ClinVar Miner

Variants from Chinese Inherited Urolithiasis Consortium, The Affiliated Yantai Yuhuangding Hospital of Qingdao University with conflicting interpretations

Location: China  Primary collection method: clinical testing
Minimum review status of the submission from Chinese Inherited Urolithiasis Consortium, The Affiliated Yantai Yuhuangding Hospital of Qingdao University: Collection method of the submission from Chinese Inherited Urolithiasis Consortium, The Affiliated Yantai Yuhuangding Hospital of Qingdao University:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
64 33 0 28 0 0 17 44

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
Chinese Inherited Urolithiasis Consortium, The Affiliated Yantai Yuhuangding Hospital of Qingdao University pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 16 3 0 0
likely pathogenic 12 0 12 5 1

Submitter to submitter summary #

Total submitters: 24
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 24 0 7 0 0 9 16
Clinical Biochemistry Laboratory, Health Services Laboratory 0 25 0 8 0 0 0 8
Illumina Laboratory Services, Illumina 0 0 0 0 0 0 8 8
Natera, Inc. 0 26 0 2 0 0 4 6
Baylor Genetics 0 12 0 5 0 0 0 5
Labcorp Genetics (formerly Invitae), Labcorp 0 3 0 2 0 0 2 4
Rare Kidney Stone Consortium and the Mayo Clinic Hyperoxaluria Center, Mayo Clinic 0 5 0 2 0 0 1 3
3billion 0 4 0 2 0 0 0 2
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 1 0 1 0 0 1 2
OMIM 0 8 0 2 0 0 0 2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 3 0 2 0 0 0 2
Arcensus 0 0 0 1 0 0 0 1
Counsyl 0 5 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 1 0 0 0 1
Department of Urology, Hunan Children's Hospital 0 1 0 0 0 0 1 1
Genetics and Genomic Medicine Centre, NeuroGen Healthcare, NeuroGen Healthcare 0 0 0 1 0 0 0 1
Juno Genomics, Hangzhou Juno Genomics, Inc 0 4 0 1 0 0 0 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 0 0 0 0 0 1 1
Laboratory of Cyto-molecular Genetics, Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 0 0 0 1 0 0 0 1
Myriad Genetics, Inc. 0 3 0 1 0 0 0 1
Revvity Omics, Revvity 0 5 0 1 0 0 0 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 3 0 1 0 0 0 1
Yan Lab, Department of Urology, Pediatric Urolith Center, National Clinical Research Center for Child Health, The Children’s Hospital of Zhejiang University School of Medicine 0 2 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 44
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000341.4(SLC3A1):c.566C>T (p.Thr189Met) rs140317484 0.00287
NM_012203.2(GRHPR):c.512G>A (p.Arg171His) rs200106110 0.00151
NM_014270.5(SLC7A9):c.1403C>T (p.Pro468Leu) rs80283711 0.00089
NM_014270.5(SLC7A9):c.-26G>T rs375495587 0.00042
NM_014270.5(SLC7A9):c.829G>A (p.Val277Met) rs147344717 0.00024
NM_138413.4(HOGA1):c.554C>T (p.Thr185Met) rs115282699 0.00024
NM_000203.5(IDUA):c.299+3558C>T rs201219683 0.00017
NM_001177316.2(SLC34A3):c.1612C>T (p.Arg538Trp) rs140319849 0.00017
NM_000341.4(SLC3A1):c.1136+2T>C rs766198611 0.00012
NM_138413.4(HOGA1):c.834G>A (p.Ala278=) rs770050262 0.00006
NM_000341.4(SLC3A1):c.1093C>T (p.Arg365Trp) rs765828196 0.00005
NM_138413.4(HOGA1):c.811C>T (p.Arg271Cys) rs367741588 0.00005
NM_000030.3(AGXT):c.484G>A (p.Val162Met) rs147497484 0.00004
NM_000342.4(SLC4A1):c.2102G>A (p.Gly701Asp) rs121912748 0.00004
NM_014270.5(SLC7A9):c.511C>T (p.Arg171Trp) rs758242098 0.00004
NM_138413.4(HOGA1):c.443C>T (p.Ala148Val) rs149896778 0.00004
NM_138413.4(HOGA1):c.769T>G (p.Cys257Gly) rs267606764 0.00004
NM_000379.4(XDH):c.445C>T (p.Arg149Cys) rs72549369 0.00003
NM_138413.4(HOGA1):c.763C>T (p.Arg255Ter) rs796052086 0.00003
NM_138413.4(HOGA1):c.812G>A (p.Arg271His) rs750974539 0.00003
NM_000341.4(SLC3A1):c.1011G>A (p.Pro337=) rs772810111 0.00002
NM_000341.4(SLC3A1):c.1085G>A (p.Arg362His) rs121912697 0.00002
NM_000030.3(AGXT):c.2T>C (p.Met1Thr) rs138584408 0.00001
NM_006580.4(CLDN16):c.437G>A (p.Arg146His) rs772241737 0.00001
NM_012203.2(GRHPR):c.181G>A (p.Asp61Asn) rs371660673 0.00001
NM_012203.2(GRHPR):c.337G>A (p.Glu113Lys) rs180177307 0.00001
NM_138413.4(HOGA1):c.290G>A (p.Arg97His) rs752252343 0.00001
NM_000030.3(AGXT):c.1049G>A (p.Gly350Asp) rs180177156
NM_000030.3(AGXT):c.1161C>A (p.Cys387Ter) rs2528766716
NM_000030.3(AGXT):c.32C>G (p.Pro11Arg) rs34116584
NM_000030.3(AGXT):c.577del (p.Leu193fs) rs180177241
NM_000030.3(AGXT):c.662_664del (p.Ser221del) rs796052071
NM_000341.4(SLC3A1):c.1364C>T (p.Ser455Leu)
NM_000341.4(SLC3A1):c.1373G>T (p.Gly458Val)
NM_000341.4(SLC3A1):c.283G>A (p.Ala95Thr)
NM_000341.4(SLC3A1):c.430+1G>A
NM_000341.4(SLC3A1):c.679C>T (p.Arg227Trp)
NM_000342.4(SLC4A1):c.1765C>T (p.Arg589Cys) rs121912745
NM_012203.2(GRHPR):c.160G>A (p.Gly54Ser) rs756085471
NM_012203.2(GRHPR):c.404+3_404+6del rs180177309
NM_012203.2(GRHPR):c.83+1G>C rs1822898131
NM_014270.5(SLC7A9):c.878T>C (p.Phe293Ser) rs1968696030
NM_138413.4(HOGA1):c.110G>A (p.Gly37Asp) rs772722925
NM_138413.4(HOGA1):c.212-1G>A rs1209105017

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