ClinVar Miner

Variants from Pars Genome Lab with conflicting interpretations

Location: Iran  Primary collection method: clinical testing
Minimum review status of the submission from Pars Genome Lab: Collection method of the submission from Pars Genome Lab:
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
218 217 1 57 67 0 18 119

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
Pars Genome Lab pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 1 8 1 0 0
likely pathogenic 3 0 4 0 1
uncertain significance 4 6 0 14 13
likely benign 2 3 35 0 27
benign 1 1 12 19 0

Submitter to submitter summary #

Total submitters: 49
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
Illumina Laboratory Services, Illumina 0 133 0 19 31 0 0 49
Labcorp Genetics (formerly Invitae), Labcorp 0 83 1 17 17 0 2 37
Natera, Inc. 0 101 0 12 8 0 1 21
Mendelics 0 12 0 2 3 0 4 9
Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic 0 0 0 0 8 0 0 8
Counsyl 0 14 0 2 4 0 2 8
Fulgent Genetics, Fulgent Genetics 0 12 0 4 0 0 4 8
Baylor Genetics 0 10 0 0 2 0 5 7
OMIM 0 3 0 1 2 0 2 5
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 2 0 0 0 0 4 4
3billion 0 4 0 2 0 0 1 3
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 27 0 2 1 0 0 3
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 1 0 0 1 2
ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen 0 0 0 1 0 0 1 2
Department of Pathology and Laboratory Medicine, Sinai Health System 0 7 0 1 0 0 1 2
Eurofins-Biomnis 0 0 0 1 0 0 1 2
First Genomix Gene Laboratory, Genetic Diagnostics Department 0 1 0 0 0 0 2 2
GeneReviews 0 1 0 0 0 0 2 2
Genome-Nilou Lab 0 147 0 1 1 0 0 2
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 0 0 1 0 0 1 2
Johns Hopkins Genomics, Johns Hopkins University 0 1 0 0 2 0 0 2
KCCC/NGS Laboratory, Kuwait Cancer Control Center 0 0 0 2 0 0 0 2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 4 0 0 0 0 2 2
Ambry Genetics 0 5 0 0 1 0 0 1
Breda Genetics srl, Breda Genetics srl 0 0 0 1 0 0 0 1
Clinical Biochemistry Laboratory, Health Services Laboratory 0 0 0 0 1 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 1 0 0 1 0 0 1
Clinical Laboratory, Xuzhou Maternity and Child Health Care Hospital 0 0 0 0 0 0 1 1
Color Diagnostics, LLC DBA Color Health 0 1 0 1 0 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 11 0 0 1 0 0 1
GENinCode PLC 0 0 0 1 0 0 0 1
Genetics and Molecular Pathology, SA Pathology 0 0 0 0 0 0 1 1
Genome Diagnostics Laboratory, The Hospital for Sick Children 0 4 0 1 0 0 0 1
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia 0 2 0 1 0 0 0 1
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 6 0 1 0 0 0 1
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 0 0 0 0 0 1 1
Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino" 0 0 0 0 0 0 1 1
LDLR-LOVD, British Heart Foundation 0 0 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 1 0 0 0 0 1 1
Medical Genetics Laboratory, Etlik City Hospital 0 0 0 1 0 0 0 1
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals 0 0 0 1 0 0 0 1
Myriad Genetics, Inc. 0 2 0 0 0 0 1 1
OLLIN Analises Genomicas, OLLIN 0 1 0 0 0 0 1 1
PROSPAX: an integrated multimodal progression chart in spastic ataxias, Center for Neurology; Hertie-Institute for Clinical Brain Research 0 0 0 0 0 0 1 1
Revvity Omics, Revvity 0 6 0 0 1 0 0 1
Sema4, Sema4 0 0 0 1 0 0 0 1
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center 0 1 0 0 1 0 0 1
St. Jude Molecular Pathology, St. Jude Children's Research Hospital 0 1 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

