ClinVar Miner

Variants in gene NPHP4 with conflicting interpretations

See also:
Y axis minimum submission review status: Y axis collection method:
X axis minimum submission review status: X axis collection method:
Minimum conflict level:
Gene type:

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
1702 159 0 37 65 0 4 97

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.

pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 2 1 1 1
likely pathogenic 2 0 2 0 0
uncertain significance 1 2 0 63 9
likely benign 1 0 63 0 35
benign 1 0 9 35 0

All variants with conflicting interpretations #

Total variants: 97
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_015102.5(NPHP4):c.86C>T (p.Thr29Met) rs12142270 0.04168
NM_015102.5(NPHP4):c.1631C>G (p.Ala544Gly) rs12093500 0.02840
NM_015102.5(NPHP4):c.2542C>T (p.Arg848Trp) rs17472401 0.01606
NM_015102.5(NPHP4):c.3479C>T (p.Pro1160Leu) rs113445782 0.01120
NM_015102.5(NPHP4):c.2876G>A (p.Arg959Gln) rs12084067 0.01035
NM_015102.5(NPHP4):c.1852G>A (p.Glu618Lys) rs571655 0.01009
NM_015102.5(NPHP4):c.1542G>A (p.Pro514=) rs35264155 0.00633
NM_015102.5(NPHP4):c.3674C>T (p.Thr1225Met) rs144624477 0.00576
NM_015102.5(NPHP4):c.1442-7C>T rs146078470 0.00557
NM_015102.5(NPHP4):c.3894C>T (p.Ala1298=) rs60094861 0.00450
NM_015102.5(NPHP4):c.1705C>G (p.Gln569Glu) rs113413307 0.00443
NM_015102.5(NPHP4):c.2293G>A (p.Val765Ile) rs149244006 0.00420
NM_015102.5(NPHP4):c.511G>A (p.Ala171Thr) rs113765431 0.00408
NM_015102.5(NPHP4):c.279+11G>A rs113902159 0.00401
NM_015102.5(NPHP4):c.1503+10G>A rs41307782 0.00367
NM_015102.5(NPHP4):c.3329C>T (p.Ala1110Val) rs139767853 0.00362
NM_015102.5(NPHP4):c.2914A>G (p.Ser972Gly) rs187947581 0.00330
NM_015102.5(NPHP4):c.4237G>A (p.Asp1413Asn) rs115910810 0.00311
NM_015102.5(NPHP4):c.1622C>T (p.Pro541Leu) rs145255635 0.00265
NM_015102.5(NPHP4):c.2882G>A (p.Arg961His) rs183885357 0.00200
NM_015102.5(NPHP4):c.4179T>A (p.Phe1393Leu) rs35641267 0.00163
NM_015102.5(NPHP4):c.2519G>A (p.Ser840Asn) rs147588666 0.00147
NM_015102.5(NPHP4):c.800A>T (p.His267Leu) rs201124357 0.00124
NM_015102.5(NPHP4):c.3168C>T (p.His1056=) rs376351293 0.00121
NM_015102.5(NPHP4):c.3911A>G (p.His1304Arg) rs115488133 0.00115
NM_015102.5(NPHP4):c.271T>C (p.Phe91Leu) rs201065230 0.00109
NM_015102.5(NPHP4):c.945G>A (p.Thr315=) rs115272639 0.00105
NM_015102.5(NPHP4):c.2653A>C (p.Ser885Arg) rs112206586 0.00098
NM_015102.5(NPHP4):c.2940G>A (p.Thr980=) rs146948888 0.00087
NM_015102.5(NPHP4):c.1867A>G (p.Thr623Ala) rs35959882 0.00081
NM_015102.5(NPHP4):c.2820G>A (p.Ala940=) rs35575973 0.00078
NM_015102.5(NPHP4):c.3843G>T (p.Leu1281=) rs9662691 0.00076
NM_015102.5(NPHP4):c.2257G>A (p.Asp753Asn) rs148424288 0.00074
NM_015102.5(NPHP4):c.3851G>A (p.Arg1284His) rs61739637 0.00069
NM_015102.5(NPHP4):c.2965G>A (p.Glu989Lys) rs116606479 0.00062
NM_015102.5(NPHP4):c.4114C>T (p.Leu1372=) rs374146357 0.00061
NM_015102.5(NPHP4):c.1482G>A (p.Gln494=) rs199557439 0.00060
NM_015102.5(NPHP4):c.2259C>T (p.Asp753=) rs199628481 0.00060
NM_015102.5(NPHP4):c.1966G>A (p.Asp656Asn) rs191602135 0.00050
NM_015102.5(NPHP4):c.1935A>G (p.Leu645=) rs200104274 0.00046
NM_015102.5(NPHP4):c.3837C>T (p.Phe1279=) rs375237454 0.00040
NM_015102.5(NPHP4):c.1478C>T (p.Pro493Leu) rs201801114 0.00038
NM_015102.5(NPHP4):c.3612G>A (p.Pro1204=) rs374003717 0.00036
