ClinVar Miner

Variants from Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics with conflicting interpretations

Location: Russian Federation  Primary collection method: clinical testing
Minimum review status of the submission from Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics: Collection method of the submission from Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics:
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
274 60 0 41 3 0 21 59

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
Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 27 6 1 0
likely pathogenic 14 0 11 0 0
uncertain significance 1 3 0 2 1

Submitter to submitter summary #

Total submitters: 34
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
Labcorp Genetics (formerly Invitae), Labcorp 0 18 0 7 3 0 8 18
Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova 0 33 0 9 0 0 3 12
Natera, Inc. 0 6 0 4 1 0 2 7
Counsyl 0 0 0 1 0 0 5 6
Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences 0 1 0 6 0 0 0 6
Fulgent Genetics, Fulgent Genetics 0 3 0 5 0 0 0 5
Baylor Genetics 0 4 0 4 0 0 0 4
3billion 0 1 0 1 0 0 2 3
Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences 0 0 0 2 0 0 0 2
Mendelics 0 0 0 2 0 0 0 2
Revvity Omics, Revvity 0 3 0 1 0 0 1 2
All of Us Research Program, National Institutes of Health 0 0 0 1 0 0 0 1
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 0 0 1 0 0 0 1
Blueprint Genetics 0 1 0 1 0 0 0 1
CENTOGENE GmbH and LLC - Guiding Precision Medicine 0 1 0 1 0 0 0 1
Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University 0 0 0 0 0 0 1 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 1 0 0 0 1
Clinical Biomedical Laboratory, Shriners Hospital For Children - Canada 0 1 0 1 0 0 0 1
Color Diagnostics, LLC DBA Color Health 0 0 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 1 0 0 0 1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 0 0 1 0 0 0 1
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 1 0 1 0 0 0 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 0 0 0 0 0 1 1
Institute of Human Genetics Munich, TUM University Hospital 0 0 0 1 0 0 0 1
Institute of Human Genetics, Heidelberg University 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
Kariminejad - Najmabadi Pathology & Genetics Center 0 0 0 1 0 0 0 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 0 0 1 0 0 0 1
Laboratory of Functional Genomics, Research Centre for Medical Genetics 0 2 0 1 0 0 0 1
Myriad Genetics, Inc. 0 0 0 1 0 0 0 1
OLLIN Analises Genomicas, OLLIN 0 0 0 0 0 0 1 1
OMIM 0 0 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 3 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 59
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000512.5(GALNS):c.121-210C>T rs75552025 0.00908
NM_000532.5(PCCB):c.882C>T (p.Pro294=) rs142730126 0.00080
NM_014780.5(CUL7):c.3041T>G (p.Leu1014Arg) rs61752334 0.00011
NM_147127.5(EVC2):c.1470+3A>T rs370769794 0.00007
NM_000282.4(PCCA):c.819+9A>G rs372739944 0.00004
NM_000330.4(RS1):c.326+1131G>A rs267608664 0.00004
NM_000512.5(GALNS):c.181C>T (p.Arg61Trp) rs145798311 0.00004
NM_000023.4(SGCA):c.502G>A (p.Gly168Arg) rs199810179 0.00001
NM_000187.4(HGD):c.536T>G (p.Ile179Ser) rs1031569954 0.00001
NM_000282.4(PCCA):c.2119-9A>G rs1389933015 0.00001
NM_000512.5(GALNS):c.1483-15A>G rs1461992033 0.00001
NM_002496.4(NDUFS8):c.307C>T (p.Arg103Trp) rs867723941 0.00001
NM_021830.5(TWNK):c.737A>G (p.Asn246Ser) rs754081544 0.00001
NM_000047.3(ARSL):c.1289+1G>A rs2147349066
NM_000095.3(COMP):c.1315G>T (p.Asp439Tyr) rs1601054002
NM_000095.3(COMP):c.886C>T (p.Pro296Ser) rs749583854
NM_000187.4(HGD):c.1114G>A (p.Gly372Arg) rs1940645842
NM_000187.4(HGD):c.127C>G (p.Gln43Glu) rs1243059404
NM_000187.4(HGD):c.131T>C (p.Leu44Pro) rs1708095030
NM_000187.4(HGD):c.665C>A (p.Ala222Asp) rs1576294110
NM_000187.4(HGD):c.753C>T (p.Gly251=) rs1357020990
NM_000202.8(IDS):c.1028G>A (p.Gly343Glu) rs2089343063
NM_000202.8(IDS):c.1034G>C (p.Trp345Ser) rs2089342988
NM_000202.8(IDS):c.103G>C (p.Asp35His) rs2089514224
NM_000202.8(IDS):c.104-1_104delinsT rs2089505743
NM_000202.8(IDS):c.117TCT[1] (p.Leu41del) rs2089505317
NM_000202.8(IDS):c.136G>T (p.Asp46Tyr) rs2089504816
NM_000202.8(IDS):c.1426_1437del (p.Asn476_Lys479del) rs2089305217
NM_000202.8(IDS):c.1491_1492dup (p.Arg498fs) rs2089304532
NM_000202.8(IDS):c.241-9C>G rs2089497858
NM_000202.8(IDS):c.307T>G (p.Tyr103Asp) rs2089496667
NM_000202.8(IDS):c.590C>T (p.Pro197Leu) rs2089451912
NM_000282.4(PCCA):c.1353+5_1353+9del rs764045674
NM_000282.4(PCCA):c.1643+1_1643+2dup rs1555425626
NM_000282.4(PCCA):c.183+4_183+7del rs1555342581
NM_000282.4(PCCA):c.1899+2_1899+3insCT rs2081058900
NM_000282.4(PCCA):c.2040G>A (p.Ala680=) rs369982920
NM_000282.4(PCCA):c.717-2A>G rs2062611307
NM_000466.3(PEX1):c.2633TGT[1] (p.Leu879del) rs886043984
NM_000512.5(GALNS):c.423-862C>T rs1597575641
NM_000512.5(GALNS):c.899-167A>G rs2142999330
NM_000527.5(LDLR):c.1186+1G>T rs730880131
NM_000527.5(LDLR):c.1691A>C (p.Asn564Thr) rs758194385
NM_000527.5(LDLR):c.940+3_940+6del rs2077315885
NM_000532.5(PCCB):c.1091-8_1091-3del rs1249235758
NM_000532.5(PCCB):c.655-2A>G rs1553778865
NM_000532.5(PCCB):c.763G>A (p.Gly255Ser) rs1553778909
NM_001040716.2(PC):c.1876C>T (p.Arg626Trp) rs1591122325
NM_001130987.2(DYSF):c.5547-2A>G rs1238293747
NM_001323289.2(CDKL5):c.290T>C (p.Leu97Pro) rs1925418549
NM_001323289.2(CDKL5):c.554+1G>A rs1555950083
NM_001323289.2(CDKL5):c.89G>A (p.Cys30Tyr) rs1555940536
NM_001353921.2(ARHGEF9):c.331C>T (p.Arg111Trp) rs1556401730
NM_001377.3(DYNC2H1):c.2T>C (p.Met1Thr) rs2134667452
NM_002693.3(POLG):c.2591A>T (p.Asn864Ile) rs121918050
NM_004544.4(NDUFA10):c.604dup (p.His202fs) rs746019378
NM_005138.3(SCO2):c.227_230del (p.Leu76fs) rs780824645
NM_021830.5(TWNK):c.1272C>G (p.Phe424Leu) rs773918715
NM_153717.3(EVC):c.2561+1G>A rs1553894457

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