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
215 41 0 19 1 0 8 25

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
pathogenic 0 9 1 0
likely pathogenic 10 0 4 0
uncertain significance 3 0 0 1

Submitter to submitter summary #

Total submitters: 22
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 17 0 6 0 0 3 9
Invitae 0 16 0 3 1 0 1 5
Center for Human Genetics, Inc,Center for Human Genetics, Inc 0 2 0 3 0 0 0 3
Counsyl 0 0 0 2 0 0 1 3
Baylor Genetics 0 10 0 1 0 0 1 2
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City 0 0 0 2 0 0 0 2
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 1 0 1 0 0 0 1
GeneDx 0 4 0 1 0 0 0 1
Institute of Medical Molecular Genetics, University of Zurich 0 0 0 1 0 0 0 1
Integrated Genetics/Laboratory Corporation of America 0 5 0 1 0 0 0 1
Fulgent Genetics,Fulgent Genetics 0 0 0 0 0 0 1 1
Illumina Clinical Services Laboratory,Illumina 0 2 0 1 0 0 0 1
Laboratory of Human Genetics,Universidade de São Paulo 0 0 0 0 0 0 1 1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 0 0 0 0 0 1 1
Laboratory of Prof. Karen Avraham,Tel Aviv University 0 0 0 1 0 0 0 1
Institute for Genomic Medicine, Columbia University,Columbia University Medical Center 0 0 0 1 0 0 0 1
Undiagnosed Diseases Network,NIH 0 1 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 4 0 0 0 0 1 1
SIB Swiss Institute of Bioinformatics 0 2 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
Autoinflammatory diseases unit,CHU de Montpellier 0 2 0 1 0 0 0 1
GenomeConnect - Simons Searchlight 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 25
Download table as spreadsheet
HGVS dbSNP
NM_000104.3(CYP1B1):c.1103G>A (p.Arg368His) rs79204362
NM_000104.3(CYP1B1):c.1159G>A (p.Glu387Lys) rs55989760
NM_000303.3(PMM2):c.178G>T (p.Val60Leu) rs759513930
NM_000836.2(GRIN2D):c.1999G>A (p.Val667Ile) rs886040861
NM_001032280.3(TFAP2A):c.742C>T (p.Arg248Trp) rs151344528
NM_001079866.2(BCS1L):c.269G>A (p.Arg90His) rs747956412
NM_001190737.2(NFIB):c.265C>T (p.Arg89Ter) rs764333096
NM_001277269.1(OTOG):c.2500C>T (p.Gln834Ter) rs554847663
NM_001848.3(COL6A1):c.850G>A 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_003482.3(KMT2D):c.12469C>T (p.Gln4157Ter) rs1555188080
NM_003482.3(KMT2D):c.16342C>T (p.Arg5448Ter) rs1422752351
NM_004321.7(KIF1A):c.914C>T (p.Pro305Leu) rs1131690804
NM_005585.5(SMAD6):c.531C>G (p.Tyr177Ter) rs760571406
NM_006978.3(RNF113A):c.903_910del (p.Gln302fs) rs1603374549
NM_012434.5(SLC17A5):c.533del (p.Thr178fs) rs727504156
NM_018055.5(NODAL):c.778G>A (p.Gly260Arg) rs121909283
NM_019597.5(HNRNPH2):c.617G>A (p.Arg206Gln) rs886039764
NM_025103.4(IFT74):c.1685-1G>T rs200699377
NM_032271.3(TRAF7):c.1964G>A (p.Arg655Gln) rs1331463984
NM_033310.3(KCNK4):c.515C>A (p.Ala172Glu) rs1565369746
NM_138694.4(PKHD1):c.353del (p.Ser118fs) rs398124483

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