ClinVar Miner

Variants from National Health Laboratory Service, Universitas Academic Hospital and University of the Free State with conflicting interpretations

Location: South Africa  Primary collection method: clinical testing
Minimum review status of the submission from National Health Laboratory Service, Universitas Academic Hospital and University of the Free State: Collection method of the submission from National Health Laboratory Service, Universitas Academic Hospital and University of the Free State:
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
704 181 0 88 42 1 2 125

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
National Health Laboratory Service, Universitas Academic Hospital and University of the Free State pathogenic likely pathogenic uncertain significance likely benign benign pathogenic, low penetrance
pathogenic 0 3 1 0 0 1
likely pathogenic 1 0 0 1 1 0
uncertain significance 0 0 0 12 8 0
likely benign 0 0 18 0 44 0
benign 0 0 7 40 0 0

Submitter to submitter summary #

Total submitters: 15
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
Invitae 0 208 0 53 29 1 2 85
Genetics Program, Instituto Nacional de Cancer 0 62 0 19 5 0 0 24
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C. 0 26 0 15 4 0 0 19
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia 0 5 0 10 5 0 0 15
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 102 0 10 0 0 0 10
Mendelics 0 6 0 0 3 0 1 4
Hereditary Cancer Genetics group, Vall d'Hebron Institute of Oncology 0 1 0 2 1 0 0 3
CSER _CC_NCGL, University of Washington 0 1 0 1 1 0 0 2
Molecular Oncology Research Center, Barretos Cancer Hospital 0 0 0 0 2 0 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 16 0 1 0 0 0 1
Illumina Laboratory Services, Illumina 0 4 0 1 0 0 0 1
Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency 0 2 0 0 1 0 0 1
Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto 0 29 0 1 0 0 0 1
Cancer Variant Interpretation Group UK, Institute of Cancer Research, London 0 0 0 1 0 0 0 1
Cancer Genomics Group, Japanese Foundation For Cancer Research 0 2 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 125
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000059.4(BRCA2):c.5744C>T (p.Thr1915Met) rs4987117 0.01834
NM_007294.4(BRCA1):c.*36C>G rs3092995 0.01385
NM_007294.4(BRCA1):c.3119G>A (p.Ser1040Asn) rs4986852 0.01109
NM_000059.4(BRCA2):c.8487+19A>G rs11571743 0.01055
NM_007294.4(BRCA1):c.3418A>G (p.Ser1140Gly) rs2227945 0.01054
NM_007294.4(BRCA1):c.212+23T>A rs8176128 0.01018
NM_000059.4(BRCA2):c.7319A>G (p.His2440Arg) rs4986860 0.00984
NM_007294.4(BRCA1):c.2458A>G (p.Lys820Glu) rs56082113 0.00964
NM_000059.4(BRCA2):c.3264T>C (p.Pro1088=) rs36060526 0.00793
NM_000059.4(BRCA2):c.7017G>C (p.Lys2339Asn) rs45574331 0.00792
NM_000059.4(BRCA2):c.9730G>A (p.Val3244Ile) rs11571831 0.00792
NM_000059.4(BRCA2):c.1788T>C (p.Asp596=) rs11571642 0.00768
NM_000059.4(BRCA2):c.9976A>T (p.Lys3326Ter) rs11571833 0.00597
NM_000059.4(BRCA2):c.7008-62A>G rs76584943 0.00439
NM_000051.4(ATM):c.1810C>T (p.Pro604Ser) rs2227922 0.00431
NM_007294.4(BRCA1):c.4039A>G (p.Arg1347Gly) rs28897689 0.00419
NM_000059.4(BRCA2):c.9648+54G>A rs11571823 0.00369
