ClinVar Miner

Variants from Molecular Genetics laboratory, Necker Hospital with conflicting interpretations

Location: France  Primary collection method: clinical testing
Minimum review status of the submission from Molecular Genetics laboratory, Necker Hospital: Collection method of the submission from Molecular Genetics laboratory, Necker 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
160 37 0 26 0 0 13 35

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
Molecular Genetics laboratory, Necker Hospital pathogenic likely pathogenic uncertain significance
pathogenic 0 10 8
likely pathogenic 16 0 5

Submitter to submitter summary #

Total submitters: 18
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
GeneDx 0 32 0 13 0 0 2 15
Invitae 0 14 0 7 0 0 2 9
CeGaT Center for Human Genetics Tuebingen 0 14 0 2 0 0 2 4
Athena Diagnostics Inc 0 1 0 1 0 0 2 3
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 5 0 2 0 0 0 2
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 3 0 1 0 0 1 2
Baylor Genetics 0 0 0 1 0 0 0 1
PreventionGenetics, part of Exact Sciences 0 7 0 1 0 0 0 1
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes 0 1 0 1 0 0 0 1
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden 0 2 0 1 0 0 0 1
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 0 3 0 1 0 0 0 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 0 0 1 0 0 0 1
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System 0 0 0 0 0 0 1 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 4 0 0 0 0 1 1
AiLife Diagnostics, AiLife Diagnostics 0 0 0 1 0 0 0 1
Genome-Nilou Lab 0 1 0 0 0 0 1 1
Neuberg Centre For Genomic Medicine, NCGM 0 0 0 0 0 0 1 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 1 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 35
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_025216.3(WNT10A):c.682T>A (p.Phe228Ile) rs121908120 0.01450
NM_001278512.2(AP3B2):c.2978_2979del (p.Pro993fs) rs1347618037 0.00001
NM_020451.3(SELENON):c.1396C>T (p.Arg466Trp) rs752156505 0.00001
NM_000188.3(HK1):c.1334C>T (p.Ser445Leu) rs1064794848
NM_000531.6(OTC):c.1009G>T (p.Val337Phe) rs72558487
NM_000531.6(OTC):c.608C>T (p.Ser203Phe) rs72558410
NM_000531.6(OTC):c.77+5G>C rs72552302
NM_001012426.2(FOXP4):c.1540G>A (p.Ala514Thr) rs2127404974
NM_001039591.3(USP9X):c.82dup (p.Leu28fs) rs758083405
NM_001101.5(ACTB):c.1043C>T (p.Ser348Leu) rs886041309
NM_001123385.2(BCOR):c.4936dup (p.Leu1646fs) rs748074364
NM_001130021.3(ATP6V0A1):c.2219G>A (p.Arg740Gln) rs1567871600
NM_001136035.4(TRMT1):c.1168C>T (p.Arg390Ter)
NM_001170629.2(CHD8):c.727C>T (p.Arg243Ter) rs1555318552
NM_001172509.2(SATB2):c.1573G>A (p.Glu525Lys)
NM_001197104.2(KMT2A):c.3460C>T (p.Arg1154Trp) rs1555038090
NM_001282531.3(ADNP):c.2496_2499del (p.Asn832fs) rs587777523
NM_001348323.3(TRIP12):c.4302_4303del (p.Tyr1435fs) rs2154259932
NM_001353345.2(SETD1B):c.4170_4171del (p.Gly1392fs) rs2137578021
NM_002804.5(PSMC3):c.782T>C (p.Ile261Thr)
NM_003002.4(SDHD):c.436G>C (p.Asp146His)
NM_003042.4(SLC6A1):c.1531G>A (p.Val511Met) rs1064794981
NM_003470.3(USP7):c.841A>G (p.Lys281Glu) rs2141203936
NM_006306.4(SMC1A):c.793_795del (p.Glu265del) rs1602413408
NM_006772.3(SYNGAP1):c.1167_1168del (p.Gly391fs) rs1060503378
NM_006940.6(SOX5):c.1711C>T (p.Arg571Trp) rs1565669640
NM_012154.5(AGO2):c.2140C>T (p.Arg714Trp) rs866981753
NM_013328.4(PYCR2):c.596G>A (p.Arg199Gln)
NM_016188.5(ACTL6B):c.1027G>A (p.Gly343Arg) rs1131692228
NM_017934.7(PHIP):c.328C>T (p.Arg110Cys) rs768324201
NM_020771.4(HACE1):c.2487TCT[1] (p.Leu832del) rs869025283
NM_052867.4(NALCN):c.4004G>A (p.Ser1335Asn) rs2139471533
NM_078480.3(PUF60):c.449_457del (p.Ala150_Phe152del) rs1131692232
NM_078480.3(PUF60):c.590dup (p.Arg198fs) rs1057518046
NM_138927.4(SON):c.5753_5756del (p.Val1918fs) rs886039773

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