ClinVar Miner

Variants from Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS with conflicting interpretations

Location: India  Primary collection method: research
Minimum review status of the submission from Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS: Collection method of the submission from Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

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
132 15 0 28 1 0 13 39

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
Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 8 2 1 0
likely pathogenic 19 0 7 4 1
uncertain significance 0 0 0 0 1
likely benign 0 0 0 0 1

Submitter to submitter summary #

Total submitters: 28
Download table as spreadsheet
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 5 0 12 1 0 5 18
OMIM 0 1 0 5 0 0 0 5
Baylor Genetics 0 6 0 5 0 0 0 5
Counsyl 0 4 0 3 0 0 1 4
Illumina Laboratory Services, Illumina 0 0 0 0 0 0 4 4
Revvity Omics, Revvity 0 0 0 1 0 0 1 2
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 1 0 2 0 0 0 2
Fulgent Genetics, Fulgent Genetics 0 2 0 1 0 0 1 2
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 1 0 1 0 0 1 2
Myriad Genetics, Inc. 0 2 0 2 0 0 0 2
Genome-Nilou Lab 0 0 0 2 0 0 0 2
Neuberg Centre For Genomic Medicine, NCGM 0 3 0 2 0 0 0 2
Genetic Services Laboratory, University of Chicago 0 0 0 1 0 0 0 1
GeneDx 0 0 0 0 0 0 1 1
Centogene AG - the Rare Disease Company 0 0 0 1 0 0 0 1
Courtagen Diagnostics Laboratory, Courtagen Life Sciences 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
Natera, Inc. 0 3 0 1 0 0 0 1
Blueprint Genetics 0 0 0 1 0 0 0 1
Pediatric Department, Peking University First Hospital 0 0 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 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
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 0 0 1 0 0 0 1
New York Genome Center 0 0 0 1 0 0 0 1
Department of Pediatrics, University of Modena and Reggio Emilia 0 0 0 1 0 0 0 1
3billion 0 1 0 1 0 0 0 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 0 0 0 0 0 1 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 39
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000310.4(PPT1):c.451C>T (p.Arg151Ter) rs137852700 0.00038
NM_002860.4(ALDH18A1):c.1273C>T (p.Arg425Cys) rs762742204 0.00009
NM_024312.5(GNPTAB):c.2019A>G (p.Lys673=) rs551905649 0.00005
NR_023343.1:n.30G>A rs374299350 0.00005
NM_006371.5(CRTAP):c.634C>T (p.Arg212Ter) rs137853944 0.00004
NM_020975.6(RET):c.1438G>A (p.Glu480Lys) rs537874538 0.00004
NM_001377.3(DYNC2H1):c.7784A>G (p.His2595Arg) rs755505546 0.00003
NM_000543.5(SMPD1):c.1492C>T (p.Arg498Cys) rs769904764 0.00002
NM_004722.4(AP4M1):c.953G>A (p.Arg318Gln) rs531148057 0.00002
NM_000543.5(SMPD1):c.1148A>G (p.Asn383Ser) rs776442314 0.00001
NM_000543.5(SMPD1):c.1529C>T (p.Ser510Phe) rs200652683 0.00001
NM_000543.5(SMPD1):c.1730A>G (p.His577Arg) rs1554935669 0.00001
NM_001114753.3(ENG):c.790G>A (p.Asp264Asn) rs1210433339 0.00001
NM_002317.7(LOX):c.760G>A (p.Val254Ile) rs575190694 0.00001
NM_006623.4(PHGDH):c.357-1G>A rs766427173 0.00001
NM_019109.5(ALG1):c.652C>T (p.Pro218Ser) rs528261173 0.00001
NM_024312.5(GNPTAB):c.2956C>T (p.Arg986Cys) rs769587233 0.00001
NM_000199.5(SGSH):c.1375C>T (p.Gln459Ter) rs1567914459
NM_000540.3(RYR1):c.4481T>C (p.Val1494Ala) rs767928113
NM_000540.3(RYR1):c.5628GGA[2] (p.Glu1878del) rs371047178
NM_000543.5(SMPD1):c.1493G>A (p.Arg498His) rs120074117
NM_000543.5(SMPD1):c.1598C>A (p.Pro533Gln) rs199915216
NM_000543.5(SMPD1):c.1817del (p.Pro606fs) rs1554935746
NM_000543.5(SMPD1):c.314T>C (p.Leu105Pro) rs751269562
NM_000543.5(SMPD1):c.505dup (p.His169fs) rs781535659
NM_000543.5(SMPD1):c.518dup (p.Ser174fs) rs786204733
NM_000543.5(SMPD1):c.698C>T (p.Ser233Phe) rs1847925080
NM_001079802.2(FKTN):c.1106del (p.Phe369fs) rs750176716
NM_001164405.1(BHLHA9):c.220_221delinsTT (p.Glu74Leu) rs886037856
NM_001184880.2(PCDH19):c.462C>G (p.Tyr154Ter) rs1569315876
NM_001257096.2(PAX1):c.1169_1173dup (p.Pro392fs) rs1555804780
NM_002485.5(NBN):c.935T>A (p.Leu312Ter) rs371480039
NM_024312.5(GNPTAB):c.1144A>C (p.Thr382Pro) rs112543062
NM_024312.5(GNPTAB):c.1408+1G>T rs1060499680
NM_024312.5(GNPTAB):c.1613-25del rs546802775
NM_024312.5(GNPTAB):c.2550_2554del (p.Lys850fs) rs281864996
NM_024312.5(GNPTAB):c.3602G>A (p.Trp1201Ter) rs1952850511
NM_144596.4(TTC8):c.114+2T>C rs1273244823
NM_152393.4(KLHL40):c.931C>A (p.Arg311Ser) rs763283033

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