Variants from 3DMed Clinical Laboratory Inc with conflicting interpretations

Minimum review status of the submission from 3DMed Clinical Laboratory Inc:	★☆☆☆ criteria provided ★★★☆ reviewed by expert panel ★★★★ practice guideline	Collection method of the submission from 3DMed Clinical Laboratory Inc:	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
110	27	2	3	12	0	1	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
3DMed Clinical Laboratory Inc		likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	1	0	0	0
	uncertain significance	1	2	9	7
	likely benign	0	1	0	2

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
GeneDx	0	14	0	0	8	0	0	8
Quest Diagnostics Nichols Institute San Juan Capistrano	0	10	0	2	6	0	0	8
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	0	7	0	2	4	0	0	6
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	0	3	0	1	3	0	0	4
PreventionGenetics, part of Exact Sciences	0	4	0	0	3	0	0	3
Biesecker Lab/Clinical Genomics Section, National Institutes of Health	0	0	2	0	0	0	0	2
Genetic Services Laboratory, University of Chicago	0	2	0	0	2	0	0	2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	0	3	0	0	2	0	0	2
Department of Pathology and Laboratory Medicine, Sinai Health System	0	3	0	0	2	0	0	2
Laboratory of Molecular Epidemiology of Birth Defects, West China Second University Hospital, Sichuan University	0	0	0	0	1	0	1	2
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	0	2	0	0	1	0	0	1
Illumina Laboratory Services, Illumina	0	0	0	0	1	0	0	1
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	0	0	0	0	1	0	0	1
Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University	0	4	0	0	1	0	0	1
CeGaT Center for Human Genetics Tuebingen	0	1	0	0	1	0	0	1
Database of Curated Mutations (DoCM)	0	0	0	1	0	0	0	1
Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency	0	0	0	0	1	0	0	1
University of Washington Department of Laboratory Medicine, University of Washington	0	0	0	0	1	0	0	1

All variants with conflicting interpretations #

HGVS	dbSNP	gnomAD frequency
NM_000038.6(APC):c.3511C>T (p.Arg1171Cys)	rs201830995	0.00028
NM_000059.4(BRCA2):c.440A>G (p.Gln147Arg)	rs80358674	0.00025
NM_000038.6(APC):c.3374T>C (p.Val1125Ala)	rs377278397	0.00018
NM_000038.6(APC):c.2204C>T (p.Ala735Val)	rs147655929	0.00012
NM_000059.4(BRCA2):c.1568A>G (p.His523Arg)	rs80358443	0.00009
NM_000038.6(APC):c.8332G>T (p.Ala2778Ser)	rs587778046	0.00006
NM_000059.4(BRCA2):c.6325G>A (p.Val2109Ile)	rs79456940	0.00006
NM_000059.4(BRCA2):c.7522G>A (p.Gly2508Ser)	rs80358978	0.00004
NM_007294.4(BRCA1):c.811G>A (p.Val271Met)	rs80357244	0.00003
NM_000059.4(BRCA2):c.353G>A (p.Arg118His)	rs80358603	0.00002
NM_000038.6(APC):c.3378C>G (p.Ser1126Arg)	rs149353082	0.00001
NM_000059.4(BRCA2):c.10150C>T (p.Arg3384Ter)	rs397507568	0.00001
NM_000059.4(BRCA2):c.2186T>C (p.Ile729Thr)	rs431825296	0.00001
NM_020975.6(RET):c.2753T>C (p.Met918Thr)	rs74799832