ClinVar Miner

Variants with conflicting interpretations between Gharavi Laboratory,Columbia University and GeneDx

Minimum review status of the submission from Gharavi Laboratory,Columbia University: Collection method of the submission from Gharavi Laboratory,Columbia University:
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
0 102 0 20 17 0 15 52

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 10 1 0 0
likely pathogenic 9 0 7 1 0
uncertain significance 2 3 0 11 5
likely benign 0 1 1 0 0
benign 0 0 0 1 0

All variants with conflicting interpretations #

Total variants: 52
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_014625.4(NPHS2):c.686G>A (p.Arg229Gln) rs61747728 0.02863
NM_001360.3(DHCR7):c.199G>A (p.Ala67Thr) rs143999854 0.00093
NM_000169.3(GLA):c.376A>G (p.Ser126Gly) rs149391489 0.00063
NM_001177316.2(SLC34A3):c.575C>T (p.Ser192Leu) rs199690076 0.00059
NM_001126108.2(SLC12A3):c.37G>C (p.Ala13Pro) rs147200024 0.00048
NM_000091.5(COL4A3):c.4981C>T (p.Arg1661Cys) rs201697532 0.00038
NM_001009944.3(PKD1):c.9829C>T (p.Arg3277Cys) rs148812376 0.00032
NM_000168.6(GLI3):c.2119C>T (p.Pro707Ser) rs121917716 0.00028
NM_153240.5(NPHP3):c.2694-2_2694-1del rs751527253 0.00026
NM_020975.6(RET):c.785T>C (p.Val262Ala) rs139790943 0.00024
NM_000092.5(COL4A4):c.5045G>A (p.Arg1682Gln) rs368404711 0.00010
NM_001110556.2(FLNA):c.2609A>G (p.His870Arg) rs200679107 0.00009
NM_002968.3(SALL1):c.1738A>G (p.Ile580Val) rs761575154 0.00008
NM_017780.4(CHD7):c.2194C>G (p.Pro732Ala) rs200277422 0.00008
NM_001110556.2(FLNA):c.5116G>A (p.Gly1706Ser) rs781993685 0.00005
NM_138694.4(PKHD1):c.9530T>C (p.Ile3177Thr) rs200511261 0.00005
NM_138694.4(PKHD1):c.2414C>T (p.Pro805Leu) rs199531851 0.00004
NM_001126108.2(SLC12A3):c.1844C>T (p.Ser615Leu) rs779160677 0.00003
NM_003000.3(SDHB):c.136C>T (p.Arg46Ter) rs74315370 0.00003
NM_017780.4(CHD7):c.8356G>A (p.Gly2786Arg) rs765315726 0.00003
NM_138694.4(PKHD1):c.4870C>T (p.Arg1624Trp) rs200391019 0.00003
NM_170784.3(MKKS):c.830T>C (p.Leu277Pro) rs74315398 0.00003
NM_000069.3(CACNA1S):c.3795G>T (p.Gln1265His) rs201627041 0.00001
NM_000091.5(COL4A3):c.2452G>A (p.Gly818Arg) rs868002181 0.00001
NM_000368.5(TSC1):c.397G>A (p.Val133Ile) rs118203381 0.00001
NM_000388.4(CASR):c.1189G>A (p.Gly397Arg) rs1064794291 0.00001
NM_015559.3(SETBP1):c.2612T>C (p.Ile871Thr) rs267607038 0.00001
NM_033380.3(COL4A5):c.1276G>A (p.Gly426Arg) rs104886111 0.00001
NM_153240.5(NPHP3):c.3287T>C (p.Leu1096Pro) rs777276873 0.00001
NM_000059.4(BRCA2):c.8488-1G>A rs397507404
NM_000091.5(COL4A3):c.1504+1G>A rs1559882199
NM_000091.5(COL4A3):c.3546_3548dup (p.Gly1183dup) rs1175052474
NM_000256.3(MYBPC3):c.3815-1G>A rs397516044
NM_000335.5(SCN5A):c.3943C>T (p.Arg1315Ter) rs1553695764
NM_001005242.3(PKP2):c.1379-2047_1379-2043del rs775995156
NM_001009944.3(PKD1):c.1261C>T (p.Arg421Cys) rs1567216536
NM_001009944.3(PKD1):c.2180T>C (p.Leu727Pro) rs1616940
NM_001009944.3(PKD1):c.2494dup (p.Arg832fs) rs1567210630
NM_001009944.3(PKD1):c.7546C>T (p.Arg2516Cys) rs797044902
NM_001009944.3(PKD1):c.8447T>C (p.Leu2816Pro) rs1567177684
NM_001123385.2(BCOR):c.2423_2424delinsAC (p.Leu808His) rs1569155643
NM_001166355.2(LFNG):c.163_166dup (p.Glu56delinsGlyTer) rs34637446
NM_001374828.1(ARID1B):c.1211GAG[4] (p.Gly408_Gly411del) rs747790383
NM_001374828.1(ARID1B):c.1281GGC[5] (p.Ala433dup) rs764418312
NM_001374828.1(ARID1B):c.594GCAGCAGCAGCAGCAGCAACAGCA[1] (p.Gln207_Gln214del) rs770869529
NM_003361.4(UMOD):c.628G>A (p.Gly210Ser) rs1567309965
NM_004985.5(KRAS):c.108A>G (p.Ile36Met) rs727503109
NM_006015.6(ARID1A):c.48GCC[7] (p.Pro20_Pro21dup) rs748085214
NM_033380.3(COL4A5):c.3427G>A (p.Gly1143Ser) rs104886228
NM_033380.3(COL4A5):c.4282C>T (p.Arg1428Cys) rs144282156
NM_139058.3(ARX):c.306GGC[5] (p.Ala111_Ala115del) rs387906492
NM_139058.3(ARX):c.451_465del (p.Ala151_Ala155del) rs757588621

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