ClinVar Miner

Variants from Centre for Genomic and Experimental Medicine,University of Edinburgh with conflicting interpretations

Location: United Kingdom — Primary collection method: research
Minimum review status of the submission from Centre for Genomic and Experimental Medicine,University of Edinburgh: Collection method of the submission from Centre for Genomic and Experimental Medicine,University of Edinburgh:
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 Variants with at least 2 submissions 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 kind of conflict
45 9 0 13 2 2 15 30

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 Genomic and Experimental Medicine,University of Edinburgh pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 6 3 0 0
likely pathogenic 6 0 11 5 2
uncertain significance 0 0 0 1 0
likely benign 0 0 1 0 1
other 2 0 0 0 0

Submitter to submitter summary #

Total submitters: 27
Download table as spreadsheet
Submitter Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
GeneDx 0 8 0 4 0 1 9 14
Invitae 0 6 0 3 1 0 9 13
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 3 0 0 1 0 5 6
Integrated Genetics/Laboratory Corporation of America 0 2 0 2 0 0 3 5
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 1 0 3 0 0 1 4
Ambry Genetics 0 4 0 2 0 0 2 4
OMIM 0 5 0 3 0 0 0 3
Fulgent Genetics 0 0 0 2 0 0 1 3
CeGaT Praxis fuer Humangenetik Tuebingen 0 0 0 0 1 0 2 3
Center for Human Genetics, Inc 0 4 0 0 0 0 2 2
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 4 0 0 1 0 1 2
CSER_CC_NCGL; University of Washington Medical Center 0 0 0 0 0 0 2 2
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital 0 0 0 1 0 0 0 1
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario 0 0 0 1 0 0 0 1
Genetic Services Laboratory, University of Chicago 0 1 0 0 0 0 1 1
Genome Diagnostics Laboratory,University Medical Center Utrecht 0 0 0 0 0 0 1 1
Counsyl 0 0 0 1 0 0 0 1
GeneReviews 0 1 0 1 0 0 0 1
Blueprint Genetics, 0 1 0 1 0 0 0 1
Illumina Clinical Services Laboratory,Illumina 0 1 0 0 0 0 1 1
Center for Medical Genetics Ghent,University of Ghent 0 6 0 1 0 0 0 1
Stanford Center for Inherited Cardiovascular Disease,Stanford University 0 0 0 1 0 0 0 1
University of Washington Center for Mendelian Genomics,University of Washington 0 0 0 1 0 0 0 1
Color 0 0 0 0 0 0 1 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Dan Cohn Lab,University Of California Los Angeles 0 0 0 0 0 1 0 1
Genome Diagnostics Laboratory,VU University Medical Center Amsterdam 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 30
Download table as spreadsheet
HGVS dbSNP
NM_000088.3(COL1A1):c.1042G>A (p.Ala348Thr) rs139955975
NM_000088.3(COL1A1):c.2932C>T (p.Pro978Ser) rs193922153
NM_000090.3(COL3A1):c.1204G>A (p.Gly402Ser) rs1064797017
NM_000090.3(COL3A1):c.1744G>A (p.Gly582Ser) rs121912923
NM_000138.4(FBN1):c.1468+5G>A rs397515757
NM_000138.4(FBN1):c.2306G>A (p.Cys769Tyr) rs794728190
NM_000138.4(FBN1):c.2645C>T (p.Ala882Val) rs794728195
NM_000138.4(FBN1):c.3012C>G (p.Tyr1004Ter) rs397515784
NM_000138.4(FBN1):c.3193delG (p.Glu1065Lysfs) rs193922198
NM_000138.4(FBN1):c.59A>G (p.Tyr20Cys) rs201309310
NM_000138.4(FBN1):c.7039_7040delAT (p.Met2347Valfs) rs794728319
NM_001008212.1(OPTN):c.941A>T (p.Gln314Leu) rs142812715
NM_001040113.1(MYH11):c.5294G>A (p.Arg1765Gln) rs142546324
NM_002474.2(MYH11):c.4861A>C (p.Lys1621Gln) rs34321232
NM_003242.5(TGFBR2):c.1489C>T (p.Arg497Ter) rs863223852
NM_003242.5(TGFBR2):c.1609C>T (p.Arg537Cys) rs104893809
NM_007375.3(TARDBP):c.859G>A (p.Gly287Ser) rs80356719
NM_012224.2(NEK1):c.1021G>A (p.Ala341Thr) rs189186475
NM_012224.2(NEK1):c.1137T>A (p.Asp379Glu) rs372585344
NM_012224.2(NEK1):c.1705T>A (p.Phe569Ile) rs776098853
NM_012224.2(NEK1):c.2053G>A (p.Val685Met) rs199827465
NM_012224.2(NEK1):c.214+1G>A rs1049502301
NM_012224.2(NEK1):c.2151T>G (p.Asn717Lys) rs34324114
NM_012224.2(NEK1):c.695G>A (p.Arg232His) rs772747361
NM_012224.2(NEK1):c.782G>A (p.Arg261His) rs200161705
NM_013254.3(TBK1):c.1330C>T (p.Arg444Ter) rs142030898
NM_013254.3(TBK1):c.829C>G (p.Leu277Val) rs905184241
NM_030777.3(SLC2A10):c.394C>T (p.Arg132Trp) rs121908173
NM_053025.3(MYLK):c.5275T>C (p.Ser1759Pro) rs387906781
NM_147127.4(EVC2):c.3141G>A (p.Trp1047Ter) rs886037764

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