ClinVar Miner

Variants from Cohesion Phenomics with conflicting interpretations

Location: United States  Primary collection method: clinical testing
Minimum review status of the submission from Cohesion Phenomics: Collection method of the submission from Cohesion Phenomics:
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
62 131 0 47 16 0 2 58

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
Cohesion Phenomics pathogenic likely pathogenic uncertain significance likely benign benign
likely benign 0 0 8 0 23
benign 2 1 8 24 0

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 63 0 12 3 0 1 16
Illumina Laboratory Services, Illumina 0 23 0 15 1 0 0 16
Laboratory of Genetics and Molecular Cardiology, University of São Paulo 0 12 0 1 7 0 0 8
Color Diagnostics, LLC DBA Color Health 0 81 0 8 0 0 0 8
Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge 0 25 0 1 6 0 0 7
All of Us Research Program, National Institutes of Health 0 23 0 5 0 0 1 6
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 9 0 3 0 0 1 4
Robarts Research Institute, Western University 0 6 0 4 0 0 0 4
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia 0 1 0 2 1 0 0 3
Fundacion Hipercolesterolemia Familiar 0 0 0 0 3 0 0 3
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum 0 18 0 1 0 0 2 3
Department of Human Genetics, Laborarztpraxis Dres. Walther, Weindel und Kollegen 0 6 0 3 0 0 0 3
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario 0 16 0 2 0 0 0 2
Mendelics 0 2 0 2 0 0 0 2
LDLR-LOVD, British Heart Foundation 0 9 0 1 0 0 1 2
Cardiovascular Biomarker Research Laboratory, Mayo Clinic 0 0 0 2 0 0 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 0 0 0 1 0 0 1
Revvity Omics, Revvity 0 0 0 0 0 0 1 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 0 0 0 0 0 1 1
CSER _CC_NCGL, University of Washington 0 1 0 1 0 0 0 1
Agnes Ginges Centre for Molecular Cardiology, Centenary Institute 0 1 0 1 0 0 0 1
Center for Human Genetics, University of Leuven 0 0 0 0 1 0 0 1
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille 0 0 0 0 0 0 1 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 1 0 0 0 0 1 1
ClinGen Cardiomyopathy Variant Curation Expert Panel 0 8 0 0 1 0 0 1
Iberoamerican FH Network 0 6 0 0 1 0 0 1
Center for Advanced Laboratory Medicine, UC San Diego Health, University of California San Diego 0 1 0 1 0 0 0 1
Molecular Genetics, Royal Melbourne Hospital 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 58
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_174936.4(PCSK9):c.1026A>G (p.Gln342=) rs509504 0.98223
NM_001276345.2(TNNT2):c.348C>T (p.Ile116=) rs3729547 0.69444
NM_002294.3(LAMP2):c.156A>T (p.Val52=) rs12097 0.39324
NM_000527.5(LDLR):c.1959T>C (p.Val653=) rs5925 0.37370
NM_000527.5(LDLR):c.1773C>T (p.Asn591=) rs688 0.33392
NM_000218.3(KCNQ1):c.1638G>A (p.Ser546=) rs1057128 0.16286
