Variants from Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, University Tunis El Manar with conflicting interpretations

Minimum review status of the submission from Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, University Tunis El Manar:	★☆☆☆ criteria provided ★★★☆ reviewed by expert panel ★★★★ practice guideline	Collection method of the submission from Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, University Tunis El Manar:	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: 2024-06-30

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
9	19	0	4	2	0	5	10

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
Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, University Tunis El Manar		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	3	2	0	0
	likely pathogenic	0	0	0	1	1
	uncertain significance	2	0	0	2	0
	likely benign	0	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
Invitae	0	6	0	2	1	0	1	4
Baylor Genetics	0	3	0	2	0	0	0	2
GeneDx	0	1	0	1	1	0	0	2
Myriad Genetics, Inc.	0	0	0	2	0	0	0	2
OMIM	0	1	0	0	0	0	1	1
Ambry Genetics	0	2	0	0	0	0	1	1
PreventionGenetics, part of Exact Sciences	0	1	0	0	1	0	0	1
MGZ Medical Genetics Center	0	1	0	1	0	0	0	1
Counsyl	0	4	0	0	0	0	1	1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	0	0	0	0	0	0	1	1
Genomic Research Center, Shahid Beheshti University of Medical Sciences	0	0	0	0	0	0	1	1
Illumina Laboratory Services, Illumina	0	1	0	0	1	0	0	1
CeGaT Center for Human Genetics Tuebingen	0	0	0	0	1	0	0	1
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	0	0	0	0	1	0	0	1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	0	3	0	0	1	0	0	1

All variants with conflicting interpretations #

HGVS	dbSNP	gnomAD frequency
NM_152618.3(BBS12):c.355G>A (p.Gly119Ser)	rs77731085	0.00439
NM_144596.4(TTC8):c.194A>G (p.Asp65Gly)	rs114557412	0.00354
NM_000209.4(PDX1):c.226G>A (p.Asp76Asn)	rs137852783	0.00320
NM_173560.4(RFX6):c.1733G>C (p.Arg578Pro)	rs146115506	0.00143
NM_017547.4(FOXRED1):c.1261G>A (p.Val421Met)	rs199542988	0.00004
NM_006005.3(WFS1):c.2206G>A (p.Gly736Ser)	rs71532864	0.00003
NM_032380.5(GFM2):c.569G>A (p.Arg190Gln)	rs761283105	0.00003
NM_007194.4(CHEK2):c.592+3A>T	rs587782849	0.00001
NM_000051.4(ATM):c.6115G>A (p.Glu2039Lys)	rs864622251
NM_000070.3(CAPN3):c.1681T>C (p.Tyr561His)