ClinVar Miner

Variants with conflicting interpretations studied for Anophthalmia-microphthalmia syndrome

Coded as:
Minimum review status of the submission for Anophthalmia-microphthalmia syndrome: Collection method of the submission for Anophthalmia-microphthalmia syndrome:
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
182 96 0 24 42 1 6 68

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
Anophthalmia-microphthalmia syndrome pathogenic likely pathogenic uncertain significance likely benign benign protective other
pathogenic 0 1 2 0 0 0 0
likely pathogenic 1 0 1 3 1 1 1
uncertain significance 0 1 0 17 18 0 0
likely benign 0 0 12 0 16 0 0
benign 0 0 2 6 0 0 0

Condition to condition summary #

Total conditions: 41
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 31 0 8 27 1 5 38
carboxymethyl-dextran-A2-gadolinium-DOTA 0 86 0 8 18 0 0 26
not specified 0 6 0 7 3 0 1 10
OTX2-Related Syndromic Microphthalmia 0 2 0 2 2 0 0 4
Syndromic Microphthalmia, Dominant 0 1 0 1 2 0 0 3
16p13.2-p13.13 microduplication syndrome 0 0 0 1 0 0 0 1
1q24q25 microdeletion syndrome 0 0 0 1 0 0 0 1
22q13.3 interstitial deletion 0 0 0 1 0 0 0 1
ATAD3 gene cluster related condition 0 0 0 0 0 0 1 1
Abnormality of refraction 0 0 0 0 1 0 0 1
Aminoaciduria 0 0 0 1 0 0 0 1
Arthrogryphosis 0 0 0 0 0 0 1 1
Atypical behavior; Low-set ears; Prominent nasal bridge; Underdeveloped nasal alae; Intellectual disability, mild; Secondary microcephaly 0 0 0 0 0 0 1 1
Atypical behavior; Moderate global developmental delay 0 0 0 0 0 0 1 1
Autistic behavior; Absent speech 0 0 0 0 0 0 1 1
Epileptic encephalopathy 0 0 0 1 0 0 0 1
Global developmental delay 0 0 0 1 0 0 1 1
Global developmental delay; Expressive language delay; Secondary microcephaly 0 0 0 1 0 0 0 1
Global developmental delay; Seizure; Hypotelorism; Short philtrum; Infantile muscular hypotonia 0 0 0 0 0 0 1 1
Growth abnormality 0 0 0 0 0 0 1 1
Hirschsprung disease, susceptibility to, 1 0 0 0 0 1 0 0 1
Immunodeficiency 33; Ectodermal dysplasia and immunodeficiency 1; Incontinentia pigmenti syndrome; Immunodeficiency 47 0 0 0 1 0 0 0 1
Intellectual disability, mild 0 0 0 1 0 0 1 1
Intellectual disability, severe 0 0 0 1 0 0 0 1
Internal malformations 0 0 0 0 0 0 1 1
Interstitial 6q microdeletion syndrome 0 0 0 1 0 0 0 1
MBD5 associated neurodevelopmental disorder 0 0 0 1 0 0 0 1
MKS1-related condition 0 0 0 0 0 0 1 1
Male infertility with azoospermia or oligozoospermia due to single gene mutation 0 0 0 0 0 0 1 1
PTCH1-related condition 0 0 0 0 0 0 1 1
Primary amenorrhea 0 0 0 0 0 0 1 1
RHD DEL 0 0 0 1 0 0 0 1
SIX6-related condition 0 0 0 0 1 0 0 1
See cases 0 0 0 1 0 0 1 1
Seizure 0 0 0 0 0 0 1 1
Silver Russell Syndrome-related disorder 0 0 0 0 0 0 1 1
Spastic paraplegia 0 0 0 0 0 0 1 1
Spinocerebellar ataxia, X-linked 0 0 0 0 0 1 0 1
Splenomegaly; Decreased circulating antibody level 0 0 0 1 0 0 0 1
VSX2-related Microphthalmia 0 0 0 1 0 0 1 1
ZNF331 deletion 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 68
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HGVS dbSNP gnomAD frequency
NM_001368894.2(PAX6):c.808-12C>T rs667773 0.05916
NM_001368894.2(PAX6):c.-129+9G>A rs56139994 0.02711
NM_007374.3(SIX6):c.21G>A (p.Leu7=) rs61746410 0.02217
NM_001368894.2(PAX6):c.*842G>A rs115045926 0.01172
NM_001368894.2(PAX6):c.369G>A (p.Glu123=) rs114384476 0.01168
NM_021728.4(OTX2):c.459C>T (p.Ser153=) rs34537598 0.00961
