Malaysian Node of the Human Variome Project Database
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Individual #00000055
Reference
E George et al. (1992)
Gender
-
Geographic origin
Malaysia
Ethnic origin
Malay
Population
-
Remarks
-
Microattribution
-
Panel size
1
Diseases
HBB
Owner name
Nuur Athirah Binti Mohd Daud
Database submission
license
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Created by
Nuur Athirah Binti Mohd Daud
Phenotypes
Beta-thalassaemia (
HBB
)
Add phenotype for this disease
No phenotypes found!
Screenings
Legend
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Template
: Template(s) used to detect the sequence variant; DNA = genomic DNA, RNA = RNA (cDNA).
All options:
DNA
RNA = RNA (cDNA)
Protein
? = unknown
Technique
: Technique(s) used to identify the sequence variant.
All options:
? = Unknown
arrayCGH = array for Comparative Genomic Hybridisation
arraySEQ = array for resequencing
arraySNP = array for SNP typing
arrayCNV = array for Copy Number Variation (SNP and CNV probes)
BESS = Base Excision Sequence Scanning
CMC = Chemical Mismatch Cleavage
CSCE = Conformation Sensitive Capillary Electrophoresis
DGGE = Denaturing-Gradient Gel-Electrophoresis
DHPLC = Denaturing High-Performance Liquid Chromatography
DOVAM = Detection Of Virtually All Mutations (SSCA variant)
ddF = dideoxy Fingerprinting
DSCA = Double-Strand DNA Conformation Analysis
EMC = Enzymatic Mismatch Cleavage
HD = HeteroDuplex analysis
MCA = high-resolution Melting Curve Analysis (hrMCA)
IHC = Immuno-Histo-Chemistry
MAPH = Multiplex Amplifiable Probe Hybridisation
MLPA = Multiplex Ligation-dependent Probe Amplification
SEQ-NG = Next-Generation Sequencing
SEQ-NG-H = Next-Generation Sequencing - Helicos
SEQ-NG-I = Next-Generation Sequencing - Illumina/Solexa
SEQ-NG-R = Next-Generation Sequencing - Roche/454
SEQ-NG-S = Next-Generation Sequencing - SOLiD
Northern = Northern blotting
PCR = Polymerase Chain Reaction
PCRdig = PCR + restriction enzyme digestion
PCRlr = PCR, long-range
PCRm = PCR, multiplex
PCRq = PCR, quantitative
PAGE = Poly-Acrylamide Gel-Electrophoresis
PTT = Protein Truncation Test
PFGE = Pulsed-Field Gel-Electrophoresis (+Southern)
RT-PCR = Reverse Transcription and PCR
SEQ = SEQuencing
SBE = Single Base Extension
SSCA = Single-Strand DNA Conformation polymorphism Analysis (SSCP)
SSCAf = SSCA, fluorescent (SSCP)
Southern = Southern blotting
TaqMan = TaqMan assay
Western = Western Blotting
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Date
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Numeric
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Numeric
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Numeric
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Numeric
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Numeric
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Numeric
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Numeric
>=23
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Numeric
>=20 <30 !23
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Example
Matches
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all entries containing 'Asian', 'asian', including 'Caucasian', 'caucasian', etc.
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all entries containing 'Asian' but not containing 'Caucasian'
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Screening ID
Template
Technique
Genes screened
Variants found
Owner
0000000068
DNA
PCRm
HBB
12
Nuur Athirah Binti Mohd Daud
Variants
Legend
Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.
Allele
: On which allele is the variant located? Does not necessarily imply inheritance! 'Paternal' (confirmed or inferred), 'Maternal' (confirmed or inferred), 'Parent #1' or #2 for compound heterozygosity without having screened the parents, 'Unknown' for heterozygosity without having screened the parents, 'Both' for homozygozity.
Effect
: The variant's effect on the function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.Values used: '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect was not classified.
DNA change (genomic) (hg38)
: Description of variant at DNA level, based on the genomic DNA reference sequence (following HGVS recommendations).
g.12345678C>T
g.12345678_12345890del
g.12345678_12345890dup
Published as
: Variant as originally reported (e.g. 521delT); listed only when different from "DNA change". Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G).
Reference
: Reference to publication describing the variant, including links to OMIM (when available), PubMed or or other source, e.g. "den Dunnen ASHG2003 P2346".
DB-ID
: Database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro.
dbSNP ID
: The dbSNP ID.
Frequency
: Frequency in which the variant was found; e.g 5/760 chromosomes (in 5 of 760 chromosomes tested), 1/33 patients (in 1 of 33 patients analysed in study), 0.05 controls (in 5% of control cases tested).
Variant remarks
: Remarks regarding the variant described, e.g. germline mosaicism in mother, 345 kb deletion, muscle RNA analysed, not in 200 control chromosomes tested, on founder haplotype, etc.
Exon
: Number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = exons 3 to 7, 8i_9 = border intron 8/exon 9.
DNA change (cDNA)
: Description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup.
Published as
: Variant as originally reported (e.g. 521delT); listed only when different from "DNA change". Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G).
RNA change
: Description of variant at RNA level (following HGVS recommendations).
r.123c>u
r.? = unknown
r.(?) = RNA not analysed but probably transcribed copy of DNA variant
r.spl? = RNA not analysed but variant probably affects splicing
r.(spl?) = RNA not analysed but variant may affect splicing
r.0? = change expected to abolish transcription
Protein
: Description of variant at protein level (following HGVS recommendations).
p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
p.Arg345Pro = change derived from RNA analysis
p.? = unknown effect
p.0? = probably no protein produced
GVS function
: The functional annotation of this position from the Genome Variation Server.
