ClinVar Miner

Variants from Phosphorus, Inc. with conflicting interpretations

Location: United States  Primary collection method: clinical testing
Minimum review status of the submission from Phosphorus, Inc.: Collection method of the submission from Phosphorus, Inc.:
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
81 88 0 22 31 2 5 56

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
Phosphorus, Inc. pathogenic likely pathogenic uncertain significance likely benign benign uncertain risk allele other
pathogenic 0 2 0 0 0 0 0
likely pathogenic 2 0 2 1 0 0 0
uncertain significance 2 1 0 17 8 1 0
likely benign 0 0 5 0 14 0 0
benign 1 0 3 4 0 0 1

Submitter to submitter summary #

Total submitters: 33
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 38 0 3 12 1 0 16
Illumina Laboratory Services, Illumina 0 28 0 6 7 0 1 14
Ambry Genetics 0 35 0 2 4 0 1 7
GeneDx 0 22 0 5 1 0 0 6
Clinical Genetics, Academic Medical Center 0 0 0 4 1 0 1 6
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 11 0 2 3 0 1 6
OMIM 0 4 0 1 3 0 0 4
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 3 0 2 2 0 0 4
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 6 0 1 3 0 0 4
Natera, Inc. 0 22 0 1 2 0 0 3
Laboratory of Genetics and Molecular Cardiology, University of São Paulo 0 2 0 2 0 0 1 3
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 10 0 0 2 0 0 2
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 11 0 1 0 0 1 2
Genome-Nilou Lab 0 27 0 1 1 0 0 2
Baylor Genetics 0 2 0 0 0 0 1 1
Athena Diagnostics Inc 0 1 0 1 0 0 0 1
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 6 0 1 0 0 0 1
PreventionGenetics, part of Exact Sciences 0 8 0 0 0 0 1 1
Mayo Clinic Laboratories, Mayo Clinic 0 0 0 0 0 0 1 1
Quest Diagnostics Nichols Institute San Juan Capistrano 0 0 0 0 1 0 0 1
LDLR-LOVD, British Heart Foundation 0 0 0 0 1 0 0 1
Laboratory of Human Genetics, Universidade de São Paulo 0 0 0 0 0 0 1 1
Color Diagnostics, LLC DBA Color Health 0 4 0 0 1 0 0 1
CeGaT Center for Human Genetics Tuebingen 0 5 0 0 0 0 1 1
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille 0 0 0 0 0 0 1 1
Robarts Research Institute, Western University 0 0 0 0 1 0 0 1
Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix 0 0 0 0 1 0 0 1
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum 0 0 0 0 1 0 0 1
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 0 0 0 1 0 0 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 1 0 0 1 0 0 1
Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia 0 0 0 0 0 0 1 1
Genomics England Pilot Project, Genomics England 0 0 0 1 0 0 0 1
Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 56
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000152.3(GAA):c.2065G>A (p.Glu689Lys) rs1800309 0.04051
NM_002230.4(JUP):c.425G>A (p.Arg142His) rs41283425 0.03910
NM_015627.3(LDLRAP1):c.712C>T (p.Arg238Trp) rs41291058 0.03285
NM_004006.3(DMD):c.8734A>G (p.Asn2912Asp) rs1800278 0.02976
NM_004006.3(DMD):c.8729A>T (p.Glu2910Val) rs41305353 0.02876