NM_000059.4(BRCA2):c.6412G>T (p.Val2138Phe) rs11571659 0.00346
NM_000059.4(BRCA2):c.1275A>G (p.Glu425=) rs34355306 0.00335
NM_000059.4(BRCA2):c.3869G>A (p.Cys1290Tyr) rs41293485 0.00307
NM_007294.4(BRCA1):c.557C>A (p.Ser186Tyr) rs55688530 0.00301
NM_000059.4(BRCA2):c.4068G>A (p.Leu1356=) rs28897724 0.00295
NM_000059.4(BRCA2):c.4681C>A (p.His1561Asn) rs2219594 0.00292
NM_000059.4(BRCA2):c.7805+6C>G rs81002819 0.00290
NM_000059.4(BRCA2):c.5640T>G (p.Asn1880Lys) rs11571657 0.00288
NM_000059.4(BRCA2):c.68-7T>A rs81002830 0.00277
NM_000059.4(BRCA2):c.6100C>T (p.Arg2034Cys) rs1799954 0.00268
NM_000059.4(BRCA2):c.6220C>A (p.His2074Asn) rs34309943 0.00264
NM_007294.4(BRCA1):c.4535G>T (p.Ser1512Ile) rs1800744 0.00240
NM_000059.4(BRCA2):c.7626G>A (p.Thr2542=) rs61754138 0.00228
NM_007294.4(BRCA1):c.2167A>G (p.Asn723Asp) rs4986845 0.00209
NM_000059.4(BRCA2):c.7150C>A (p.Gln2384Lys) rs55977008 0.00203
NM_000059.4(BRCA2):c.231T>G (p.Thr77=) rs114446594 0.00191
NM_007294.4(BRCA1):c.5277+48_5277+59dup rs572766355 0.00187
NM_007294.4(BRCA1):c.2814A>G (p.Pro938=) rs80356851 0.00183
NM_007294.4(BRCA1):c.21C>T (p.Arg7=) rs149402012 0.00165
NM_000059.4(BRCA2):c.125A>G (p.Tyr42Cys) rs4987046 0.00158
NM_000059.4(BRCA2):c.8567A>C (p.Glu2856Ala) rs11571747 0.00158
NM_007294.4(BRCA1):c.4113G>A (p.Gly1371=) rs147448807 0.00150
NM_007294.4(BRCA1):c.4682C>T (p.Thr1561Ile) rs56158747 0.00150
NM_007294.4(BRCA1):c.4600G>A (p.Val1534Met) rs55815649 0.00145
NM_000059.4(BRCA2):c.9634G>C (p.Gly3212Arg) rs55775473 0.00141
NM_000059.4(BRCA2):c.2138A>T (p.Gln713Leu) rs55816687 0.00138
NM_000059.4(BRCA2):c.10110G>A (p.Arg3370=) rs28897762 0.00132
NM_000546.6(TP53):c.139C>T (p.Pro47Ser) rs1800371 0.00123
NM_007294.4(BRCA1):c.591C>T (p.Cys197=) rs1799965 0.00117
NM_000059.4(BRCA2):c.175C>G (p.Pro59Ala) rs56091799 0.00108
NM_000059.4(BRCA2):c.9235G>A (p.Val3079Ile) rs55933907 0.00106
NM_007294.4(BRCA1):c.3083G>A (p.Arg1028His) rs80357459 0.00106
NM_000059.4(BRCA2):c.2883G>A (p.Gln961=) rs11571655 0.00097
NM_000059.4(BRCA2):c.-15A>C rs138705202 0.00066
NM_007294.4(BRCA1):c.81-12C>G rs80358055 0.00066
NM_007294.4(BRCA1):c.3024G>A (p.Met1008Ile) rs1800704 0.00065
NM_007294.4(BRCA1):c.4840C>T (p.Pro1614Ser) rs70953660 0.00065
NM_007294.4(BRCA1):c.5348T>C (p.Met1783Thr) rs55808233 0.00058
NM_007294.4(BRCA1):c.301+8T>C rs80358101 0.00054
NM_000059.4(BRCA2):c.7435+6G>A rs81002852 0.00053
NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) rs77130927 0.00051
NM_000059.4(BRCA2):c.9720T>C (p.Val3240=) rs80359810 0.00048
NM_000059.4(BRCA2):c.7976+12G>A rs81002827 0.00045
NM_000059.4(BRCA2):c.322A>C (p.Asn108His) rs80358567 0.00034
NM_000059.4(BRCA2):c.6853A>G (p.Ile2285Val) rs56272235 0.00026
NM_000059.4(BRCA2):c.317-22C>T rs81002794 0.00024
NM_000059.4(BRCA2):c.467A>G (p.Asp156Gly) rs68071147 0.00022
NM_000059.4(BRCA2):c.5312G>A (p.Gly1771Asp) rs80358755 0.00021
NM_007294.4(BRCA1):c.2477C>A (p.Thr826Lys) rs28897683 0.00021
NM_007294.4(BRCA1):c.3804T>C (p.Asn1268=) rs140588714 0.00021
NM_000059.4(BRCA2):c.1123C>T (p.Pro375Ser) rs80358408 0.00019
NM_000059.4(BRCA2):c.7805+13A>G rs149769332 0.00019
NM_000059.4(BRCA2):c.9770A>G (p.Lys3257Arg) rs55847618 0.00019
