ClinVar Miner

Variants with conflicting interpretations studied for Holoprosencephaly sequence

Coded as:
Minimum review status of the submission for Holoprosencephaly sequence: Y axis collection method of the submission for Holoprosencephaly sequence:
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 Variants with at least 2 submissions 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 kind of conflict
282 121 2 79 29 0 4 105

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
Holoprosencephaly sequence pathogenic uncertain significance likely benign benign
likely pathogenic 1 0 0 0
uncertain significance 0 1 19 5
likely benign 4 7 0 78
benign 0 0 8 1

Condition to condition summary #

Total conditions: 12
Download table as spreadsheet
Condition Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
not specified 0 30 0 63 12 0 0 75
Gorlin syndrome 0 68 0 27 14 0 0 41
not provided 0 12 2 19 8 0 0 29
Hereditary cancer-predisposing syndrome 0 12 0 19 5 0 0 24
Holoprosencephaly 9; Culler-Jones syndrome 0 0 0 9 0 0 0 9
Holoprosencephaly sequence 495 5 0 8 0 0 0 8
Holoprosencephaly 11 0 1 0 6 0 0 0 6
Holoprosencephaly 4 0 0 0 3 0 0 0 3
Visceral heterotaxy 5, autosomal 0 0 0 3 0 0 0 3
Holoprosencephaly 7 0 0 0 0 0 0 2 2
Holoprosencephaly 9 0 0 0 1 0 0 2 2
Kallmann syndrome 6 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 105
Download table as spreadsheet
HGVS dbSNP
NM_000264.3(PTCH1):c.2183C>T (p.Thr728Met) rs115556836
NM_000264.3(PTCH1):c.3155C>T (p.Thr1052Met) rs138911275
NM_000264.3(PTCH1):c.3944C>T (p.Pro1315Leu) rs357564
NM_000264.4(PTCH1):c.1074T>C (p.His358=) rs2066832
NM_000264.4(PTCH1):c.109G>C (p.Gly37Arg) rs199976372
NM_000264.4(PTCH1):c.1119C>T (p.Tyr373=) rs2066831
NM_000264.4(PTCH1):c.1216-6C>A rs186008764
NM_000264.4(PTCH1):c.1348-4G>A rs772826555
NM_000264.4(PTCH1):c.1504-8T>C rs2277184
NM_000264.4(PTCH1):c.1641C>T (p.Ser547=) rs2066830
NM_000264.4(PTCH1):c.1653G>A (p.Thr551=) rs766039170
NM_000264.4(PTCH1):c.1665T>C (p.Asn555=) rs1805155
NM_000264.4(PTCH1):c.1686C>T (p.Ala562=) rs2066836
NM_000264.4(PTCH1):c.1710G>T (p.Leu570=) rs374924167
NM_000264.4(PTCH1):c.1808G>A (p.Arg603His) rs199523893
NM_000264.4(PTCH1):c.1847+14C>T rs202007968
NM_000264.4(PTCH1):c.1854C>T (p.Cys618=) rs62637628
NM_000264.4(PTCH1):c.2184G>A (p.Thr728=) rs201103723
NM_000264.4(PTCH1):c.2199A>G (p.Ser733=) rs2227970
NM_000264.4(PTCH1):c.2270T>C (p.Phe757Ser) rs547954117
NM_000264.4(PTCH1):c.2304C>T (p.Thr768=) rs1805156
NM_000264.4(PTCH1):c.2460C>T (p.Tyr820=) rs766227557
NM_000264.4(PTCH1):c.2484C>T (p.Asn828=) rs143305989
NM_000264.4(PTCH1):c.2678G>A (p.Arg893His) rs138154222
NM_000264.4(PTCH1):c.2692G>A (p.Asp898Asn) rs531947455
NM_000264.4(PTCH1):c.2787C>T (p.Asn929=) rs145196322
NM_000264.4(PTCH1):c.2887+10G>A rs202081420
NM_000264.4(PTCH1):c.2913T>C (p.Tyr971=) rs2229062
NM_000264.4(PTCH1):c.2937C>T (p.Asn979=) rs58629309
NM_000264.4(PTCH1):c.3141T>G (p.Leu1047=) rs2066835
NM_000264.4(PTCH1):c.318C>T (p.Leu106=) rs1805153
NM_000264.4(PTCH1):c.3387C>T (p.Gly1129=) rs28446339
NM_000264.4(PTCH1):c.3423G>A (p.Ala1141=) rs745948150
NM_000264.4(PTCH1):c.3567C>T (p.Gly1189=) rs62637630
NM_000264.4(PTCH1):c.3583A>T (p.Thr1195Ser) rs2236405
NM_000264.4(PTCH1):c.3606C>T (p.Pro1202=) rs138240178
NM_000264.4(PTCH1):c.3692T>C (p.Val1231Ala) rs182045135
NM_000264.4(PTCH1):c.3805-9C>T rs2236404
NM_000264.4(PTCH1):c.3845C>T (p.Pro1282Leu) rs2227968
NM_000264.4(PTCH1):c.3907C>T (p.Arg1303Cys) rs56102979