All variants with conflicting interpretations #

Total variants: 119
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000352.6(ABCC8):c.2390+219T>C rs4148632 0.89203
NM_000352.6(ABCC8):c.2256-50T>C rs4148626 0.89141
NM_000352.6(ABCC8):c.2390+123C>T rs4148631 0.71455
NM_000352.6(ABCC8):c.2390+93C>T rs4148630 0.71434
NM_000525.4(KCNJ11):c.1009G>A (p.Val337Ile) rs5215 0.70936
NM_000352.6(ABCC8):c.2820+17A>G rs2106865 0.62022
NM_000352.6(ABCC8):c.4120-27T>C rs739689 0.45032
NM_000277.3(PAH):c.441+47C>T rs1718301 0.37849
NM_000352.6(ABCC8):c.4609-40A>G rs1109591 0.36267
NM_000277.3(PAH):c.60+62C>T rs1522296 0.34408
NM_138413.4(HOGA1):c.912C>A (p.Ala304=) rs12261752 0.29673
NM_000352.6(ABCC8):c.4119+93G>T rs4148644 0.21307
NM_000404.4(GLB1):c.1233+8T>C rs13093698 0.21250
NM_001369.3(DNAH5):c.11372C>T (p.Thr3791Ile) rs17263496 0.10158
NM_003060.4(SLC22A5):c.1052+101A>G rs2073645 0.06948
NM_000352.6(ABCC8):c.4714G>A (p.Val1572Ile) rs8192690 0.05059
NM_000404.4(GLB1):c.1594A>G (p.Ser532Gly) rs73826339 0.04924
NM_000525.4(KCNJ11):c.808C>G (p.Leu270Val) rs1800467 0.03694
NM_004006.3(DMD):c.8734A>G (p.Asn2912Asp) rs1800278 0.02886
NM_004006.3(DMD):c.8729A>T (p.Glu2910Val) rs41305353 0.02876
NM_000784.4(CYP27A1):c.1151C>T (p.Pro384Leu) rs41272687 0.01532
NM_000525.4(KCNJ11):c.801C>G (p.Leu267=) rs5216 0.01521
NM_001370658.1(BTD):c.820A>G (p.Ile274Val) rs35976361 0.01107
NM_003659.4(AGPS):c.147C>T (p.Pro49=) rs34442536 0.01033
NM_000525.4(KCNJ11):c.1154C>G (p.Ser385Cys) rs41282930 0.00987
NM_024996.7(GFM1):c.127A>G (p.Asn43Asp) rs35942089 0.00886
NM_001365088.1(SLC12A6):c.408T>C (p.Phe136=) rs145186782 0.00819
NM_000492.4(CFTR):c.4272C>T (p.Tyr1424=) rs1800135 0.00634
NM_014363.6(SACS):c.4466A>G (p.Asn1489Ser) rs147099630 0.00597
NM_000318.3(PEX2):c.748T>C (p.Trp250Arg) rs142645936 0.00573
NM_001164508.2(NEB):c.5905T>C (p.Tyr1969His) rs34532796 0.00550
NM_000441.2(SLC26A4):c.1790T>C (p.Leu597Ser) rs55638457 0.00545
NM_001365088.1(SLC12A6):c.1412G>C (p.Ser471Thr) rs140916001 0.00534
NM_017739.4(POMGNT1):c.-11G>A rs80107141 0.00484
NM_006019.4(TCIRG1):c.1515C>T (p.Thr505=) rs34211419 0.00447
NM_004004.6(GJB2):c.457G>A (p.Val153Ile) rs111033186 0.00414
NM_002529.4(NTRK1):c.2339G>A (p.Arg780Gln) rs35669708 0.00406
NM_001384140.1(PCDH15):c.2625G>A (p.Ser875=) rs111033516 0.00386
NM_003060.4(SLC22A5):c.1463G>A (p.Arg488His) rs28383481 0.00347
NM_001692.4(ATP6V1B1):c.1394G>A (p.Arg465His) rs142905621 0.00310
