Variants from Laboratory of Human Genetics, Universidade de São Paulo with conflicting interpretations

Minimum review status of the submission from Laboratory of Human Genetics, Universidade de São Paulo:	★☆☆☆ criteria provided ★★★☆ reviewed by expert panel ★★★★ practice guideline	Collection method of the submission from Laboratory of Human Genetics, Universidade de São Paulo:	clinical testing curation literature only research other
Minimum review status of the other submission:	★☆☆☆ criteria provided ★★★☆ reviewed by expert panel ★★★★ practice guideline	Collection method of the other submission:	clinical testing curation literature only research other
Minimum conflict level: confidence conflict (e.g. benign vs likely benign) benign or likely benign vs uncertain conflict category conflict (e.g. benign vs affects) clinically significant conflict (e.g. benign vs pathogenic) Report conflict between different conditions
Show significances as they were submitted (without aggregation into standard terms)
		ClinVar version: 2025-03-05

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
87	14	0	14	1	0	3	16

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 Human Genetics, Universidade de São Paulo		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	10	3	1	2
	likely pathogenic	4	0	0	0	0
	uncertain significance	0	0	0	1	0

Submitter to submitter summary #

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
Mendelics	0	0	0	3	0	0	0	3
Baylor Genetics	0	3	0	1	0	0	1	2
Center for Human Genetics, Inc, Center for Human Genetics, Inc	0	2	0	2	0	0	0	2
Genetic Services Laboratory, University of Chicago	0	1	0	2	0	0	0	2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	0	0	0	2	0	0	0	2
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	0	2	0	1	0	0	1	2
Institute of Human Genetics, University of Leipzig Medical Center	0	0	0	1	0	0	1	2
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City	0	0	0	2	0	0	0	2
OMIM	0	6	0	1	0	0	0	1
Labcorp Genetics (formerly Invitae), Labcorp	0	2	0	0	0	0	1	1
Natera, Inc.	0	0	0	0	0	0	1	1
Fulgent Genetics, Fulgent Genetics	0	2	0	0	0	0	1	1
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre	0	0	0	0	0	0	1	1
LDLR-LOVD, British Heart Foundation	0	0	0	0	0	0	1	1
Illumina Laboratory Services, Illumina	0	1	0	0	0	0	1	1
Knight Diagnostic Laboratories, Oregon Health and Sciences University	0	0	0	1	0	0	0	1
Laboratory of Genetics and Molecular Cardiology, University of São Paulo	0	0	0	0	0	0	1	1
Color Diagnostics, LLC DBA Color Health	0	0	0	0	0	0	1	1
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	0	0	0	1	0	0	0	1
Centre for Mendelian Genomics, University Medical Centre Ljubljana	0	0	0	0	0	0	1	1
Robarts Research Institute, Western University	0	0	0	0	0	0	1	1
Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix	0	0	0	0	0	0	1	1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	0	0	0	1	0	0	0	1
Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation	0	0	0	0	0	0	1	1
Genetics and Molecular Pathology, SA Pathology	0	0	0	0	0	0	1	1
Phosphorus, Inc.	0	0	0	0	0	0	1	1
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	0	0	0	0	0	0	1	1
Genetic Endocrinology Unit / Unidade de Endocrinologia Genetica - LIM25, Universidade de Sao Paulo (USP)	0	0	0	0	0	0	1	1
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University	0	0	0	1	0	0	0	1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens	0	2	0	0	0	0	1	1
Genomic Medicine Lab, University of California San Francisco	0	1	0	0	0	0	1	1
ClinGen Hearing Loss Variant Curation Expert Panel	0	1	0	1	0	0	0	1
Johns Hopkins Genomics, Johns Hopkins University	0	0	0	1	0	0	0	1
Department of Human Genetics, Laborarztpraxis Dres. Walther, Weindel und Kollegen	0	0	0	0	0	0	1	1
INGEBI, INGEBI / CONICET	0	0	0	1	0	0	0	1
Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia	0	0	0	1	0	0	0	1
New York Genome Center	0	0	0	0	0	0	1	1
Genome-Nilou Lab	0	0	0	0	0	0	1	1
3billion, Medical Genetics	0	3	0	0	1	0	0	1
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	0	0	0	0	0	0	1	1
Neuberg Centre For Genomic Medicine, NCGM	0	0	0	0	0	0	1	1

All variants with conflicting interpretations #

HGVS	dbSNP	gnomAD frequency
NM_004004.6(GJB2):c.109G>A (p.Val37Ile)	rs72474224	0.00354
NM_000104.4(CYP1B1):c.1103G>A (p.Arg368His)	rs79204362	0.00125
NM_144508.5(KNL1):c.6416-13T>G	rs370035611	0.00041
NM_014444.5(TUBGCP4):c.1746G>T (p.Leu582=)	rs200092283	0.00034
NM_001195263.2(PDZD7):c.2211del (p.Gln737fs)	rs1157689930	0.00004
NM_000266.4(NDP):c.109C>T (p.Arg37Ter)	rs398123283
NM_000527.5(LDLR):c.2479G>A (p.Val827Ile)	rs137853964
NM_001029896.2(WDR45):c.397C>T (p.Arg133Ter)	rs797046101
NM_001354604.2(MITF):c.649C>T (p.Arg217Ter)	rs1553702006
NM_001356.5(DDX3X):c.113A>G (p.Tyr38Cys)	rs1555951993
NM_001367721.1(CASK):c.1609C>T (p.Arg537Ter)	rs1555981717
NM_001371928.1(AHDC1):c.994C>T (p.Gln332Ter)	rs1571242220
NM_004187.5(KDM5C):c.807del (p.Thr270fs)	rs1569278313
NM_004975.4(KCNB1):c.1222C>T (p.Pro408Ser)	rs1601071085
NM_173602.3(DIP2B):c.2962-2_2962-1del	rs768972285
NM_181458.4(PAX3):c.142G>C (p.Gly48Arg)	rs1419548558