NM_000098.3(CPT2):c.1055T>G (p.Phe352Cys) rs2229291 0.01469
NM_020433.5(JPH2):c.1513G>A (p.Gly505Ser) rs140740776 0.01003
NM_005477.3(HCN4):c.2648C>G (p.Pro883Arg) rs148398509 0.00737
NM_001148.6(ANK2):c.2377-8C>T rs139893914 0.00682
NM_000642.3(AGL):c.3758G>A (p.Arg1253His) rs12043139 0.00515
NM_000384.3(APOB):c.3383G>A (p.Arg1128His) rs12713843 0.00356
NM_001308093.3(GATA4):c.825C>T (p.Cys275=) rs55980825 0.00275
NM_020297.4(ABCC9):c.2093-7T>C rs185235724 0.00261
NM_053025.4(MYLK):c.24C>G (p.Ala8=) rs78118111 0.00229
NM_001037.5(SCN1B):c.448+193G>A rs66876876 0.00227
NM_002471.4(MYH6):c.2928+5G>A rs28730772 0.00172
NM_001267550.2(TTN):c.30718G>T (p.Val10240Phe) rs111671438 0.00153
NM_002230.4(JUP):c.567C>T (p.Val189=) rs35297577 0.00090
NM_006440.5(TXNRD2):c.858G>C (p.Arg286Ser) rs201503021 0.00064
NM_013266.4(CTNNA3):c.1900G>A (p.Glu634Lys) rs77165728 0.00058
NM_001005242.3(PKP2):c.1379-2019C>T rs149930872 0.00049
NM_001114753.3(ENG):c.-9G>A rs368423516 0.00040
NM_001378454.1(ALMS1):c.4329G>T (p.Leu1443Phe) rs192499639 0.00036
NM_002230.4(JUP):c.633C>T (p.Asn211=) rs372145644 0.00036
NM_001035.3(RYR2):c.13291G>A (p.Glu4431Lys) rs571985775 0.00028
NM_001378454.1(ALMS1):c.9389C>G (p.Pro3130Arg) rs200586877 0.00017
NM_000138.5(FBN1):c.6380-3A>G rs567703513 0.00016
NM_001134363.3(RBM20):c.1455A>G (p.Ser485=) rs751559376 0.00016
NM_006514.4(SCN10A):c.4849G>T (p.Val1617Phe) rs375940680 0.00015
NM_024422.6(DSC2):c.1521-7C>T rs374810953 0.00015
NM_000257.4(MYH7):c.957C>T (p.Thr319=) rs368699342 0.00014
NM_000256.3(MYBPC3):c.442G>A (p.Gly148Arg) rs397516050 0.00011
NM_001267550.2(TTN):c.266C>G (p.Ala89Gly) rs200165636 0.00010
NM_001267550.2(TTN):c.105383C>T (p.Ala35128Val) rs758458467 0.00007
NM_001267550.2(TTN):c.31456A>T (p.Ile10486Phe) rs772882862 0.00006
NM_000256.3(MYBPC3):c.772G>A (p.Glu258Lys) rs397516074 0.00004
NM_001458.5(FLNC):c.4140C>T (p.Thr1380=) rs183668401 0.00004
NM_001458.5(FLNC):c.6864C>T (p.Val2288=) rs761269440 0.00004
NM_001943.5(DSG2):c.1688T>G (p.Leu563Arg) rs780469370 0.00004
NM_001042492.3(NF1):c.7910G>A (p.Arg2637Gln) rs560262404 0.00003
NM_001134363.3(RBM20):c.2905G>A (p.Val969Ile) rs369747752 0.00003
NM_000256.3(MYBPC3):c.502G>A (p.Val168Met) rs569740494 0.00002
NM_024422.6(DSC2):c.1680G>A (p.Thr560=) rs567202599 0.00002
NM_000257.4(MYH7):c.728G>A (p.Arg243His) rs267606910 0.00001
NM_001458.5(FLNC):c.5670G>A (p.Gly1890=) rs369881758 0.00001
NM_001927.4(DES):c.894G>A (p.Ser298=) rs747073500 0.00001
NM_006939.4(SOS2):c.2161+10A>G rs201629454 0.00001
NM_170707.4(LMNA):c.1633C>T (p.Arg545Cys) rs267607613 0.00001
NM_000257.4(MYH7):c.746G>A (p.Arg249Gln) rs3218713
NM_000258.3(MYL3):c.466G>T (p.Val156Leu) rs199474707
NM_000527.5(LDLR):c.2479G>A (p.Val827Ile) rs137853964
NM_001943.5(DSG2):c.1280+4AG[3] rs876657791
NM_002230.4(JUP):c.1281G>A (p.Thr427=) rs373544304
NM_053025.4(MYLK):c.3637G>C (p.Val1213Leu) rs368390254
NM_174936.4(PCSK9):c.1099G>C (p.Asp367His) rs141867978
NM_174936.4(PCSK9):c.212C>T (p.Pro71Leu) rs569379713

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.