NM_001360.3(DHCR7):c.399C>T (p.Ala133=) rs147424205 0.00245
NM_001378454.1(ALMS1):c.9822C>G (p.Thr3274=) rs201446579 0.00245
NM_031885.5(BBS2):c.1422G>A (p.Ser474=) rs117033008 0.00243
NM_153676.4(USH1C):c.403G>A (p.Val135Ile) rs145013633 0.00234
NM_005609.4(PYGM):c.1537A>G (p.Ile513Val) rs139570786 0.00232
NM_138694.4(PKHD1):c.2853C>T (p.Thr951=) rs139815340 0.00230
NM_022124.6(CDH23):c.4068C>G (p.Thr1356=) rs143136329 0.00226
NM_000318.3(PEX2):c.209A>G (p.Tyr70Cys) rs35689779 0.00225
NM_001039396.2(MPEG1):c.217A>G (p.Thr73Ala) rs143527301 0.00210
NM_000492.4(CFTR):c.2991G>C (p.Leu997Phe) rs1800111 0.00208
NM_001033855.3(DCLRE1C):c.1284A>C (p.Lys428Asn) rs113870881 0.00202
NM_014363.6(SACS):c.10982C>T (p.Ala3661Val) rs36061856 0.00198
NM_001164508.2(NEB):c.21720C>T (p.Tyr7240=) rs34718443 0.00171
NM_001142800.2(EYS):c.6119T>A (p.Val2040Asp) rs201580493 0.00166
NM_201253.3(CRB1):c.2307C>T (p.Arg769=) rs151104285 0.00151
NM_005957.5(MTHFR):c.1761C>T (p.Ala587=) rs115049252 0.00145
NM_000527.5(LDLR):c.1194C>T (p.Ile398=) rs13306498 0.00138
NM_025114.4(CEP290):c.3654T>C (p.Leu1218=) rs201838492 0.00133
NM_000098.3(CPT2):c.338C>T (p.Ser113Leu) rs74315294 0.00131
NM_001384474.1(LOXHD1):c.4217C>T (p.Ala1406Val) rs146739496 0.00111
NM_022124.6(CDH23):c.510C>T (p.Ser170=) rs143341423 0.00096
NM_000198.4(HSD3B2):c.500C>T (p.Ala167Val) rs35486059 0.00095
NM_000261.2(MYOC):c.1102C>T (p.Gln368Ter) rs74315329 0.00086
NM_000023.4(SGCA):c.843C>A (p.Ala281=) rs149487996 0.00075
NM_000018.4(ACADVL):c.1824C>T (p.Ile608=) rs146115467 0.00070
NM_201253.3(CRB1):c.1533C>T (p.Ala511=) rs142224492 0.00051
NM_004646.4(NPHS1):c.2869G>C (p.Val957Leu) rs114849139 0.00044
NM_000466.3(PEX1):c.3031G>A (p.Val1011Met) rs141650598 0.00036
NM_023036.6(DNAI2):c.1574C>T (p.Ala525Val) rs145602856 0.00036
NM_000492.4(CFTR):c.2421A>G (p.Ile807Met) rs1800103 0.00034
NM_000271.5(NPC1):c.3717C>T (p.His1239=) rs34624018 0.00033
NM_001378454.1(ALMS1):c.10238A>G (p.Glu3413Gly) rs184779459 0.00032
NM_206933.4(USH2A):c.1530C>T (p.Asp510=) rs200940197 0.00032
NM_001386140.1(MTTP):c.2657C>T (p.Pro886Leu) rs144600401 0.00028
NM_000051.4(ATM):c.5975A>C (p.Lys1992Thr) rs150757822 0.00025
NM_152564.5(VPS13B):c.1440C>T (p.Phe480=) rs141324814 0.00024
NM_000135.4(FANCA):c.2236G>T (p.Ala746Ser) rs575108446 0.00019
NM_014363.6(SACS):c.4302A>G (p.Leu1434=) rs34559250 0.00016
NM_000057.4(BLM):c.274A>G (p.Asn92Asp) rs200690226 0.00015