NM_015102.5(NPHP4):c.1120-13G>T rs192450719 0.00034
NM_015102.5(NPHP4):c.2811C>T (p.Ser937=) rs758757125 0.00034
NM_015102.5(NPHP4):c.944C>T (p.Thr315Met) rs200684272 0.00033
NM_015102.5(NPHP4):c.909C>T (p.Val303=) rs201488441 0.00030
NM_015102.5(NPHP4):c.138C>T (p.Gly46=) rs201069164 0.00028
NM_015102.5(NPHP4):c.3705C>T (p.Arg1235=) rs199925943 0.00028
NM_015102.5(NPHP4):c.1632C>T (p.Ala544=) rs201903713 0.00025
NM_015102.5(NPHP4):c.3105G>A (p.Pro1035=) rs151151838 0.00025
NM_015102.5(NPHP4):c.3175G>A (p.Ala1059Thr) rs202004152 0.00024
NM_015102.5(NPHP4):c.2142T>A (p.Ala714=) rs199912631 0.00023
NM_015102.5(NPHP4):c.1440G>A (p.Ser480=) rs374690894 0.00021
NM_015102.5(NPHP4):c.1196A>G (p.Glu399Gly) rs117898549 0.00020
NM_015102.5(NPHP4):c.3044+20C>T rs372051668 0.00019
NM_015102.5(NPHP4):c.1923C>T (p.Asn641=) rs372430727 0.00017
NM_015102.5(NPHP4):c.2716C>T (p.Arg906Cys) rs199992272 0.00017
NM_015102.5(NPHP4):c.3028G>A (p.Asp1010Asn) rs200166175 0.00017
NM_015102.5(NPHP4):c.4107G>A (p.Pro1369=) rs200569946 0.00016
NM_015102.5(NPHP4):c.3309C>T (p.His1103=) rs200320780 0.00014
NM_015102.5(NPHP4):c.3174C>T (p.Thr1058=) rs374354239 0.00013
NM_015102.5(NPHP4):c.279+6C>T rs199856317 0.00012
NM_015102.5(NPHP4):c.122C>T (p.Pro41Leu) rs754311690 0.00011
NM_015102.5(NPHP4):c.2029C>T (p.Pro677Ser) rs547495754 0.00011
NM_015102.5(NPHP4):c.1462C>T (p.Arg488Ter) rs778043242 0.00009
NM_015102.5(NPHP4):c.1764-5C>T rs370899989 0.00009
NM_015102.5(NPHP4):c.2807C>T (p.Thr936Met) rs201074950 0.00008
NM_015102.5(NPHP4):c.2952G>A (p.Thr984=) rs375493384 0.00008
NM_015102.5(NPHP4):c.2902G>A (p.Ala968Thr) rs375090704 0.00007
NM_015102.5(NPHP4):c.3012G>A (p.Thr1004=) rs185162256 0.00007
NM_015102.5(NPHP4):c.3160C>T (p.Arg1054Cys) rs373369949 0.00007
NM_015102.5(NPHP4):c.2238C>T (p.Thr746=) rs756449736 0.00006
NM_015102.5(NPHP4):c.3960C>T (p.Leu1320=) rs778306754 0.00006
NM_015102.5(NPHP4):c.-8C>T rs375807896 0.00005
NM_015102.5(NPHP4):c.1408C>T (p.Arg470Trp) rs367686843 0.00005
NM_015102.5(NPHP4):c.1851C>T (p.Ala617=) rs201192584 0.00005
NM_015102.5(NPHP4):c.2886G>A (p.Thr962=) rs368320071 0.00005
NM_015102.5(NPHP4):c.1653C>T (p.Ala551=) rs751732786 0.00004
NM_015102.5(NPHP4):c.267C>T (p.Ile89=) rs372171438 0.00004
NM_015102.5(NPHP4):c.4075C>T (p.Arg1359Trp) rs369162678 0.00004
NM_015102.5(NPHP4):c.2611+1G>A rs374141736 0.00003
NM_015102.5(NPHP4):c.2646C>T (p.Asp882=) rs774354969 0.00003
NM_015102.5(NPHP4):c.3417G>A (p.Pro1139=) rs371527260 0.00003
NM_015102.5(NPHP4):c.3348C>T (p.Ile1116=) rs751938743 0.00002
NM_015102.5(NPHP4):c.578C>T (p.Pro193Leu) rs779760001 0.00002
NM_015102.5(NPHP4):c.1075C>T (p.Gln359Ter) rs1430741326 0.00001
NM_015102.5(NPHP4):c.3234C>G (p.Ala1078=) rs1036816659 0.00001
NM_015102.5(NPHP4):c.3927C>T (p.Asp1309=) rs377183096 0.00001
NM_015102.5(NPHP4):c.4143C>T (p.Val1381=) rs766613810 0.00001
NM_015102.5(NPHP4):c.4182G>A (p.Ala1394=) rs754549864 0.00001
NM_015102.5(NPHP4):c.510C>T (p.Pro170=) rs545943420 0.00001
NM_015102.5(NPHP4):c.1257C>T (p.His419=) rs768393994
NM_015102.5(NPHP4):c.136-4del rs143323188
NM_015102.5(NPHP4):c.2250C>T (p.Asp750=) rs201090359
NM_015102.5(NPHP4):c.3758G>A (p.Arg1253Gln) rs560944258
NM_015102.5(NPHP4):c.594G>C (p.Ala198=) rs141538649

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