ClinVar Miner

Variants from Laboratorio de I+D, Fundación Centro Médico de Asturias with conflicting interpretations

Location: Spain  Primary collection method: clinical testing
Minimum review status of the submission from Laboratorio de I+D, Fundación Centro Médico de Asturias: Collection method of the submission from Laboratorio de I+D, Fundación Centro Médico de Asturias:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
19 22 0 52 31 0 5 75

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
Laboratorio de I+D, Fundación Centro Médico de Asturias pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 1 1 0 0
likely pathogenic 2 0 0 0 0
uncertain significance 2 4 0 7 3
likely benign 0 0 13 0 11
benign 0 0 11 38 0

Submitter to submitter summary #

Total submitters: 31
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
Ambry Genetics 0 44 0 22 11 0 1 34
Sema4, Sema4 0 32 0 18 7 0 0 25
True Health Diagnostics 0 3 0 13 6 0 0 19
Color Diagnostics, LLC DBA Color Health 0 23 0 8 7 0 1 16
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C. 0 5 0 10 3 0 0 13
GeneKor MSA 0 1 0 4 2 0 0 6
Mendelics 0 1 0 2 1 0 2 5
Molecular Diagnostics Laboratory, Catalan Institute of Oncology 0 3 0 3 2 0 0 5
Labcorp Genetics (formerly Invitae), Labcorp 0 3 0 1 2 0 1 4
Vantari Genetics 0 3 0 2 2 0 0 4
Baylor Genetics 0 1 0 0 1 0 2 3
Counsyl 0 1 0 2 0 0 1 3
Department of Pathology and Laboratory Medicine, Sinai Health System 0 1 0 1 2 0 0 3
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 3 0 2 0 0 1 3
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 0 0 0 1 0 1 2
St. Jude Molecular Pathology, St. Jude Children's Research Hospital 0 0 0 0 2 0 0 2
Center of Medical Genetics and Primary Health Care 0 0 0 0 0 0 1 1
Department of Genetics, HCU Lozano Blesa 0 0 0 0 0 0 1 1
Dipartimento Di Medicina Di Precisione, Università Degli Studi Della Campania Luigi Vanvitelli 0 0 0 1 0 0 0 1
Fulgent Genetics, Fulgent Genetics 0 1 0 1 0 0 0 1
Genetics and Molecular Pathology, SA Pathology 0 1 0 1 0 0 0 1
Hereditary Cancer Laboratory, Hospital Universitario 12 de Octubre 0 0 0 0 1 0 0 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 0 0 0 0 0 1 1
Institute of Human Genetics, Heidelberg University 0 0 0 0 0 0 1 1
KCCC/NGS Laboratory, Kuwait Cancer Control Center 0 0 0 0 1 0 0 1
Medical Genetics Laboratory, Umraniye Training and Research Hospital, University of Health Sciences 0 0 0 0 0 0 1 1
Myriad Genetics, Inc. 0 1 0 0 1 0 0 1
Pathway Genomics 0 0 0 0 0 0 1 1
Praxis Für Humangenetik, Biosciencia MVZ Labor Saar 0 1 0 1 0 0 0 1
Spanish ATM Cancer Susceptibility Variant Interpretation Working Group 0 1 0 1 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 75
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HGVS dbSNP gnomAD frequency
NM_000535.7(PMS2):c.52A>G (p.Ile18Val) rs63750123 0.00861
NM_000051.4(ATM):c.2119T>C (p.Ser707Pro) rs4986761 0.00782
NM_000051.4(ATM):c.146C>G (p.Ser49Cys) rs1800054 0.00712
NM_058216.3(RAD51C):c.859A>G (p.Thr287Ala) rs28363317 0.00653
NM_000059.4(BRCA2):c.9976A>T (p.Lys3326Ter) rs11571833 0.00597
NM_000051.4(ATM):c.1810C>T (p.Pro604Ser) rs2227922 0.00431
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) rs17879961 0.00408
NM_005591.4(MRE11):c.1475C>A (p.Ala492Asp) rs61749249 0.00399
NM_001042492.3(NF1):c.528T>A (p.Asp176Glu) rs112306990 0.00380
NM_032043.3(BRIP1):c.517C>T (p.Arg173Cys) rs4988345 0.00363
NM_001048174.2(MUTYH):c.1103G>A (p.Gly368Asp) rs36053993 0.00341
NM_006231.4(POLE):c.4259C>T (p.Ala1420Val) rs41561818 0.00325
NM_004360.5(CDH1):c.1774G>A (p.Ala592Thr) rs35187787 0.00311
NM_020975.6(RET):c.166C>A (p.Leu56Met) rs145633958 0.00310
NM_006231.4(POLE):c.16G>C (p.Gly6Arg) rs202220778 0.00291