All options:
intergenic
near-gene-5
utr-5
start-lost
coding
non-coding-exon
coding-near-splice
non-coding-exon-near-splice
coding-synonymous
coding-synonymous-near-splice
codingComplex
codingComplex-near-splice
frameshift
frameshift-near-splice
missense
missense-near-splice
splice-5
splice
non-coding-intron-near-splice
intron
splice-3
stop-gained
stop-gained-near-splice
stop-lost
stop-lost-near-splice
utr-3
near-gene-3
Clinical classification
: Clinical classification of variant
12 entries on 1 page. Showing entries 1 - 12.
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Chr
Allele
Effect
DNA change (genomic) (hg38)
Published as
Reference
DB-ID
dbSNP ID
Frequency
Variant remarks
Owner
Gene
Exon
DNA change (cDNA)
Published as
RNA change
Protein
GVS function
Clinical classification
11
Unknown
+/.
g.63632_71046del
Hb Lepore
E George et al. (1992)
,
(OMIM 0020)
HBB_000029
-
1/141
-
Nuur Athirah Binti Mohd Daud
HBB
-
NM_000518.4:c.*5154552_*5161966del
Hb Lepore
r.(=)
p.(=)
-
-
11
Unknown
+/.
g.5225486T>C
Poly A (A>G) AATAAA>AATAGA
E George et al. (1992)
,
dbSNP
,
(OMIM 0386)
HBB_000030
rs63750954
1/141
-
Nuur Athirah Binti Mohd Daud
HBB
-
NM_000518.4:c.*112A>G
Poly A (A>G) AATAAA>AATAGA
r.(=)
p.(=)
-
ClinVar
11
Unknown
+/.
g.5225923G>A
IVS II-654 C>T
E George et al. (1992)
,
dbSNP
,
(OMIM 0368)
,
ClinVar
HBB_000015
rs34451549
4/141
-
Nuur Athirah Binti Mohd Daud
HBB
2i
NM_000518.4:c.316-197C>T
IVS II-654 C>T
r.(=)
p.(=)
-
ClinVar
11
Unknown
./.
g.5226763_5226766delAAAG
CD 41/42 (-CTTT)
E George et al. (1992)
,
dbSNP
,
(OMIM 0326)
,
ClinVar
HBB_000014
rs80356821
7/141
-
Nuur Athirah Binti Mohd Daud
HBB
2
NM_000518.4:c.126_129delCTTT
CD 41/42 (-CTTT)
r.(?)
p.(Phe42Leufs*19)
-
ClinVar
11
Unknown
+/.
g.5226925C>G
IVS I-5 (G>C)
E George et al. (1992)
,
dbSNP
,
(OMIM 0357)
,
ClinVar
HBB_000003
rs33915217
45/141
-
Nuur Athirah Binti Mohd Daud
HBB
1i
NM_000518.4:c.92+5G>C
IVS I-5 (G>C)
r.spl?
p.?
-
ClinVar
11
Unknown
+/.
g.5226928A>G
IVS I-2 (T>C)
E George et al. (1992)
,
dbSNP
,
(OMIM 0350)
,
ClinVar
HBB_000032
rs33956879
9/141
-
Nuur Athirah Binti Mohd Daud
HBB
1i
NM_000518.4:c.92+2T>C
IVS I-2 (T>C)
r.spl?
p.?
-
ClinVar
11
Unknown
./.
g.5226929C>A
IVS I-1 (G>T)
E George et al. (1992)
,
dbSNP
,
(OMIM 0347)
,
ClinVar
HBB_000004
rs33971440
9/141
-
Nuur Athirah Binti Mohd Daud
HBB
1i
NM_000518.4:c.92+1G>T
IVS I-1 (G>T)
r.spl?
p.?
-
ClinVar
11
Unknown
+/.
g.5226943C>T
CD 26 GAG>AAG / HbE
E George et al. (1992)
,
dbSNP
,
(OMIM 0071)
,
ClinVar
HBB_000006
rs33950507
42/141
-
Nuur Athirah Binti Mohd Daud
HBB
1
NM_000518.4:c.79G>A
CD 26 GAG>AAG / HbE
r.(?)
p.(Glu27Lys)
-
ClinVar
11
Unknown
+/.
g.5226963T>C
CD 19 (AAC>AGC) / Hb Malay
E George et al. (1992)
,
dbSNP
,
(OMIM 0168)
HBB_000012
rs33972047
10/141
-
Nuur Athirah Binti Mohd Daud
HBB
1
NM_000518.4:c.59A>G
CD 19 (AAC>AGC) / Hb Malay
r.(?)
p.(Asn20Ser)
-
ClinVar
11
Unknown
+/.
g.5226970T>A
CD 17 (AAG>TAG)
E George et al. (1992)
,
dbSNP
,
(OMIM 0311)
,
ClinVar
HBB_000011
rs33986703
7/141
-
Nuur Athirah Binti Mohd Daud
HBB
1
NM_000518.4:c.52A>T
CD 17 (AAG>TAG)
r.(?)
p.(Lys18*)
-
ClinVar
11
Unknown
./.
g.5227071T>G
CAP +1 (A>C)
E George et al. (1992)
,
dbSNP
,
(OMIM 0387)
HBB_000008
rs34305195
2/141
-
Nuur Athirah Binti Mohd Daud
HBB
-
NM_000518.4:c.-50A>C
CAP +1 (A>C)
r.(=)
p.(=)
-
ClinVar
11
Unknown
./.
g.5227099T>C
-28 (A>G)
E George et al. (1992)
,
dbSNP
,
(OMIM 0381)
,
ClinVar
HBB_000005
rs33931746
3/141
-
Nuur Athirah Binti Mohd Daud
HBB
-
NM_000518.4:c.-78A>G
-28 (A>G)
r.(=)
p.(=)
-
ClinVar
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