Malaysian Node of the Human Variome Project Database
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Individual #00000414
Reference
Wei Xiong Wen et al. (2018)
Gender
-
Geographic origin
Malaysia
Ethnic origin
Chinese
Population
-
Remarks
-
Microattribution
-
Panel size
1
Diseases
BRCA2
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
No phenotypes found for this individual!
Screenings
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.
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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Screening ID
Template
Technique
Genes screened
Variants found
Owner
0000000431
DNA
MLPA;SEQ-NG-I
BRCA2
44
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
44 entries on 1 page. Showing entries 1 - 44.
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How to query
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
13
Unknown
+/.
g.32316421_32316422del
c.-39-1_-39delGA
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000140
rs758732038
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.-39-1_-39del
c.-39-1_-39delGA
r.spl?
p.?
-
Likely pathogenic
13
Unknown
+/.
g.32326614G>A
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
(OMIM 0033)
,
ClinVar
BRCA2_000141
rs81002897
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.631+1G>A
-
r.spl?
p.?
-
Pathogenic
13
Unknown
+/.
g.32331011_32331012delAA
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000131
rs75096777
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.774_775delAA
-
r.(?)
p.(Glu260Serfs*15)
-
Pathogenic
13
Unknown
+/.
g.32332287C>G
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000125
rs276174902
2/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.809C>G
-
r.(?)
p.(Ser270*)
-
Pathogenic
13
Unknown
+/.
g.32332434dupA
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000002
rs80359770
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.956dupA
-
r.(?)
p.(Asn319Lysfs*8)
-
Pathogenic
13
Unknown
+/.
g.32333251_32333254del
c.1773_1776delTTAT
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000097
rs80359304
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.1773_1776del
c.1773_1776delTTAT
r.(?)
p.(Ile591Metfs*22)
-
Pathogenic
13
Unknown
+/.
g.32336950del
2595delA
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000100
rs483353111
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.2595del
2595delA
r.(?)
p.(Glu866Lysfs*8)
-
Pathogenic
13
Unknown
+/.
g.32336967C>A
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000142
rs397507634
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.2612C>A
-
r.(?)
p.(Ser871*)
-
Pathogenic
13
Unknown
+/.
g.32337163_32337166del
2808_2811delACAA
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000068
rs80359351
2/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.2808_2811del
2808_2811delACAA
r.(?)
p.(Ala938Profs*21)
-
Pathogenic
13
Unknown
+/.
g.32337185A>T
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000102
rs80358533
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.2830A>T
-
r.(?)
p.(Lys944*)
-
Pathogenic
13
Unknown
+/.
g.32337464C>T
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000054
rs80358557
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.3109C>T
-
r.(?)
p.(Gln1037*)
-
Pathogenic
13
Unknown
+/.
g.32337746A>G
-
Wei Xiong Wen et al. (2018)
,
ClinVar
BRCA2_000156
-
1/1726
VUS (variants of unknown significance)
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.3391A>G
-
r.(?)
p.(Arg1131Gly)
missense
Uncertain significance
13
Unknown
+/.
g.32338202_32338203del
3847_3848delGT
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000143
rs80359405
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.3847_3848del
3847_3848delGT
r.(?)
p.(Val1283Lysfs*2)
-
Pathogenic
13
Unknown
+/.
g.32338277G>T
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000144
rs80358638
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.3922G>T
-
r.(?)
p.(Glu1308*)
-
Pathogenic
13
Unknown
+/.
g.32338312_32338313del
3957_3958delTG
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000105
rs886040504
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.3957_3958del
3957_3958delTG
r.(?)
p.(Asn1319Lysfs*3)
-
Pathogenic
13
Unknown
+/.
g.32338822_32338829delinsTGTTTTT
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000109
rs886040533
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.4467_4474delinsTGTTTTT
-
r.(?)
p.(Lys1489Asnfs*15)
-
Pathogenic
13
Unknown
+/.
g.32338880C>T
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000110
rs80358683
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.4525C>T
-
r.(?)
p.(Gln1509*)
-
Pathogenic
13
Unknown
+/.
g.32339227_32339228delTG
-
Wei Xiong Wen et al. (2018)
BRCA2_000145
-
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.4872_4873delTG
-
r.(?)
p.(Glu1625Lysfs*13)
-
-
13
Unknown
+/.
g.32339428dupA
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000134
rs80359479
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.5073dupA
-
r.(?)
p.(Trp1692Metfs*3)
-
Pathogenic
13
Unknown
+/.
g.32339931_32339934del
5576_5579delTTAA
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000065
rs80359520
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.5576_5579del
5576_5579delTTAA
r.(?)
p.(Ile1859Lysfs*3)
-
Pathogenic
13
Unknown
+/.
g.32340000C>A
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000114
rs80358785
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.5645C>A
-
r.(?)
