ClinVar Miner

Variants from Laboratory of Prof. Karen Avraham, Tel Aviv University with conflicting interpretations

Location: Israel  Primary collection method: research
Minimum review status of the submission from Laboratory of Prof. Karen Avraham, Tel Aviv University: Collection method of the submission from Laboratory of Prof. Karen Avraham, Tel Aviv University:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic) 		Variants with a confidence conflict
(e.g. benign vs likely benign) 		Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects) 		Variants with a clinically significant conflict
(e.g. benign vs pathogenic) 		Variants with any conflict
228 26 0 25 3 1 41 61

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

All submitters
Laboratory of Prof. Karen Avraham, Tel Aviv University pathogenic likely pathogenic uncertain significance likely benign benign other
pathogenic 0 24 22 6 1 1
likely pathogenic 1 0 12 3 3 0
uncertain significance 0 0 0 1 2 0

Submitter to submitter summary #

Total submitters: 45
Download table as spreadsheet
Submitter Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic) 		Variants with a confidence conflict
(e.g. benign vs likely benign) 		Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects) 		Variants with a clinically significant conflict
(e.g. benign vs pathogenic) 		Variants with any conflict
Illumina Laboratory Services, Illumina 0 8 0 3 0 0 16 19
Labcorp Genetics (formerly Invitae), Labcorp 0 1 0 0 2 0 7 9
Natera, Inc. 0 7 0 2 0 0 7 9
Genome-Nilou Lab 0 4 0 0 1 0 6 7
Counsyl 0 1 0 1 0 0 4 5
3billion 0 5 0 3 0 0 1 4
Baylor Genetics 0 3 0 1 0 0 3 4
Dubai Health Genomic Medicine Center, Dubai Health 0 0 0 0 0 0 3 3
Fulgent Genetics, Fulgent Genetics 0 4 0 1 0 0 2 3
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 3 0 3 0 0 0 3
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 0 0 0 2 2
First Genomix Gene Laboratory, Genetic Diagnostics Department 0 3 0 2 0 0 0 2
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 2 0 1 0 0 1 2
Institute of Human Genetics, University of Leipzig Medical Center 0 1 0 1 0 0 1 2
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare 0 0 0 0 0 0 1 1
CENTOGENE GmbH and LLC - Guiding Precision Medicine 0 0 0 0 0 0 1 1
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 0 0 1 0 0 0 1
Center of Genomic medicine, Geneva, University Hospital of Geneva 0 1 0 1 0 0 0 1
ClinGen Hearing Loss Variant Curation Expert Panel 0 1 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 1 0 0 0 0 1 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 0 0 1 0 0 0 1
GeneDx 0 0 0 0 0 0 1 1
Genetics Research Center, University of Social Welfare and Rehabilitation Sciences 0 3 0 1 0 0 0 1
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia 0 0 0 0 0 0 1 1
Genomic Medicine Lab, University of California San Francisco 0 0 0 1 0 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 0 0 1 0 0 0 1
Institute of Human Genetics Munich, TUM University Hospital 0 0 0 1 0 0 0 1
Johns Hopkins Genomics, Johns Hopkins University 0 0 0 0 0 0 1 1
Juno Genomics, Hangzhou Juno Genomics, Inc 0 2 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 1 0 1 0 0 0 1
MGZ Medical Genetics Center 0 0 0 1 0 0 0 1
Miami Human Genetics, University Of Miami Miller School Of Medicine 0 0 0 0 0 0 1 1
Molecular Biology Laboratory, Fundació Puigvert 0 0 0 0 0 0 1 1
Molecular Diagnosis Center for Deafness 0 1 0 0 0 0 1 1
Molecular Genetics and NGS Laboratory, Hospital Fundacion Valle Del Lili 0 0 0 0 0 0 1 1
National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center 0 0 0 0 0 1 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 1 0 0 0 0 1 1
Neurogenetic Laboratory, Second Faculty of Medicine, Charles University 0 0 0 0 0 0 1 1
New York Genome Center 0 0 0 1 0 0 0 1
OMIM 0 10 0 1 0 0 0 1
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center 0 1 0 1 0 0 0 1
PreventionGenetics, part of Exact Sciences 0 0 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 0 0 0 0 0 1 1
