Individual #00003486

Ethnic origin	Spanish/Swiss German
Reference	-
Remarks	-
Cuadro familiar	Breast cancer
Panel size	1
Diseases	Breast cancer
Owner name	Marcela Lopez-CEMAFE
Database submission license
Created by	Instituto Nacional del Cancer

No phenotypes found for this individual!

Screenings

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DNA
RNA = RNA (cDNA)
Protein
? = unknown

Technique: Technique(s) used to identify the sequence variant.
All options:

? = Unknown
SEQ-NG = Next-Generation Sequencing
SEQ = SEQuencing
MLPA = Multiplex Ligation-dependent Probe Amplification
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
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
CNV
CSCE = Conformation Sensitive Capillary Electrophoresis
DECoN = Detection of Exon Copy Number variants
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
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
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
in-house algorithm for CNV
z-score-CNV = z-score based algorithm for CNV detection in targeted NGS

Lab: Name of the Laboratory that performed the screening.
All options:

ARGENETICS
ARGENOMICS - Fundacion Investigar
Biocodices S.A.
Biogenotec
BIOMAKERS Molecular Pathology & Research
Bionet
Centro de Diagnostico Molecular (CDM)
Centro de Educación Médica e Investigaciones Clínicas (CEMIC)
Centro de Estudios Geneticos (CEG)
Centro de Investigaciones Endocrinologicas “Dr. Cesar Bergada” (CEDIE)
Centro Nacional de Genetica Medica "Dr. Eduardo E. Castilla" (CENAGEM)
Centro Privado Internacional de Medicina Personalizada - CEPIMP Genomics
CIBIC – Centro de Diagnóstico Médico de Alta Complejidad S.A. - HERITAS
CITOGEN.LAB
Clínica Universitaria Reina Fabiola
Dasa Genómica - Genia
Diagnus Lab
Domeq&Lafage
Fundacion BIOGEN
Fundación para el Progreso de la Medicina
FUNDAGEN S.A.
Gammalab - Grupo Gamma S.A.
GENDA
Genesia - Progenitest
Genologica laboratorio de análisis genéticos
GENOS
Grupo de investigacion en Genetica Aplicada (GIGA)
Hospital Alemán
Hospital de Alta Complejidad El Calafate - SAMIC
Hospital de Gastroenterología Dr. Carlos Bonorino Udaondo
Hospital Italiano de Buenos Aires
Hospital Privado Centro Médico de Córdoba
Hospital Universitario Austral
IACA Laboratorios
IBC Laboratorios
Instituto Alexander Fleming
Laboratorio Barros
Laboratorio de Biologia Celular y Molecular IHEM-CONICET CCT Mendoza
Laboratorio de Medicina Genomica - Facultad de Medicina - UNNE
Laboratorio Dr. Rapela
Laboratorio Dra. Marta Cortelezzi
Laboratorio Fares Taie
Laboratorio Flores
Laboratorio Hidalgo S.A.
Laboratorio High Medic Group S.A.
Laboratorio Integral SRL
Laboratorio Maipu
Laboratorio Motter
Laboratorio NANNI
Laboratorio PampaGEN
Laboratorio Primagen
Laboratorio Tucumán
Laboratorios Turner
Labsis
LACE Laboratorios
LEB (Laboratorio de Especialidades Bioquimicas)
MANLAB
MEDgenomica
PRICAI-Primer Centro Argentino de Inmunogenética-Fundación Favaloro
Sanatorio Allende
Stamboulian Laboratorio
STEM
VZ Laboratorios
Zoigen
AMBRY GENETICS
Baylor Genetics
Blueprint Genetics
CENTOGENE
COLOR
GENE ONE
Health in code
Iden Gene
IMEGEN
INVITAE
Laboratorio ATGen (E)
Laboratorio ATGen
MACROGEN
Myriad Genetics
SENTIS
Sistemas Genómicos
------
Color
Genda
Genda/Color
Genesia
Genesia/Invitae
Genia/Invitae
Genia/Color
Genia
Genos
Genos/Color
Hospital Privado Centro Médico de Córdoba
Hospital Privado Centro médico de Córdoba/IACA
Héritas
IACA
Invitae
AbaCid
Ambry Genetics
Alexander Fleming
Alexander Fleming/Baylor College
Alexander Fleming/Genesia-INVITAE
Argenomics
Baylor Genetics
BIOGEN
Biogenotec
BIOMAKERS Molecular Pathology & Research
BIONET
Blueprint Genetics
CEDIE
CEG
CEMIC
Centro de diagnóstico molecular
CEPIMP Genomics
CeNaGeM
Centogene
CIBIC
CIBIC/Héritas
Ciscato&Sharovsky
Clinica Universitaria Reina Fabiola
DIAGNUS LAB
Domeq&Lafage
Dr. Rapela
Fares Taie
FARESTAIE/Héritas
FAVALORO-PRICAI
Fundación para el Progreso de la Medicina
Fundación para el Progreso de la Medicina/CIBIC/Héritas
Fundagen
Gammalab
GeneDx
GIGA
Health in code
Hidalgo
High Medic Group
Hospital Alemán
Hospital de Gastroenterologia
Sanatorio Allende
MEDgenomica
LACE
HEMA
Centro médico de Córdoba
DASA-INVITAE
Bioscreen Rosario
x

Remarks: Remarks

Date of test: Date in which the results of the test were informed to the pacient

Type of test: Type of test
All options:

Known familial mutation
Multigenetic panel
Specific pathology
Ashkenazi panel
Germline variant found in somatic testing
Whole exome