p.(Ser1882*)
-
Pathogenic
13
Unknown
+/.
g.32340036dupA
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000146
rs80359527
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.5681dupA
-
r.(?)
p.(Tyr1894*)
-
Pathogenic
13
Unknown
+/.
g.32340680_32340681delGT
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000008
rs276174871
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.6325_6326delGT
-
r.(?)
p.(Val2109*)
-
Pathogenic
13
Unknown
+/.
g.32340760_32340764del
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000147
rs80359584
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.6405_6409del
-
r.(?)
p.(Asn2135Lysfs*3)
-
Pathogenic
13
Unknown
+/.
g.32340946_32340947del
6591_6592delTG
Wei Xiong Wen et al. (2018)
,
dbSNP
,
(OMIM 0003)
,
ClinVar
BRCA2_000148
rs80359605
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.6591_6592del
6591_6592delTG
r.(?)
p.(Glu2198Asnfs*4)
-
Pathogenic
13
Unknown
+/.
g.32341028delA
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000009
rs276174875
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.6673delA
-
r.(?)
p.(Thr2225Glnfs*4)
-
Pathogenic
13
Unknown
+/.
g.32346896G>T
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000149
rs28897743
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.7007G>T
-
r.(?)
p.(Arg2336Leu)
-
Pathogenic
13
Unknown
+/.
g.32355232_32355235del
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000150
rs80359648
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.7379_7382del
7379_7382delACAA
r.(?)
p.(Asn2460Thrfs*6)
-
Pathogenic
13
Unknown
+/.
g.32356514G>A
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000087
rs80358978
5/1762
VUS (variants of unknown significance)
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.7522G>A
-
r.(?)
p.(Gly2508Ser)
missense
Uncertain significance
13
Unknown
+/.
g.32356550C>T
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000057
rs80358981
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.7558C>T
-
r.(?)
p.(Arg2520*)
-
Pathogenic
13
Unknown
+/.
g.32357753T>G
-
Wei Xiong Wen et al. (2018)
BRCA2_000151
-
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.7629T>G
-
r.(?)
p.(Tyr2543*)
-
-
13
Unknown
+/.
g.32362694G>A
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000040
rs81002873
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.7976+1G>A
-
r.spl?
p.?
-
Pathogenic
13
Unknown
+/.
g.32363225A>G
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000086
rs397507954
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.8023A>G
-
r.(?)
p.(Ile2675Val)
-
Pathogenic
13
Unknown
+/.
g.32363403C>T
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000157
rs876658732
1/1726
VUS (variants of unknown significance)
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.8201C>T
-
r.(?)
p.(Pro2734Leu)
missense
Uncertain significance
13
Unknown
+/.
g.32363436_32363439del
8234_8237delTGAC
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000126
rs80359699
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.8234_8237del
8234_8237delTGAC
r.(?)
p.(Leu2745Glnfs*31)
-
Pathogenic
13
Unknown
+/.
g.32376739G>A
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000034
rs80359129
4/1762
VUS (variants of unknown significance)
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.8702G>A
-
r.(?)
p.(Gly2901Asp)
missense
Benign
13
Unknown
+/.
g.32379893A>C
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000158
rs766308212
2/1726
VUS (variants of unknown significance)
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.9097A>C
-
r.(?)
p.(Thr3033Pro)
missense
Uncertain significance
13
Unknown
+/.
g.32379893del
9097delA
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000069
rs397507419
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.9097del
9097delA
r.(?)
p.(Thr3033Leufs*29)
-
Pathogenic
13
Unknown
+/.
g.32379893dupA
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000152
rs397507419
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.9097dupA
-
r.(?)
p.(Thr3033Asnfs*11)
-
Pathogenic
13
Unknown
+/.
g.32379894_32379895insA
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000012
rs80359747
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.9098_9099insA
-
r.(?)
p.(Gln3034Serfs*10)
-
Pathogenic
13
Unknown
+/.
g.32379900A>G
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000035
rs80359165
3/1762
VUS (variants of unknown significance)
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.9104A>G
-
r.(?)
p.(Tyr3035Cys)
missense
Uncertain significance / Likely benign
13
Unknown
+/.
g.32394726C>A
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000154
rs80359200
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.9294C>A
-
r.(?)
p.(Tyr3098*)
-
Pathogenic
13
Unknown
+/.
g.32394726C>G
-
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000153
rs80359200
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.9294C>G
-
r.(?)
p.(Tyr3098*)
-
Pathogenic
13
Unknown
+/.
g.32394762dup
9330dupT
Wei Xiong Wen et al. (2018)
,
dbSNP
,
ClinVar
BRCA2_000155
rs1555289529
1/1726
-
Nuur Athirah Binti Mohd Daud
BRCA2
-
NM_000059.3:c.9330dup
9330dupT
r.(?)
p.(Glu3111*)
-
Pathogenic
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