ClinVar Miner

Variants from Genomic Medicine Lab, University of California San Francisco with conflicting interpretations

Location: United States  Primary collection method: clinical testing
Minimum review status of the submission from Genomic Medicine Lab, University of California San Francisco: Collection method of the submission from Genomic Medicine Lab, University of California San Francisco:
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
245 75 0 41 3 2 15 52

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
Genomic Medicine Lab, University of California San Francisco pathogenic likely pathogenic uncertain significance likely benign benign pathogenic, low penetrance
pathogenic 0 25 4 0 2 2
likely pathogenic 16 0 5 0 0 0
uncertain significance 5 0 0 1 2 0

Submitter to submitter summary #

Total submitters: 45
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
OMIM 0 33 0 6 0 0 6 12
Invitae 0 27 0 2 2 2 2 8
Baylor Genetics 0 32 0 3 0 0 0 3
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 2 0 3 0 0 0 3
Counsyl 0 1 0 2 0 0 1 3
Fulgent Genetics, Fulgent Genetics 0 4 0 2 0 0 1 3
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 1 0 1 0 0 2 3
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 3 0 1 1 0 1 3
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 10 0 1 0 0 1 2
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 10 0 2 0 0 0 2
Illumina Laboratory Services, Illumina 0 11 0 1 0 0 1 2
Institute of Human Genetics, University of Leipzig Medical Center 0 12 0 1 0 0 1 2
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 1 0 2 0 0 0 2
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 0 0 2 0 0 0 2
Myriad Genetics, Inc. 0 5 0 2 0 0 0 2
Genome-Nilou Lab 0 7 0 2 0 0 0 2
3billion 0 9 0 2 0 0 0 2
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 7 0 2 0 0 0 2
Genetic Services Laboratory, University of Chicago 0 8 0 0 0 0 1 1
GeneDx 0 6 0 1 0 0 0 1
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 2 0 1 0 0 0 1
MGZ Medical Genetics Center 0 10 0 1 0 0 0 1
Centogene AG - the Rare Disease Company 0 5 0 1 0 0 0 1
Institute of Medical Molecular Genetics, University of Zurich 0 0 0 1 0 0 0 1
Mendelics 0 4 0 1 0 0 0 1
UCLA Clinical Genomics Center, UCLA 0 2 0 1 0 0 0 1
Laboratory of Human Genetics, Universidade de São Paulo 0 1 0 0 0 0 1 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 7 0 1 0 0 0 1
Laboratory of Genetics and Molecular Cardiology, University of São Paulo 0 0 0 1 0 0 0 1
Laboratory of Prof. Karen Avraham, Tel Aviv University 0 0 0 1 0 0 0 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 3 0 1 0 0 0 1
Daryl Scott Lab, Baylor College of Medicine 0 3 0 1 0 0 0 1
Undiagnosed Diseases Network, NIH 0 1 0 1 0 0 0 1
Genetics and Molecular Pathology, SA Pathology 0 4 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 2 0 1 0 0 0 1
Dan Cohn Lab, University Of California Los Angeles 0 0 0 1 0 0 0 1
Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital 0 0 0 1 0 0 0 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 1 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 8 0 1 0 0 0 1
Johns Hopkins Genomics, Johns Hopkins University 0 5 0 1 0 0 0 1
deCODE genetics, Amgen 0 1 0 1 0 0 0 1
Autoinflammatory diseases unit, CHU de Montpellier 0 2 0 1 0 0 0 1
New York Genome Center 0 6 0 0 0 0 1 1