NM_000059.4(BRCA2):c.7712A>G (p.Glu2571Gly) rs55689095 0.00018
NM_000059.4(BRCA2):c.3445A>G (p.Met1149Val) rs80358589 0.00013
NM_000059.4(BRCA2):c.9875C>T (p.Pro3292Leu) rs56121817 0.00009
NM_000059.4(BRCA2):c.9501+3A>T rs61757642 0.00008
NM_007294.4(BRCA1):c.593+3G>A rs80358013 0.00007
NM_007294.4(BRCA1):c.692C>T (p.Thr231Met) rs80357001 0.00007
NM_000059.4(BRCA2):c.1011C>T (p.Asn337=) rs41293473 0.00006
NM_000059.4(BRCA2):c.7051G>A (p.Ala2351Thr) rs80358930 0.00006
NM_007294.4(BRCA1):c.1724A>G (p.Glu575Gly) rs111539978 0.00006
NM_000059.4(BRCA2):c.5985C>T (p.Asn1995=) rs374620036 0.00005
NM_007294.4(BRCA1):c.4046C>T (p.Thr1349Met) rs80357345 0.00005
NM_000465.4(BARD1):c.773T>C (p.Ile258Thr) rs146223579 0.00004
NM_007294.4(BRCA1):c.2669G>T (p.Gly890Val) rs80356874 0.00004
NM_000059.4(BRCA2):c.5986G>A (p.Ala1996Thr) rs80358833 0.00003
NM_000059.4(BRCA2):c.8010G>A (p.Ser2670=) rs146430937 0.00003
NM_007294.4(BRCA1):c.3362A>G (p.Asn1121Ser) rs80356919 0.00003
NM_000059.4(BRCA2):c.10154G>A (p.Arg3385His) rs80358398 0.00002
NM_000059.4(BRCA2):c.2299A>C (p.Ser767Arg) rs750755676 0.00002
NM_007294.4(BRCA1):c.509G>A (p.Arg170Gln) rs80357264 0.00002
NM_000059.4(BRCA2):c.10023C>T (p.Asp3341=) rs113507014 0.00001
NM_000059.4(BRCA2):c.6231G>C (p.Lys2077Asn) rs541826447 0.00001
NM_000059.4(BRCA2):c.7759C>T (p.Leu2587Phe) rs56335340 0.00001
NM_000059.4(BRCA2):c.927A>G (p.Ser309=) rs80359806 0.00001
NM_000059.4(BRCA2):c.9396A>G (p.Lys3132=) rs201172050 0.00001
NM_000059.4(BRCA2):c.987G>A (p.Arg329=) rs561002197 0.00001
NM_007294.4(BRCA1):c.2597G>A (p.Arg866His) rs80356911 0.00001
NM_007294.4(BRCA1):c.5096G>A (p.Arg1699Gln) rs41293459 0.00001
NM_000059.4(BRCA2):c.10102T>C (p.Ser3368Pro) rs786205482
NM_000059.4(BRCA2):c.1166C>A (p.Pro389Gln) rs397507263
NM_000059.4(BRCA2):c.1780A>G (p.Ile594Val) rs431825287
NM_000059.4(BRCA2):c.3858_3860del (p.Lys1286del) rs80359406
NM_000059.4(BRCA2):c.4143AGA[1] (p.Glu1382del) rs80359432
NM_000059.4(BRCA2):c.425+5G>C rs1388671241
NM_000059.4(BRCA2):c.4502A>G (p.Asn1501Ser) rs545444016
NM_000059.4(BRCA2):c.4795AAT[1] (p.Asn1600del) rs276174851
NM_000059.4(BRCA2):c.5095G>A (p.Asp1699Asn) rs80358731
NM_000059.4(BRCA2):c.516G>A (p.Lys172=) rs80359790
NM_000059.4(BRCA2):c.5610C>G (p.Phe1870Leu) rs1060504598
NM_000059.4(BRCA2):c.67+16A>G rs529148674
NM_000059.4(BRCA2):c.7625C>T (p.Thr2542Met) rs80358989
NM_000059.4(BRCA2):c.7762A>G (p.Ile2588Val) rs2137567485
NM_000059.4(BRCA2):c.8168A>T (p.Asp2723Val) rs41293513
NM_000059.4(BRCA2):c.8954-2A>G rs1135401928
NM_007294.4(BRCA1):c.1168G>A (p.Asp390Asn) rs2154472475
NM_007294.4(BRCA1):c.14C>T (p.Ala5Val) rs1335137805
NM_007294.4(BRCA1):c.1843TCT[1] (p.Ser616del) rs80358329
NM_007294.4(BRCA1):c.2120G>A (p.Gly707Asp) rs80357192
NM_007294.4(BRCA1):c.2619A>T (p.Ser873=) rs1597868763
NM_007294.4(BRCA1):c.3328_3330del (p.Lys1110del) rs80358335
NM_007294.4(BRCA1):c.3600G>C (p.Gln1200His) rs56214134
NM_007294.4(BRCA1):c.4186-10G>A rs80358172
NM_007294.4(BRCA1):c.4973C>A (p.Thr1658Asn) rs1015073230
NM_007294.4(BRCA1):c.663A>G (p.Ala221=) rs375952040
NM_007294.4(BRCA1):c.671-12del rs273902781
NM_007294.4(BRCA1):c.81-13C>G rs56328013

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