ClinVar Miner

Variants with conflicting interpretations studied for NPHP4-related condition

Minimum review status of the submission for NPHP4-related condition: Collection method of the submission for NPHP4-related condition:
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
87 26 0 5 43 0 1 46

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 conditions
NPHP4-related condition likely pathogenic uncertain significance likely benign benign
uncertain significance 1 0 1 0
likely benign 0 41 0 4
benign 0 1 1 0

Condition to condition summary #

Total conditions: 2
Download table as spreadsheet
Condition 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
not provided 0 24 0 0 43 0 1 44
not specified 0 5 0 5 0 0 0 5

All variants with conflicting interpretations #

Total variants: 46
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_015102.5(NPHP4):c.1622C>T (p.Pro541Leu) rs145255635 0.00265
NM_015102.5(NPHP4):c.4179T>A (p.Phe1393Leu) rs35641267 0.00163
NM_015102.5(NPHP4):c.3911A>G (p.His1304Arg) rs115488133 0.00124
NM_015102.5(NPHP4):c.800A>T (p.His267Leu) rs201124357 0.00124
NM_015102.5(NPHP4):c.2653A>C (p.Ser885Arg) rs112206586 0.00102
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.3851G>A (p.Arg1284His) rs61739637 0.00069
NM_015102.5(NPHP4):c.1482G>A (p.Gln494=) rs199557439 0.00064
NM_015102.5(NPHP4):c.2259C>T (p.Asp753=) rs199628481 0.00061
NM_015102.5(NPHP4):c.1935A>G (p.Leu645=) rs200104274 0.00048
NM_015102.5(NPHP4):c.3837C>T (p.Phe1279=) rs375237454 0.00040
NM_015102.5(NPHP4):c.1478C>T (p.Pro493Leu) rs201801114 0.00039
NM_015102.5(NPHP4):c.3612G>A (p.Pro1204=) rs374003717 0.00035
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.2142T>A (p.Ala714=) rs199912631 0.00026
NM_015102.5(NPHP4):c.1196A>G (p.Glu399Gly) rs117898549 0.00020
NM_015102.5(NPHP4):c.3028G>A (p.Asp1010Asn) rs200166175 0.00017
NM_015102.5(NPHP4):c.4107G>A (p.Pro1369=) rs200569946 0.00017
NM_015102.5(NPHP4):c.3309C>T (p.His1103=) rs200320780 0.00014
NM_015102.5(NPHP4):c.279+6C>T rs199856317 0.00012
NM_015102.5(NPHP4):c.3012G>A (p.Thr1004=) rs185162256 0.00009
NM_015102.5(NPHP4):c.1923C>T (p.Asn641=) rs372430727 0.00008
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.3160C>T (p.Arg1054Cys) rs373369949 0.00007
NM_015102.5(NPHP4):c.-8C>T rs375807896 0.00006
NM_015102.5(NPHP4):c.3960C>T (p.Leu1320=) rs778306754 0.00006
NM_015102.5(NPHP4):c.1851C>T (p.Ala617=) rs201192584 0.00005
NM_015102.5(NPHP4):c.1653C>T (p.Ala551=) rs751732786 0.00004
NM_015102.5(NPHP4):c.1764-5C>T rs370899989 0.00004
NM_015102.5(NPHP4):c.267C>T (p.Ile89=) rs372171438 0.00004
NM_015102.5(NPHP4):c.1408C>T (p.Arg470Trp) rs367686843 0.00003
NM_015102.5(NPHP4):c.2646C>T (p.Asp882=) rs774354969 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.3234C>G (p.Ala1078=) rs1036816659 0.00001
NM_015102.5(NPHP4):c.3927C>T (p.Asp1309=) rs377183096 0.00001
NM_015102.5(NPHP4):c.1257C>T (p.His419=) rs768393994
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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