NM_004004.6(GJB2):c.493C>T (p.Arg165Trp) rs376898963 0.00015
NM_014363.6(SACS):c.3345C>T (p.Val1115=) rs143287019 0.00015
NM_000158.4(GBE1):c.45G>A (p.Glu15=) rs370326965 0.00014
NM_001164508.2(NEB):c.3211A>C (p.Ile1071Leu) rs35194393 0.00014
NM_020320.5(RARS2):c.1026G>A (p.Met342Ile) rs34647222 0.00014
NM_000117.3(EMD):c.428C>T (p.Ser143Phe) rs139983160 0.00013
NM_003982.4(SLC7A7):c.339A>C (p.Gly113=) rs139270936 0.00013
NM_001352514.2(HLCS):c.951C>T (p.Ser317=) rs185480832 0.00011
NM_004004.6(GJB2):c.23C>T (p.Thr8Met) rs529500747 0.00011
NM_000051.4(ATM):c.6382T>C (p.Leu2128=) rs753646931 0.00009
NM_000159.4(GCDH):c.1299G>A (p.Ala433=) rs150271870 0.00008
NM_001164508.2(NEB):c.23840T>G (p.Leu7947Trp) rs200559481 0.00008
NM_000070.3(CAPN3):c.1947G>A (p.Glu649=) rs79440238 0.00007
NM_000492.4(CFTR):c.1043T>A (p.Met348Lys) rs142920240 0.00007
NM_002529.4(NTRK1):c.585G>A (p.Thr195=) rs182531655 0.00007
NM_000057.4(BLM):c.2898C>G (p.Leu966=) rs201220226 0.00006
NM_000152.5(GAA):c.318C>T (p.Arg106=) rs762542246 0.00006
NM_001142800.2(EYS):c.9392G>C (p.Gly3131Ala) rs772888249 0.00006
NM_020533.3(MCOLN1):c.783G>A (p.Thr261=) rs200484869 0.00006
NM_001039141.3(TRIOBP):c.3073C>T (p.Arg1025Ter) rs776962899 0.00005
NM_000057.4(BLM):c.2371C>T (p.Arg791Cys) rs55880859 0.00004
NM_001243279.3(ACSF3):c.1470G>C (p.Glu490Asp) rs147538370 0.00004
NM_054012.4(ASS1):c.786C>T (p.Gly262=) rs536799104 0.00003
NM_138694.4(PKHD1):c.9107T>G (p.Val3036Gly) rs893497345 0.00003
NM_000022.4(ADA):c.454C>A (p.Leu152Met) rs121908728 0.00002
NM_000277.3(PAH):c.1218A>G (p.Ile406Met) rs773526027 0.00002
NM_000059.4(BRCA2):c.5851_5854del (p.Ser1951fs) rs80359543
NM_000070.3(CAPN3):c.2380+2T>G rs761935462
NM_000155.4(GALT):c.-119_-116delGTCA rs111033640
NM_000228.3(LAMB3):c.1117C>T (p.Gln373Ter) rs1057517096
NM_000329.3(RPE65):c.1451-1G>A rs1317871521
NM_000404.4(GLB1):c.792+10G>T rs79518579
NM_000492.4(CFTR):c.350G>A (p.Arg117His) rs78655421
NM_002435.3(MPI):c.678C>A (p.Ala226=) rs199972529
NM_003282.4(TNNI2):c.524AGA[1] (p.Lys176del) rs199474801
NM_004006.3(DMD):c.9352G>T (p.Ala3118Ser) rs200928985
NM_004425.4(ECM1):c.806G>A (p.Cys269Tyr) rs756977475
NM_005249.5(FOXG1):c.584G>C (p.Arg195Pro) rs1001642335
NM_014363.6(SACS):c.10291G>C (p.Val3431Leu) rs144179865
NM_015506.3(MMACHC):c.766_771del (p.Ala256_Pro257del) rs796064513

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