ClinVar Miner

Variants from Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center with conflicting interpretations

Location: United States  Primary collection method: clinical testing
Minimum review status of the submission from Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center: Collection method of the submission from Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center:
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
38 21 0 14 2 0 4 18

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
Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 8 2 0 0
likely pathogenic 6 0 0 0 0
uncertain significance 1 1 0 1 1

Submitter to submitter summary #

Total submitters: 19
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
Fulgent Genetics, Fulgent Genetics 0 5 0 4 0 0 0 4
OMIM 0 4 0 2 0 0 1 3
Invitae 0 8 0 1 2 0 0 3
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 0 0 0 2 0 0 0 2
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 1 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
MGZ Medical Genetics Center 0 3 0 1 0 0 0 1
Counsyl 0 3 0 0 0 0 1 1
Natera, Inc. 0 2 0 1 0 0 0 1
Mendelics 0 0 0 1 0 0 0 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 2 0 0 0 0 1 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 3 0 0 0 0 1 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 0 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 1 0 1 0 0 0 1
Pathology and Clinical Laboratory Medicine, King Fahad Medical City 0 0 0 1 0 0 0 1
Genome-Nilou Lab 0 6 0 1 0 0 0 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 1 0 0 0 0 1 1
Clinical Cancer Genomics Laboratory, City of Hope Comprehensive Cancer Center 0 0 0 1 0 0 0 1
European Hospital Georges Pompidou Genetics Department, Assistance Publique - Hôpitaux de Paris AP-HP 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 18
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001177316.2(SLC34A3):c.575C>T (p.Ser192Leu) rs199690076 0.00059
NM_000520.6(HEXA):c.805G>A (p.Gly269Ser) rs121907954 0.00015
NM_001126108.2(SLC12A3):c.2191G>A (p.Gly731Arg) rs752101663 0.00005
NM_000335.5(SCN5A):c.1127G>A (p.Arg376His) rs199473101 0.00003
NM_001126108.2(SLC12A3):c.1844C>T (p.Ser615Leu) rs779160677 0.00003
NM_032634.4(PIGO):c.3118G>A (p.Val1040Ile) rs149439295 0.00003
NM_000092.5(COL4A4):c.1223G>A (p.Gly408Glu) rs1026613471 0.00002
NM_000092.5(COL4A4):c.489+1G>A rs1040287646 0.00001
NM_000435.3(NOTCH3):c.619C>T (p.Arg207Cys) rs775267348 0.00001
NM_001005273.3(CHD3):c.5007_5008del (p.Asp1671fs) rs967826828 0.00001
NM_007294.4(BRCA1):c.442-1G>T rs1351019392 0.00001
NM_000059.4(BRCA2):c.1796_1800del (p.Thr598_Ser599insTer) rs276174813
NM_001321075.3(DLG4):c.1878C>A (p.Cys626Ter) rs1451196379
NM_001353921.2(ARHGEF9):c.890G>A (p.Arg297His)
NM_002224.4(ITPR3):c.7570C>T (p.Arg2524Cys)
NM_005629.4(SLC6A8):c.617G>A (p.Arg206His)
NM_017825.3(ADPRS):c.530C>T (p.Ser177Leu) rs200626873
NM_020699.4(GATAD2B):c.1241G>A (p.Arg414Gln) rs1057521041

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