How to query this table

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Operator	Column type	Example	Matches
	Text	Arg	all entries containing 'Arg'
space	Text	Arg Ser	all entries containing 'Arg' and 'Ser'
\|	Text	Arg\|Ser	all entries containing 'Arg' or 'Ser'
!	Text	!fs	all entries not containing 'fs'
^	Text	^p.(Arg	all entries beginning with 'p.(Arg'
$	Text	Ser)$	all entries ending with 'Ser)'
=""	Text	=""	all entries with this field empty
=""	Text	="p.0"	all entries exactly matching 'p.0'
!=""	Text	!=""	all entries with this field not empty
!=""	Text	!="p.0"	all entries not exactly matching 'p.0?'
combination	Text	*\|Ter !fs	all entries containing '*' or 'Ter' but not containing 'fs'
	Date	2020	all entries matching the year 2020
\|	Date	2020-03\|2020-04	all entries matching March or April, 2020
!	Date	!2020-03	all entries not matching March, 2020
<	Date	<2020	all entries before the year 2020
<=	Date	<=2020-06	all entries in or before June, 2020
>	Date	>2020-06	all entries after June, 2020
>=	Date	>=2020-06-15	all entries on or after June 15th, 2020
combination	Date	2019\|2020 <2020-03	all entries in 2019 or 2020, and before March, 2020
	Numeric	23	all entries exactly matching 23
\|	Numeric	23\|24	all entries exactly matching 23 or 24
!	Numeric	!23	all entries not exactly matching 23
<	Numeric	<23	all entries lower than 23
<=	Numeric	<=23	all entries lower than, or equal to, 23
>	Numeric	>23	all entries higher than 23
>=	Numeric	>=23	all entries higher than, or equal to, 23
combination	Numeric	>=20 <30 !23	all entries with values from 20 to 29, but not equal to 23

Some more advanced examples:

Example	Matches
Asian	all entries containing 'Asian', 'asian', including 'Caucasian', 'caucasian', etc.
Asian !Caucasian	all entries containing 'Asian' but not containing 'Caucasian'
Asian\|African !Caucasian	all entries containing 'Asian' or 'African', but not containing 'Caucasian'
"South Asian"	all entries containing 'South Asian', but not containing 'South East Asian'

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Screening ID	Template	Technique	Lab	Remarks	Date of test	Type of test	Genes screened	Variants found	Owner
0000003809	DNA	SEQ-NG	GENDA	AIP, ALK, APC, ATM, AXIN2, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, CASR, CDC73, CDH1, CDK4, CDKN1B, CDKN1C, CDKN2A (p14ARF), CDKN2A (p16INK4a), CEBPA, CHEK2, CTNNA1, DICER1, DIS3L2, EGFR, EPCAM, FH, FLCN, GATA2, GPC3, GREM1, HOXB13, HRAS, KIT, MAX, MEN1, MET, MITF, MLH1, MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PHOX2B, PMS2, POLD1, POLE, POT1, PRKAR1A, PTCH1, PTEN, RAD50, RAD51C, RAD51D, RB1, RECQL4, RET, RUNX1, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, STK11, SUFU, TERC, TERT, TMEM127, TP53, TSC1, TSC2, VHL, WRN, WT1.	24-jan-2023	Multigenetic panel	-	4	Marcela Lopez-CEMAFE

Variants

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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

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.

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.

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

Zygosity: Homozygous or Heterozygous
All options:

Homo
Hetero
Not specified

Co_ocurrence: If the variant is present in co-ocurrence with a mutation, please select the name of the mutated gene. If not, please select "no".
All options:

no
N/A
BRCA1
BRCA2
CHEK2
FANCC
MLH1
MSH2
MSH6
MUTYH
PALB2
PMS2
PTEN
APC
TP53
STK11
TSC1
RET
VHL
PALB2
NBN
CDKN2A
LZTR1
ATM
ERCC5
NF1
SDHB
BARD1
NTHL1
FANCC
BLM
BRIP1
RAD51C
GJB2
G6PC
SMN1

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

Review status: prueba

4 entries on 1 page. Showing entries 1 - 4.

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How to query

Chr	Allele	Effect	DNA change (genomic) (hg38)	Reference	DB-ID	dbSNP ID	Variant remarks	Owner	Gene	Exon	DNA change (cDNA)	Protein	Zygosity	Co_ocurrence	RNA change	Review status
4	Unknown	?/?	g.54261242G>T	-	PDGFRA_000013	rs1577705273	-	Marcela Lopez-CEMAFE	PDGFRA	3	NM_006206.6:c.197G>T	p.(Ser66Ile)	Hetero	PALB2	r.?	-
11	Unknown	?/?	g.108343265C>T	-	ATM_000151	rs771781881	-	Marcela Lopez-CEMAFE	ATM	56	NM_000051.4:c.8312C>T	(p.Thr2771Ile)	Hetero	PALB2	r.(8312c>u)	-
13	Unknown	?/?	g.48373419C>T	-	RB1_000009	-	-	Marcela Lopez-CEMAFE	RB1	12	NM_000321.2:c.1142C>T	p.(Thr381Ile)	Hetero	PALB2	r.?	-
16	Unknown	+/+	g.23634893A>T	-	PALB2_000001	rs118203997	-	Marcela Lopez-CEMAFE	PALB2	4	NM_024675.4:c.1653T>A	p.(Tyr551*)	Hetero	no	r.?	-

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How to query

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