T NC_000006.12:30786634:TTTT:TTTTT (self)
31295451, 17448881, 12435324, 1064433, 6630635, 34770862, 17448881, ss499444041, ss663686960, ss666348858, ss1375318388, ss1576716353, ss1705102402, ss1705103590, ss1804350274, ss1970351697, ss2030751603, ss2626301346, ss2998774749, ss3644207587, ss3666697076, ss3733345770, ss3785418176, ss3790777811, ss3795655179, ss3829820797, ss3838387455, ss5176801555, ss5640067566, ss5842008338, ss5968571163 NC_000006.11:30754411::T NC_000006.12:30786634:TTTT:TTTTT (self)
ss558328223 NC_000006.11:30754415::T NC_000006.12:30786634:TTTT:TTTTT (self)
41084358, 48484374, 535612064, ss3064198309, ss3065076115, ss3066072564, ss3645942712, ss3648305561, ss3716886319, ss3807960661, ss3843828813, ss4139284306, ss4698234506, ss5267908759, ss5465648284, ss5553558423, ss5714647270, ss5807291269, ss5855274300, ss5883216853 NC_000006.12:30786634::T NC_000006.12:30786634:TTTT:TTTTT (self)
7990057809 NC_000006.12:30786634:TTTT:TTTTT NC_000006.12:30786634:TTTT:TTTTT (self)
ss193853837 NT_007592.15:30694411::T NC_000006.12:30786634:TTTT:TTTTT (self)
ss35527282, ss95424066, ss155041594 NT_007592.15:30694415::T NC_000006.12:30786634:TTTT:TTTTT (self)
ss4025181914 NT_113891.3:2266346::T NC_000006.12:30786634:TTTT:TTTTT (self)
ss4025223934 NT_167246.2:2096876::T NC_000006.12:30786634:TTTT:TTTTT (self)
ss4025261241 NT_167248.2:2041717::T NC_000006.12:30786634:TTTT:TTTTT (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 rs28994672

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