Variantyx, Inc. 0 3 0 1 0 0 0 1
Wonkam Laboratory, Johns Hopkins University 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 61
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000091.5(COL4A3):c.4421T>C (p.Leu1474Pro) rs200302125 0.00245
NM_153676.4(USH1C):c.403G>A (p.Val135Ile) rs145013633 0.00234
NM_194248.3(OTOF):c.2374C>T (p.Arg792Trp) rs148532589 0.00143
NM_206933.4(USH2A):c.1663C>G (p.Leu555Val) rs35818432 0.00085
NM_206933.4(USH2A):c.5858C>G (p.Ala1953Gly) rs41302239 0.00081
NM_004525.3(LRP2):c.6160G>A (p.Asp2054Asn) rs138269726 0.00078
NM_004100.5(EYA4):c.866C>T (p.Thr289Met) rs41286200 0.00067
NM_004004.6(GJB2):c.-22-2A>C rs201895089 0.00056
NM_018429.3(BDP1):c.7873T>G (p.Ter2625Glu) rs199721728 0.00055
NM_000260.4(MYO7A):c.2476G>A (p.Ala826Thr) rs368341987 0.00042
NM_000091.5(COL4A3):c.3829G>A (p.Gly1277Ser) rs190598500 0.00032
NM_030665.4(RAI1):c.3208G>A (p.Gly1070Arg) rs370633684 0.00026
NM_006383.4(CIB2):c.556C>T (p.Arg186Trp) rs370359511 0.00024
NM_001384474.1(LOXHD1):c.1571G>A (p.Arg524His) rs187658135 0.00022
NM_005422.4(TECTA):c.2827C>A (p.Leu943Met) rs139158022 0.00022
NM_006005.3(WFS1):c.1957C>T (p.Arg653Cys) rs201064551 0.00022
NM_001371623.1(TCOF1):c.1130C>T (p.Pro377Leu) rs189476787 0.00021
NM_033380.3(COL4A5):c.2692A>G (p.Met898Val) rs104886192 0.00020
NM_000441.2(SLC26A4):c.349C>T (p.Leu117Phe) rs145254330 0.00017
NM_006005.3(WFS1):c.2020G>A (p.Gly674Arg) rs200672755 0.00016
NM_001145809.2(MYH14):c.526G>A (p.Ala176Thr) rs138001307 0.00014
NM_022124.6(CDH23):c.4405A>G (p.Ile1469Val) rs200635365 0.00014
NM_001384474.1(LOXHD1):c.2863G>C (p.Glu955Gln) rs548893604 0.00013
NM_016239.4(MYO15A):c.8090T>C (p.Val2697Ala) rs200451098 0.00013
NM_016239.4(MYO15A):c.8183G>A (p.Arg2728His) rs184435771 0.00011
NM_032119.4(ADGRV1):c.155G>A (p.Arg52His) rs199798095 0.00011
NM_004004.6(GJB2):c.487A>G (p.Met163Val) rs80338949 0.00009
NM_005422.4(TECTA):c.248C>T (p.Thr83Met) rs145898158 0.00009
NM_005422.4(TECTA):c.4163G>A (p.Arg1388His) rs150016625 0.00009
NM_003482.4(KMT2D):c.10966C>T (p.Arg3656Cys) rs201283589 0.00007
NM_005422.4(TECTA):c.1621G>A (p.Val541Met) rs370652301 0.00006
NM_006005.3(WFS1):c.1673G>A (p.Arg558His) rs774265764 0.00005
NM_000260.4(MYO7A):c.2489G>A (p.Arg830His) rs371029653 0.00004
NM_001692.4(ATP6V1B1):c.319G>A (p.Glu107Lys) rs370511629 0.00004
NM_017780.4(CHD7):c.5533G>A (p.Gly1845Arg) rs753347128 0.00004
NM_000528.4(MAN2B1):c.2992C>T (p.Arg998Cys) rs758755293 0.00003
NM_003482.4(KMT2D):c.6362C>T (p.Ala2121Val) rs765985953 0.00003
NM_032119.4(ADGRV1):c.17108G>A (p.Arg5703His) rs201073459 0.00003
NM_153676.4(USH1C):c.121G>A (p.Val41Met) rs780439529 0.00003
NM_001378454.1(ALMS1):c.12442C>T (p.Arg4148Ter) rs192496253 0.00002
NM_016239.4(MYO15A):c.4642G>A (p.Ala1548Thr) rs201067821 0.00002
NM_022124.6(CDH23):c.7903G>T (p.Val2635Phe) rs763721044 0.00002
NM_000260.4(MYO7A):c.439C>T (p.Arg147Cys) rs782808261 0.00001
NM_003482.4(KMT2D):c.9101A>G (p.Asn3034Ser) rs748817042 0.00001
NM_003482.4(KMT2D):c.9377G>T (p.Gly3126Val) rs772418918 0.00001
NM_004004.6(GJB2):c.60T>G (p.Ile20Met) rs749693224 0.00001
NM_016239.4(MYO15A):c.8340G>A (p.Thr2780=) rs878853228 0.00001
NM_173477.5(USH1G):c.1373A>T (p.Asp458Val) rs397517925 0.00001
NC_012920.1(MT-TL1):m.3291T>C rs869312463
NM_000260.4(MYO7A):c.689C>T (p.Ala230Val) rs797044512
NM_000441.2(SLC26A4):c.1198del (p.Cys400fs) rs397516413
NM_000836.4(GRIN2D):c.1999G>A (p.Val667Ile) rs886040861
NM_001002295.2(GATA3):c.832G>A (p.Asp278Asn) rs1588383622
NM_001354604.2(MITF):c.953T>C (p.Leu318Pro) rs1553704097
NM_001384474.1(LOXHD1):c.4714C>T (p.Arg1572Ter) rs75949023
NM_003482.4(KMT2D):c.2992C>G (p.Pro998Ala) rs143711798
NM_005982.4(SIX1):c.746C>T (p.Pro249Leu) rs368974927
NM_015404.4(WHRN):c.2644C>A (p.Arg882Ser) rs150586098
NM_016239.4(MYO15A):c.4660G>A (p.Ala1554Thr)
NM_016239.4(MYO15A):c.7550C>G (p.Thr2517Ser) rs201119351
NM_016239.4(MYO15A):c.8467G>A (p.Asp2823Asn) rs878853238

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