Variants from GenePathDx, GenePath diagnostics with conflicting interpretations

Minimum review status of the submission from GenePathDx, GenePath diagnostics:	★☆☆☆ criteria provided ★★★☆ reviewed by expert panel ★★★★ practice guideline	Collection method of the submission from GenePathDx, GenePath diagnostics:	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: 2024-03-31

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
16	7	0	7	1	0	2	8

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
GenePathDx, GenePath diagnostics		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	4	1	0	0
	likely pathogenic	2	0	0	0	0
	uncertain significance	0	0	0	1	1
	likely benign	1	0	0	0	1

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
Illumina Laboratory Services, Illumina	0	0	0	1	1	0	0	2
Baylor Genetics	0	5	0	1	0	0	0	1
Genome Diagnostics Laboratory, The Hospital for Sick Children	0	0	0	0	1	0	0	1
Clinical Biochemistry Laboratory, Health Services Laboratory	0	0	0	1	0	0	0	1
Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital	0	0	0	1	0	0	0	1
Counsyl	0	4	0	0	0	0	1	1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	0	0	0	1	0	0	0	1
Invitae	0	3	0	1	0	0	0	1
GeneReviews	0	3	0	0	0	0	1	1
Genetics and Molecular Pathology, SA Pathology	0	0	0	1	0	0	0	1
Yale Center for Mendelian Genomics, Yale University	0	0	0	1	0	0	0	1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	0	0	0	1	0	0	0	1
Cancer Diagnostics Division, Gene Solutions	0	0	0	1	0	0	0	1
Reproductive Health Research and Development, BGI Genomics	0	0	0	1	0	0	0	1
Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital	0	0	0	1	0	0	0	1
Genome-Nilou Lab	0	0	0	1	0	0	0	1
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine	0	2	0	1	0	0	0	1

All variants with conflicting interpretations #

HGVS	dbSNP	gnomAD frequency
NM_000096.4(CP):c.1652C>T (p.Thr551Ile)	rs61733458	0.02154
NM_000088.4(COL1A1):c.613C>G (p.Pro205Ala)	rs72667032	0.00331
NM_000030.3(AGXT):c.473C>T (p.Ser158Leu)	rs180177225
NM_000038.6(APC):c.3927_3931del (p.Glu1309fs)	rs121913224
NM_000053.4(ATP7B):c.3236G>T (p.Cys1079Phe)	rs1064797072
NM_000500.9(CYP21A2):c.1118G>A (p.Ser373Asn)	rs1554305880
NM_001122955.4(BSCL2):c.844_854del (p.Ala282fs)	rs1064797076
NM_005476.7(GNE):c.2086G>A (p.Val696Met)	rs121908627