Variants from Ding PR Lab, Sun Yat-sen University Cancer Center with conflicting interpretations

Minimum review status of the submission from Ding PR Lab, Sun Yat-sen University Cancer Center:	★☆☆☆ criteria provided ★★★☆ reviewed by expert panel ★★★★ practice guideline	Collection method of the submission from Ding PR Lab, Sun Yat-sen University Cancer Center:	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
26	12	0	5	7	0	2	14

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
Ding PR Lab, Sun Yat-sen University Cancer Center		pathogenic	likely pathogenic	likely benign	benign
	pathogenic	0	2	0	0
	likely pathogenic	3	0	0	0
	uncertain significance	1	1	6	4

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
Myriad Genetics, Inc.	0	4	0	3	2	0	1	6
Baylor Genetics	0	7	0	2	0	0	2	4
Counsyl	0	7	0	1	2	0	1	4
Mendelics	0	0	0	0	4	0	0	4
KCCC/NGS Laboratory, Kuwait Cancer Control Center	0	0	0	1	2	0	0	3
OMIM	0	2	0	2	0	0	0	2
Genome Diagnostics Laboratory, Amsterdam University Medical Center	0	0	0	0	2	0	0	2
Genetic Services Laboratory, University of Chicago	0	0	0	1	0	0	0	1
Genome Diagnostics Laboratory, University Medical Center Utrecht	0	0	0	0	1	0	0	1
Illumina Laboratory Services, Illumina	0	3	0	0	1	0	0	1
Pathway Genomics	0	0	0	1	0	0	0	1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	0	0	0	1	0	0	0	1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	0	0	0	0	1	0	0	1
St. Jude Molecular Pathology, St. Jude Children's Research Hospital	0	0	0	0	0	0	1	1
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine	0	1	0	0	0	0	1	1
Human Genetics Bochum, Ruhr University Bochum	0	0	0	0	0	0	1	1
Laboratory of Molecular and Cellular Biology, University of Science and Technology Houari Boumediene	0	0	0	1	0	0	0	1

All variants with conflicting interpretations #

HGVS	dbSNP	gnomAD frequency
NM_000535.7(PMS2):c.383C>T (p.Ser128Leu)	rs116373169	0.00177
NM_000179.3(MSH6):c.2561A>T (p.Lys854Met)	rs34374438	0.00036
NM_000249.4(MLH1):c.2101C>A (p.Gln701Lys)	rs63750114	0.00016
NM_000535.7(PMS2):c.379G>A (p.Ala127Thr)	rs114090343	0.00010
NM_000249.4(MLH1):c.2059C>T (p.Arg687Trp)	rs63751275	0.00001
NM_000249.4(MLH1):c.2080G>T (p.Glu694Ter)	rs147542208	0.00001
NM_000179.3(MSH6):c.4001+2TAAC[2]	rs267608132
NM_000179.3(MSH6):c.4068_4071dup (p.Lys1358delinsAspTer)	rs55740729
NM_000249.4(MLH1):c.1038+1G>C	rs267607816
NM_000249.4(MLH1):c.1667G>A (p.Ser556Asn)	rs63751596
NM_000249.4(MLH1):c.1846AAG[2] (p.Lys618del)	rs63751247
NM_000249.4(MLH1):c.350C>T (p.Thr117Met)	rs63750781
NM_000249.4(MLH1):c.793C>T (p.Arg265Cys)	rs63751194
NM_000535.7(PMS2):c.706-4dup	rs60794673