GenomeConnect - Simons Searchlight 0 1 0 1 0 0 0 1
Genomics And Bioinformatics Analysis Resource, Columbia University 0 2 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 52
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000410.4(HFE):c.187C>G (p.His63Asp) rs1799945 0.10170
NM_000410.4(HFE):c.845G>A (p.Cys282Tyr) rs1800562 0.03880
NM_000104.4(CYP1B1):c.1103G>A (p.Arg368His) rs79204362 0.00125
NM_001377.3(DYNC2H1):c.9044A>G (p.Asp3015Gly) rs137853027 0.00026
NM_054012.4(ASS1):c.1168G>A (p.Gly390Arg) rs121908641 0.00025
NM_000104.4(CYP1B1):c.1159G>A (p.Glu387Lys) rs55989760 0.00018
NM_005912.3(MC4R):c.806T>A (p.Ile269Asn) rs79783591 0.00011
NM_012434.5(SLC17A5):c.533del (p.Thr178fs) rs727504156 0.00006
NM_025103.4(IFT74):c.1685-1G>T rs200699377 0.00005
NM_018055.5(NODAL):c.778G>A (p.Gly260Arg) rs121909283 0.00004
NM_001079866.2(BCS1L):c.269G>A (p.Arg90His) rs747956412 0.00003
NM_001377.3(DYNC2H1):c.4267C>T (p.Arg1423Cys) rs745870321 0.00003
NM_138694.4(PKHD1):c.353del (p.Ser118fs) rs398124483 0.00003
NM_000486.6(AQP2):c.190G>A (p.Gly64Arg) rs104894326 0.00002
NM_001083116.3(PRF1):c.921del (p.His308fs) rs777345151 0.00002
NM_014049.5(ACAD9):c.796C>T (p.Arg266Trp) rs753711253 0.00002
NM_000303.3(PMM2):c.178G>T (p.Val60Leu) rs759513930 0.00001
NM_000478.6(ALPL):c.532T>C (p.Tyr178His) rs1215600806 0.00001
NM_001276345.2(TNNT2):c.890G>A (p.Trp297Ter) rs727504247 0.00001
NM_002834.5(PTPN11):c.166A>G (p.Ile56Val) rs397507504 0.00001
NM_007373.4(SHOC2):c.4A>G (p.Ser2Gly) rs267607048 0.00001
NM_013382.7(POMT2):c.1976G>A (p.Arg659Gln) rs770606360 0.00001
NM_031407.7(HUWE1):c.9802C>T (p.Pro3268Ser) rs1045935059 0.00001
NM_152906.7(TANGO2):c.256C>T (p.Arg86Ter) rs1162037663 0.00001
NC_012920.1:m.3243A>G rs199474657
NM_000027.4(AGA):c.367_371del (p.Thr123fs) rs1736928101
NM_000384.3(APOB):c.10580G>A (p.Arg3527Gln)
NM_000836.4(GRIN2D):c.1999G>A (p.Val667Ile) rs886040861
NM_001190737.2(NFIB):c.265C>T (p.Arg89Ter) rs764333096
NM_001197104.2(KMT2A):c.3460C>T (p.Arg1154Trp) rs1555038090
NM_001244008.2(KIF1A):c.914C>T (p.Pro305Leu) rs1131690804
NM_001372066.1(TFAP2A):c.766C>T (p.Arg256Trp) rs151344528
NM_001848.3(COL6A1):c.850G>A (p.Gly284Arg) rs121912938
NM_002834.5(PTPN11):c.1471C>A (p.Pro491Thr) rs397507539
NM_002834.5(PTPN11):c.182A>G (p.Asp61Gly) rs121918461
NM_003042.4(SLC6A1):c.1648G>A (p.Gly550Arg) rs886042046
NM_003042.4(SLC6A1):c.863C>T (p.Ala288Val) rs794726860
NM_003482.4(KMT2D):c.12469C>T (p.Gln4157Ter) rs1555188080
NM_003482.4(KMT2D):c.16342C>T (p.Arg5448Ter) rs1422752351
NM_003924.4(PHOX2B):c.741_758dup (p.Ala255_Ala260dup) rs771383153
NM_005585.5(SMAD6):c.531C>G (p.Tyr177Ter) rs760571406
NM_006009.4(TUBA1A):c.302A>G (p.Asn101Ser) rs1565627526
NM_006245.4(PPP2R5D):c.598G>A (p.Glu200Lys) rs863225079
NM_006941.4(SOX10):c.404G>A (p.Ser135Asn) rs74315515
NM_006978.3(RNF113A):c.903_910del (p.Gln302fs) rs1603374549
NM_012205.3(HAAO):c.128G>A (p.Arg43Lys) rs1672558841
NM_013382.7(POMT2):c.2197C>T (p.Gln733Ter) rs1452558347
NM_015425.6(POLR1A):c.3988_3990del (p.Glu1330del) rs1064794956
NM_018684.4(ZC4H2):c.592C>T (p.Arg198Trp) rs137962226
NM_019597.5(HNRNPH2):c.617G>A (p.Arg206Gln) rs886039764
NM_032271.3(TRAF7):c.1964G>A (p.Arg655Gln) rs1331463984
NM_033310.3(KCNK4):c.515C>A (p.Ala172Glu) rs1565369746

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