NM_001276345.2(TNNT2):c.237G>A (p.Ser79=) rs3729845 0.08311
NM_000218.3(KCNQ1):c.1590+14T>C rs11024034 0.07860
NM_000363.5(TNNI3):c.150+13G>A rs73617692 0.07353
NM_001018005.2(TPM1):c.486T>C (p.Tyr162=) rs11558747 0.05001
NM_000363.5(TNNI3):c.204G>T (p.Arg68=) rs3729711 0.04033
NM_174936.4(PCSK9):c.657+9G>A rs11800243 0.03991
NM_000363.5(TNNI3):c.198G>A (p.Glu66=) rs3729710 0.03372
NM_000384.3(APOB):c.10737C>T (p.Thr3579=) rs12713554 0.02896
NM_000138.5(FBN1):c.6855T>C (p.Asp2285=) rs363836 0.02755
NM_005159.5(ACTC1):c.927T>C (p.Pro309=) rs2307493 0.02473
NM_000138.5(FBN1):c.6888G>A (p.Gln2296=) rs363830 0.02418
NM_000384.3(APOB):c.8148C>T (p.Ile2716=) rs6413458 0.02288
NM_000258.3(MYL3):c.69C>T (p.Pro23=) rs2233264 0.02058
NM_001035.3(RYR2):c.1519G>A (p.Val507Ile) rs16835270 0.01462
NM_004415.4(DSP):c.2815G>A (p.Gly939Ser) rs80325569 0.01244
NM_001276345.2(TNNT2):c.294+7G>A rs45490292 0.01066
NM_000527.5(LDLR):c.90C>T (p.Asn30=) rs72658855 0.00965
NM_001005242.3(PKP2):c.76G>A (p.Asp26Asn) rs143004808 0.00716
NM_000256.3(MYBPC3):c.2686G>A (p.Val896Met) rs35078470 0.00601
NM_000138.5(FBN1):c.5343G>A (p.Val1781=) rs140649 0.00561
NM_000138.5(FBN1):c.6594C>T (p.Pro2198=) rs111844882 0.00439
NM_000138.5(FBN1):c.1746C>T (p.Cys582=) rs112366266 0.00436
NM_000138.5(FBN1):c.4905C>G (p.Thr1635=) rs113115949 0.00435
NM_000169.3(GLA):c.937G>T (p.Asp313Tyr) rs28935490 0.00308
NM_001005242.3(PKP2):c.419C>T (p.Ser140Phe) rs150821281 0.00252
NM_005159.5(ACTC1):c.454+9G>A rs148695567 0.00245
NM_001943.5(DSG2):c.2484T>C (p.Asp828=) rs201051252 0.00217
NM_024422.6(DSC2):c.2194T>G (p.Leu732Val) rs151024019 0.00138
NM_000218.3(KCNQ1):c.447C>T (p.Ala149=) rs146436765 0.00126
NM_000256.3(MYBPC3):c.2914C>T (p.Arg972Trp) rs193922382 0.00096
NM_000256.3(MYBPC3):c.624G>C (p.Gln208His) rs202139499 0.00017
NM_000169.3(GLA):c.48T>G (p.Leu16=) rs201449986 0.00011
NM_000257.4(MYH7):c.1407T>C (p.Asp469=) rs112172952 0.00008
NM_000257.4(MYH7):c.4283T>C (p.Leu1428Ser) rs727503244 0.00006
NM_000257.4(MYH7):c.1332T>C (p.Asn444=) rs397516099 0.00004
NM_000363.5(TNNI3):c.372+7C>T rs367809676 0.00004
NM_000257.4(MYH7):c.1301G>A (p.Arg434Lys) rs786205356 0.00001
NM_000218.3(KCNQ1):c.1986C>T (p.Tyr662=) rs11601907
NM_000257.4(MYH7):c.3337-4dup rs45504498
NM_000257.4(MYH7):c.5451G>A (p.Ala1817=) rs138682220
NM_000384.3(APOB):c.1223T>C (p.Ile408Thr)
NM_000384.3(APOB):c.12940A>G (p.Ile4314Val)
NM_000384.3(APOB):c.13013G>A (p.Ser4338Asn)
NM_000384.3(APOB):c.13451C>T (p.Thr4484Met)
NM_000384.3(APOB):c.2188G>A (p.Val730Ile)
NM_000384.3(APOB):c.26TGGCGCTGC[1] (p.9LAL[1])
NM_000384.3(APOB):c.9835A>G (p.Ser3279Gly)
NM_000527.5(LDLR):c.1060+10G>C
NM_000527.5(LDLR):c.1103G>A (p.Cys368Tyr)
NM_000527.5(LDLR):c.1171G>A (p.Ala391Thr)
NM_001018005.2(TPM1):c.639+13del rs397516488
NM_174936.4(PCSK9):c.1327G>A (p.Ala443Thr)

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