NM_001368894.2(PAX6):c.*356T>A rs774392481 0.00945
NM_021728.4(OTX2):c.97+12C>T rs28757218 0.00889
NM_019040.5(ELP4):c.*3994C>A rs79739975 0.00857
NM_019040.5(ELP4):c.*3425C>T rs3026399 0.00813
NM_007374.3(SIX6):c.385G>A (p.Glu129Lys) rs146737847 0.00428
NM_004557.4(NOTCH4):c.2443T>G (p.Cys815Gly) rs150079294 0.00397
NM_019040.5(ELP4):c.*2740G>A rs149777109 0.00394
NM_007374.3(SIX6):c.614T>G (p.Leu205Arg) rs45549246 0.00324
NM_019040.5(ELP4):c.*3242G>A rs187705792 0.00303
NM_019040.5(ELP4):c.*3713A>T rs138881442 0.00236
NM_019040.5(ELP4):c.*4932G>A rs181818313 0.00198
NM_019040.5(ELP4):c.*2040G>C rs183115097 0.00194
NM_019040.5(ELP4):c.*3904G>A rs3026397 0.00189
NM_021728.4(OTX2):c.831C>T (p.Asn277=) rs78559885 0.00171
NM_019040.5(ELP4):c.*4974C>T rs138035131 0.00148
NM_019040.5(ELP4):c.*1302T>C rs146579778 0.00120
NM_001368894.2(PAX6):c.-107C>T rs111270711 0.00117
NM_001374353.1(GLI2):c.1808C>T (p.Thr603Met) rs142775128 0.00099
NM_019040.5(ELP4):c.*2525C>A rs183433948 0.00096
NM_021728.4(OTX2):c.663C>T (p.Pro221=) rs142743327 0.00089
NM_020366.4(RPGRIP1):c.808A>G (p.Ile270Val) rs372615343 0.00084
NM_000264.5(PTCH1):c.1306G>A (p.Asp436Asn) rs142274954 0.00083
NM_019040.5(ELP4):c.*2982G>A rs191399467 0.00076
NM_001368894.2(PAX6):c.873G>A (p.Gln291=) rs149053004 0.00075
NM_001368894.2(PAX6):c.*891G>A rs530259403 0.00065
NM_019040.5(ELP4):c.*3528A>G rs143185259 0.00060
NM_025074.7(FRAS1):c.9364C>T (p.Arg3122Trp) rs200346497 0.00046
NM_001368894.2(PAX6):c.1179A>C (p.Thr393=) rs143477661 0.00038
NM_001368894.2(PAX6):c.753G>A (p.Val251=) rs145329506 0.00038
NM_007374.3(SIX6):c.637C>T (p.Pro213Ser) rs201560655 0.00035
NM_001368894.2(PAX6):c.*841C>T rs530931929 0.00031
NM_019040.5(ELP4):c.*1783T>G rs140971065 0.00030
NM_017617.5(NOTCH1):c.2434G>A (p.Gly812Arg) rs201620755 0.00029
NM_007374.3(SIX6):c.636G>C (p.Thr212=) rs140601427 0.00027
NM_001368894.2(PAX6):c.985T>C (p.Leu329=) rs373147550 0.00024
NM_004360.5(CDH1):c.670C>T (p.Arg224Cys) rs200310662 0.00021
NM_021728.4(OTX2):c.273+11T>C rs371958059 0.00021
NM_000264.5(PTCH1):c.3191C>T (p.Thr1064Met) rs368417828 0.00020
NM_021728.4(OTX2):c.425C>G (p.Pro142Arg) rs199761861 0.00016
NM_007374.3(SIX6):c.651C>T (p.Gly217=) rs368912930 0.00009
NM_000142.5(FGFR3):c.1879G>A (p.Glu627Lys) rs200849753 0.00007
NM_000264.5(PTCH1):c.3241G>A (p.Val1081Met) rs587778629 0.00007
NM_001368894.2(PAX6):c.-368G>A rs886048206 0.00006
NM_019040.5(ELP4):c.*3092T>C rs371438311 0.00006
NM_019040.5(ELP4):c.*2664G>A rs567720234 0.00005
NM_001128205.2(SULF1):c.529G>A (p.Gly177Ser) rs538017286 0.00004
NM_001368894.2(PAX6):c.909T>C (p.Ser303=) rs202154006 0.00004
NM_021728.4(OTX2):c.270G>T (p.Val90=) rs747916036 0.00003
NM_001291303.3(FAT4):c.7966A>C (p.Lys2656Gln) rs760398912 0.00002
NM_001368894.2(PAX6):c.-316-8C>G rs566281941 0.00002
NM_019040.5(ELP4):c.*1714C>G rs180780893 0.00002
NM_001368894.2(PAX6):c.317G>A (p.Arg106Gln) rs769095184 0.00001
NM_021728.4(OTX2):c.150G>A (p.Arg50=) rs1246931412 0.00001
NM_182894.3(VSX2):c.667G>A (p.Gly223Arg) rs755799430 0.00001
NM_001368894.2(PAX6):c.192C>A (p.Asn64Lys) rs727504064
NM_004312.3(ARR3):c.1052C>T (p.Pro351Leu) rs140505250
NM_007374.3(SIX6):c.18C>A (p.Ile6=) rs150715226
NM_007374.3(SIX6):c.573-6C>G rs770759922
NM_019040.5(ELP4):c.*1811A>C rs185968715
NM_021728.4(OTX2):c.444G>C (p.Pro148=) rs147896150
NM_177438.3(DICER1):c.2191G>A (p.Glu731Lys) rs869025262
Single allele

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