ClinVar Miner

Variants from HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas with conflicting interpretations

Location: Mexico  Primary collection method: research
Minimum review status of the submission from HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas: Collection method of the submission from HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas:
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
72 3 0 0 9 11 2 19

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
HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas pathogenic uncertain significance likely benign benign association drug response risk factor other
uncertain significance 2 0 1 9 1 4 4 1
association 0 1 0 2 0 0 0 0
likely risk allele 0 0 0 1 0 0 0 0
other 1 1 0 0 0 0 0 0

Submitter to submitter summary #

Total submitters: 21
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 0 0 0 5 2 2 9
OMIM 0 1 0 0 1 5 0 6
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan 0 0 0 0 4 2 0 6
PreventionGenetics, part of Exact Sciences 0 0 0 0 3 1 1 5
Invitae 0 0 0 0 2 2 0 4
PharmGKB 0 0 0 0 0 4 0 4
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 0 0 0 2 1 0 3
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 0 0 0 2 0 1 3
CeGaT Center for Human Genetics Tuebingen 0 0 0 0 1 1 1 3
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 0 3 0 0 3
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 0 0 0 2 0 0 2
Mayo Clinic Laboratories, Mayo Clinic 0 0 0 0 0 1 1 2
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 0 0 0 1 0 1 2
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 0 0 1 1 2
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 0 0 1 1 2
AiLife Diagnostics, AiLife Diagnostics 0 0 0 0 0 1 1 2
Mendelics 0 0 0 0 1 0 0 1
Eurofins Ntd Llc (ga) 0 1 0 0 0 0 1 1
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital 0 0 0 0 0 0 1 1
HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas 87 6 0 0 0 1 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 19
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HGVS dbSNP gnomAD frequency
NM_001065.4(TNFRSF1A):c.36A>G (p.Pro12=) rs767455 0.39963
NM_001065.4(TNFRSF1A):c.625+10A>G rs1800693 0.38055
NM_001001331.4(ATP2B2):c.1437C>T (p.Asn479=) rs2289274 0.26684
NM_005656.4(TMPRSS2):c.478G>A (p.Val160Met) rs12329760 0.25326
NM_000745.4(CHRNA5):c.1192G>A (p.Asp398Asn) rs16969968 0.24062
NM_000594.3(TNF):c.-488G>A rs1800629 0.14163
NM_001001331.4(ATP2B2):c.1551C>T (p.Gly517=) rs2289273 0.10735
NM_001289125.3(IFNAR2):c.23T>C (p.Phe8Ser) rs2229207 0.08893
NM_000602.5(SERPINE1):c.43G>A (p.Ala15Thr) rs6092 0.07905
NM_138554.5(TLR4):c.896A>G (p.Asp299Gly) rs4986790 0.06665
NM_001127701.1(SERPINA1):c.863A>T (p.Glu288Val) rs17580 0.02950
NM_000130.4(F5):c.1601G>A (p.Arg534Gln) rs6025 0.01762
NM_001127701.1(SERPINA1):c.1096G>A (p.Glu366Lys) rs28929474 0.01282
NM_000789.4(ACE):c.2306-105_2306-104insTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT rs1799752
NM_001289125.3(IFNAR2):c.-83-4640G>A
NM_001289125.3(IFNAR2):c.28T>G (p.Phe10Val) rs1051393
NM_001289125.3(IFNAR2):c.541-50A>G
NM_001289125.3(IFNAR2):c.98-43T>C
NM_002458.2(MUC5B):c.-3133G>T rs35705950

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