Variants from Codex Genetics Limited with conflicting interpretations

Minimum review status of the submission from Codex Genetics Limited:	★☆☆☆ criteria provided ★★★☆ reviewed by expert panel ★★★★ practice guideline	Collection method of the submission from Codex Genetics Limited:	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: 2024-09-02

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
4	5	0	5	0	1	5	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
Codex Genetics Limited		pathogenic	likely pathogenic	uncertain significance	likely benign	benign	risk factor
	pathogenic	0	4	4	3	2	1
	likely pathogenic	2	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
Invitae	0	1	0	1	0	0	3	4
Mendelics	0	1	0	0	0	0	3	3
OMIM	0	4	0	1	0	1	0	2
GeneDx	0	0	0	0	0	0	2	2
Illumina Laboratory Services, Illumina	0	0	0	0	0	0	2	2
Athena Diagnostics	0	0	0	0	0	0	1	1
Revvity Omics, Revvity	0	1	0	0	0	0	1	1
MGZ Medical Genetics Center	0	0	0	1	0	0	0	1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	0	2	0	1	0	0	0	1
Eurofins Ntd Llc (ga)	0	0	0	0	0	0	1	1
Mayo Clinic Laboratories, Mayo Clinic	0	0	0	0	0	0	1	1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	0	0	0	0	0	0	1	1
CeGaT Center for Human Genetics Tuebingen	0	0	0	1	0	0	0	1
Codex Genetics Limited	16	0	0	1	0	0	0	1
Molecular Genetics, Royal Melbourne Hospital	0	0	0	1	0	0	0	1
Pangenia Genomics, Pangenia Inc.	0	0	0	1	0	0	0	1
Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL)	0	0	0	1	0	0	0	1

All variants with conflicting interpretations #

HGVS	dbSNP	gnomAD frequency
NM_198578.4(LRRK2):c.7153G>A (p.Gly2385Arg)	rs34778348	0.00058
NM_002693.3(POLG):c.2890C>T (p.Arg964Cys)	rs201477273	0.00033
NM_198994.3(TGM6):c.1550T>G (p.Leu517Trp)	rs387907097	0.00006
NM_001001557.4(GDF6):c.1271A>G (p.Lys424Arg)	rs121909353	0.00003
NM_000166.6(GJB1):c.-103C>T	rs863224971
NM_007375.4(TARDBP):c.892G>A (p.Gly298Ser)	rs4884357
NM_014946.4(SPAST):c.1507C>T (p.Arg503Trp)	rs864622162
NM_198578.4(LRRK2):c.4883G>C (p.Arg1628Pro)	rs33949390