NM_024675.4(PALB2):c.2590C>T (p.Pro864Ser) rs45568339 0.00287
NM_000059.4(BRCA2):c.6100C>T (p.Arg2034Cys) rs1799954 0.00268
NM_013372.7(GREM1):c.103C>G (p.Pro35Ala) rs111262341 0.00259
NM_000038.6(APC):c.3386T>C (p.Leu1129Ser) rs143638171 0.00250
NM_007294.4(BRCA1):c.4535G>T (p.Ser1512Ile) rs1800744 0.00240
NM_000077.5(CDKN2A):c.150+37G>C rs45456595 0.00212
NM_007194.4(CHEK2):c.254C>T (p.Pro85Leu) rs17883862 0.00201
NM_058216.3(RAD51C):c.790G>A (p.Gly264Ser) rs147241704 0.00182
NM_000465.4(BARD1):c.2282G>A (p.Ser761Asn) rs142155101 0.00149
NM_002354.3(EPCAM):c.831A>G (p.Ile277Met) rs115283528 0.00135
NM_000051.4(ATM):c.998C>T (p.Ser333Phe) rs28904919 0.00133
NM_032043.3(BRIP1):c.890A>G (p.Lys297Arg) rs28997570 0.00113
NM_000051.4(ATM):c.4388T>G (p.Phe1463Cys) rs138327406 0.00098
NM_000059.4(BRCA2):c.6937+594T>G rs191253965 0.00094
NM_000321.3(RB1):c.920C>T (p.Thr307Ile) rs183898408 0.00088
NM_004655.4(AXIN2):c.1985T>C (p.Leu662Pro) rs142476324 0.00084
NM_004329.3(BMPR1A):c.1327C>T (p.Arg443Cys) rs35619497 0.00081
NM_000051.4(ATM):c.1073A>G (p.Asn358Ser) rs149636614 0.00079
NM_006231.4(POLE):c.3718G>A (p.Glu1240Lys) rs113594027 0.00074
NM_007294.4(BRCA1):c.1487G>A (p.Arg496His) rs28897677 0.00060
NM_000059.4(BRCA2):c.7994A>G (p.Asp2665Gly) rs28897745 0.00049
NM_004304.5(ALK):c.4255G>A (p.Glu1419Lys) rs56181542 0.00046
NM_002485.5(NBN):c.1720T>A (p.Leu574Ile) rs142334798 0.00044
NM_004655.4(AXIN2):c.733C>T (p.Pro245Ser) rs62640028 0.00042
NM_032043.3(BRIP1):c.2220G>T (p.Gln740His) rs45589637 0.00041
NM_007194.4(CHEK2):c.1427C>T (p.Thr476Met) rs142763740 0.00032
NM_002691.4(POLD1):c.3257G>A (p.Arg1086Gln) rs3219457 0.00025
NM_000548.5(TSC2):c.1973A>C (p.Lys658Thr) rs397515223 0.00022
NM_002691.4(POLD1):c.353C>T (p.Ser118Phe) rs780604625 0.00016
NM_007194.4(CHEK2):c.190G>A (p.Glu64Lys) rs141568342 0.00015
NM_002485.5(NBN):c.456G>A (p.Met152Ile) rs201816949 0.00014
NM_004655.4(AXIN2):c.1975C>T (p.Arg659Trp) rs142670753 0.00014
NM_017841.4(SDHAF2):c.7G>T (p.Val3Leu) rs149277592 0.00010
NM_000251.3(MSH2):c.382C>G (p.Leu128Val) rs145649774 0.00009
NM_000059.4(BRCA2):c.9501+3A>T rs61757642 0.00007
NM_000249.4(MLH1):c.1360G>C (p.Gly454Arg) rs63750527 0.00007
NM_000548.5(TSC2):c.814G>A (p.Ala272Thr) rs373818076 0.00006
NM_001042492.3(NF1):c.3686A>G (p.Asn1229Ser) rs140523180 0.00006
NM_017849.4(TMEM127):c.121A>G (p.Ile41Val) rs760633411 0.00006
NM_020937.4(FANCM):c.2452A>G (p.Ile818Val) rs199948045 0.00006
NM_006231.4(POLE):c.2645A>G (p.Asn882Ser) rs539312991 0.00005
NM_006231.4(POLE):c.6445C>T (p.Arg2149Cys) rs771490182 0.00004
NM_007294.4(BRCA1):c.4669G>C (p.Asp1557His) rs80356906 0.00004
NM_000465.4(BARD1):c.568G>A (p.Asp190Asn) rs369561166 0.00003
NM_144997.7(FLCN):c.1637A>G (p.Asn546Ser) rs775149348 0.00003
NM_007194.4(CHEK2):c.500G>A (p.Gly167Glu) rs144850845 0.00002
NM_000038.6(APC):c.4333A>G (p.Thr1445Ala) rs587780597 0.00001
NM_004656.4(BAP1):c.1769A>T (p.Gln590Leu) rs756472919 0.00001
NM_005359.6(SMAD4):c.884C>T (p.Pro295Leu) rs370176106 0.00001
NM_000051.4(ATM):c.193C>G (p.Gln65Glu) rs775248597
NM_000059.4(BRCA2):c.6024dup (p.Gln2009fs) rs80359554
NM_000249.4(MLH1):c.1852_1853delinsGC (p.Lys618Ala) rs35502531
NM_000548.5(TSC2):c.4524CTT[1] (p.Phe1510del) rs137854239
NM_002878.4(RAD51D):c.94_95del (p.Val32fs) rs786203137
NM_004304.5(ALK):c.4570AAG[1] (p.Lys1525del) rs755556501
NM_004360.5(CDH1):c.2282_2284del (p.Gly761del) rs878854683
NM_006206.6(PDGFRA):c.807C>G (p.Ile269Met) rs1553903217
NM_006231.4(POLE):c.2090C>G (p.Pro697Arg) rs36120395
NM_007194.4(CHEK2):c.844C>G (p.His282Asp) rs774068238
NM_020975.6(RET):c.3142C>G (p.Leu1048Val) rs774347808

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