NM_000264.4(PTCH1):c.4027G>A (p.Gly1343Arg) rs200100952
NM_000264.4(PTCH1):c.4080C>T (p.Ser1360=) rs62637631
NM_000264.4(PTCH1):c.4128C>T (p.Ser1376=) rs142148876
NM_000264.4(PTCH1):c.4152G>A (p.Pro1384=) rs761887390
NM_000264.4(PTCH1):c.4324C>T (p.Arg1442Trp) rs143464326
NM_000264.4(PTCH1):c.4325G>A (p.Arg1442Gln) rs56023271
NM_000264.4(PTCH1):c.735A>G (p.Thr245=) rs1805154
NM_003244.3(TGIF1):c.123C>T (p.Asn41=) rs138292737
NM_003244.3(TGIF1):c.420A>G (p.Pro140=) rs2229337
NM_003244.3(TGIF1):c.487C>T (p.Pro163Ser) rs4468717
NM_003244.3(TGIF1):c.488C>T (p.Pro163Leu) rs2229333
NM_003244.3(TGIF1):c.576C>T (p.Val192=) rs2229335
NM_003244.3(TGIF1):c.657T>G (p.Thr219=) rs2229336
NM_003923.2(FOXH1):c.1077G>A (p.Leu359=) rs7833404
NM_003923.2(FOXH1):c.15C>T (p.Ser5=) rs374587860
NM_003923.2(FOXH1):c.338G>C (p.Ser113Thr) rs144830740
NM_003923.2(FOXH1):c.361C>A (p.Arg121=) rs371301968
NM_003923.2(FOXH1):c.363G>C (p.Arg121=) rs80356380
NM_003923.2(FOXH1):c.373A>T (p.Thr125Ser) rs112028242
NM_003923.2(FOXH1):c.47C>T (p.Ser16Leu) rs180724802
NM_003923.2(FOXH1):c.771C>A (p.Gly257=) rs115750264
NM_003923.2(FOXH1):c.771C>T (p.Gly257=) rs115750264
NM_003923.2(FOXH1):c.783T>C (p.Pro261=) rs151147114
NM_005270.4(GLI2):c.1294G>A (p.Val432Met) rs142296407
NM_005270.4(GLI2):c.1761G>A (p.Thr587=) rs61732852
NM_005270.4(GLI2):c.1859C>T (p.Thr620Met) rs142775128
NM_005270.4(GLI2):c.1944C>T (p.Thr648=) rs13008360
NM_005270.4(GLI2):c.1986G>A (p.Ser662=) rs114259687
NM_005270.4(GLI2):c.2088A>G (p.Ala696=) rs146059306
NM_005270.4(GLI2):c.2708C>G (p.Thr903Ser) rs572826436
NM_005270.4(GLI2):c.2940C>T (p.Ser980=) rs146811565
NM_005270.4(GLI2):c.3018C>T (p.Gly1006=) rs373880077
NM_005270.4(GLI2):c.3048C>T (p.Asp1016=) rs140479803
NM_005270.4(GLI2):c.3349G>T (p.Val1117Leu) rs147580961
NM_005270.4(GLI2):c.3590G>A (p.Gly1197Asp) rs114823319
NM_005270.4(GLI2):c.3882G>A (p.Thr1294=) rs115052795
NM_005270.4(GLI2):c.3943C>T (p.Pro1315Ser) rs114376238
NM_005270.4(GLI2):c.4030C>T (p.Leu1344=) rs149290823
NM_005270.4(GLI2):c.4054A>G (p.Met1352Val) rs149140724
NM_005270.4(GLI2):c.4332G>A (p.Met1444Ile) rs146467786
NM_005270.4(GLI2):c.4333C>T (p.Leu1445Phe) rs146207623
NM_005270.4(GLI2):c.4497T>C (p.Thr1499=) rs151090814
NM_005270.4(GLI2):c.4558G>A (p.Asp1520Asn) rs114814747
NM_005270.4(GLI2):c.4663T>C (p.Ser1555Pro) rs144372453
NM_005270.4(GLI2):c.720C>T (p.Asp240=) rs142793481
NM_005270.4(GLI2):c.963C>G (p.Pro321=) rs149894186
NM_016952.4(CDON):c.1051C>G (p.Pro351Ala) rs35665264
NM_016952.4(CDON):c.1296G>A (p.Pro432=) rs11220313
NM_016952.4(CDON):c.1603G>A (p.Ala535Thr) rs76247998
NM_016952.4(CDON):c.1671G>A (p.Lys557=) rs35884952
NM_016952.4(CDON):c.197A>G (p.Lys66Arg) rs7122277
NM_016952.4(CDON):c.2057C>T (p.Ala686Val) rs12274923
NM_016952.4(CDON):c.2623A>G (p.Ser875Gly) rs115533243
NM_016952.4(CDON):c.330T>C (p.Pro110=) rs35131477
NM_016952.4(CDON):c.350-13T>C rs3740910
NM_016952.4(CDON):c.3526G>A (p.Val1176Ile) rs78304400
NM_016952.4(CDON):c.484G>A (p.Glu162Lys) rs3740909
NM_016952.4(CDON):c.640+12G>A rs4426144
NM_018055.4(NODAL):c.216C>T (p.Asn72=) rs138195571
NM_018055.4(NODAL):c.357C>T (p.Pro119=) rs77151171
NM_018055.4(NODAL):c.588C>G (p.Leu196=) rs2231959
NM_033163.3(FGF8):c.385C>T (p.Arg129Ter) rs876661330
NM_033164.3(FGF8):c.86_103dup (p.Arg34_Glu35insGlyProAlaLeuGlyArg) rs762175290
NM_173208.2(TGIF1):c.489G>A (p.Pro163=) rs2229334
NM_173208.2(TGIF1):c.723G>A (p.Pro241=) rs114912664

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