ClinVar Miner

Variants from Centre for Inherited Metabolic Diseases, Karolinska University Hospital with conflicting interpretations

Location: Sweden — Primary collection method: clinical testing
Minimum review status of the submission from Centre for Inherited Metabolic Diseases, Karolinska University Hospital: Collection method of the submission from Centre for Inherited Metabolic Diseases, Karolinska University Hospital:
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
46 22 8 21 0 0 8 31

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
Centre for Inherited Metabolic Diseases, Karolinska University Hospital pathogenic likely pathogenic uncertain significance
pathogenic 8 18 6
likely pathogenic 3 0 2

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
Counsyl 0 3 0 9 0 0 3 12
GeneReviews 0 5 8 0 0 0 0 8
Invitae 0 29 0 4 0 0 1 5
OMIM 0 17 0 2 0 0 0 2
Baylor Genetics 0 10 0 1 0 0 1 2
Laboratory of Diagnosis and Therapy of Lysosomal Disorders,University of Padova 0 1 0 2 0 0 0 2
Myriad Women's Health, Inc. 0 10 0 2 0 0 0 2
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital 0 0 0 1 0 0 0 1
Natera, Inc. 0 14 0 1 0 0 0 1
Fulgent Genetics,Fulgent Genetics 0 6 0 1 0 0 0 1
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 0 0 0 1 0 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 2 0 1 0 0 0 1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 0 0 0 0 0 1 1
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 2 0 1 0 0 0 1
Undiagnosed Diseases Network,NIH 0 0 0 0 0 0 1 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Genome Diagnostics Laboratory,VU University Medical Center Amsterdam 0 2 0 1 0 0 0 1
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center 0 4 0 0 0 0 1 1
Pathology and Clinical Laboratory Medicine,King Fahad Medical City 0 1 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 31
Download table as spreadsheet
HGVS dbSNP
NM_000018.4(ACADVL):c.1405C>T (p.Arg469Trp) rs113994170
NM_000018.4(ACADVL):c.1468G>C (p.Ala490Pro) rs759775666
NM_000153.4(GALC):c.1586C>T (p.Thr529Met) rs200960659
NM_000153.4(GALC):c.1591C>T (p.Arg531Cys) rs749893889
NM_000199.5(SGSH):c.220C>T (p.Arg74Cys) rs104894636
NM_000199.5(SGSH):c.364G>A (p.Gly122Arg) rs761607612
NM_000271.5(NPC1):c.3019C>G (p.Pro1007Ala) rs80358257
NM_000282.4(PCCA):c.2040G>A (p.Ala680=) rs369982920
NM_000303.3(PMM2):c.317A>T (p.Tyr106Phe) rs387906824
NM_000303.3(PMM2):c.357C>A (p.Phe119Leu) rs80338701
NM_000303.3(PMM2):c.422G>A (p.Arg141His) rs28936415
NM_000303.3(PMM2):c.44G>C (p.Gly15Ala) rs958073558
NM_000303.3(PMM2):c.691G>A (p.Val231Met) rs80338707
NM_000310.3(PPT1):c.364A>T (p.Arg122Trp) rs137852695
NM_000310.4(PPT1):c.541G>A rs148412181
NM_000481.4(AMT):c.217C>T (p.Arg73Cys) rs386833679
NM_000487.6(ARSA):c.1114C>T (p.Arg372Trp) rs74315476
NM_000487.6(ARSA):c.465+1G>A rs80338815
NM_000744.7(CHRNA4):c.851C>T (p.Ser284Leu) rs28931591
NM_001282225.2(ADA2):c.139G>A (p.Gly47Arg) rs202134424
NM_001918.4(DBT):c.5C>T (p.Ala2Val) rs398123672
NM_002769.5(PRSS1):c.346C>T (p.Arg116Cys) rs387906698
NM_002936.6(RNASEH1):c.424G>A (p.Val142Ile) rs766294940
NM_006920.6(SCN1A):c.602+1G>A
NM_007055.4(POLR3A):c.1771-7C>G rs201314157
NM_014233.4(UBTF):c.628G>A (p.Glu210Lys) rs1555582065
NM_017882.3(CLN6):c.791CCT[1] (p.Ser265del) rs768422260
NM_020117.11(LARS1):c.1292T>A (p.Val431Asp) rs150429680
NM_183050.4(BCKDHB):c.832G>A (p.Gly278Ser) rs386834233
NM_183050.4(BCKDHB):c.853C>T (p.Arg285Ter) rs398124598
NM_206933.3(USH2A):c.15017C>T (p.Thr5006Met) rs757676723

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.