ClinVar Miner

Variants with conflicting interpretations studied for Hirschsprung disease, susceptibility to, 1

Coded as:
Minimum review status of the submission for Hirschsprung disease, susceptibility to, 1: Collection method of the submission for Hirschsprung disease, susceptibility to, 1:
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
154 96 2 34 36 10 7 77

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
Hirschsprung disease, susceptibility to, 1 pathogenic likely pathogenic uncertain significance likely benign benign drug response protective risk factor
pathogenic 0 7 1 0 0 0 0 0
likely pathogenic 5 0 1 3 1 0 0 0
uncertain significance 1 1 2 26 10 1 0 0
likely benign 1 1 9 0 16 0 1 1
benign 0 0 2 10 0 0 0 0
risk factor 1 1 4 2 3 0 0 0

Condition to condition summary #

Total conditions: 25
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 78 2 22 22 4 5 49
not specified 0 37 0 19 18 4 2 40
RET-related condition 0 12 0 5 5 1 0 11
Hirschsprung disease, susceptibility to, 1 312 9 0 4 1 1 0 6
Aganglionic megacolon 0 6 0 1 1 3 1 5
Hirschsprung disease, susceptibility to, 1; MULTIPLE ENDOCRINE NEOPLASIA, TYPE IIB; Pheochromocytoma; Familial medullary thyroid carcinoma; MULTIPLE ENDOCRINE NEOPLASIA, TYPE IIA 0 42 0 3 0 2 0 5
Hereditary cancer 0 1 0 0 2 0 0 2
Anophthalmia-microphthalmia syndrome 0 0 0 0 1 0 0 1
Congenital central hypoventilation; Hirschsprung disease, susceptibility to, 1; MULTIPLE ENDOCRINE NEOPLASIA, TYPE IIB; Pheochromocytoma; Familial medullary thyroid carcinoma; MULTIPLE ENDOCRINE NEOPLASIA, TYPE IIA 0 2 0 1 0 0 0 1
DYNC2H1-related condition 0 0 0 0 1 0 0 1
Ewing sarcoma of soft tissue 0 0 0 0 1 0 0 1
Fluorouracil response 0 0 0 0 0 0 1 1
Hirschsprung disease, protection against 0 0 0 0 0 1 0 1
LRBA-related condition 0 0 0 0 1 0 0 1
NOTCH2-related condition 0 0 0 0 1 0 0 1
NRP2-related condition 0 0 0 0 1 0 0 1
RET-related disease 0 0 0 1 0 0 0 1
SOX10-related condition 0 0 0 0 0 0 1 1
See cases 0 0 0 0 1 0 0 1
TSC2-related condition 0 0 0 0 1 0 0 1
Thyroid carcinoma, sporadic medullary 0 0 0 1 0 0 0 1
capecitabine response - Toxicity 0 0 0 0 0 1 0 1
fluorouracil response - Other 0 0 0 0 0 1 0 1
fluorouracil response - Toxicity 0 0 0 0 0 1 0 1
tegafur response - Toxicity 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 77
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_020975.6(RET):c.73+9277T>C rs2435357 0.79636
NM_020975.6(RET):c.135= (p.Ala45=) rs1800858 0.20726
NM_020975.6(RET):c.337+9G>A rs2435351 0.20641
NM_020975.6(RET):c.2071G>A (p.Gly691Ser) rs1799939 0.16640
NM_020975.6(RET):c.*1969T>C rs3026785 0.04255
NM_020975.6(RET):c.2508C>T (p.Ser836=) rs1800862 0.03791
NM_020975.6(RET):c.*1591G>A rs76759170 0.03751
NM_020975.6(RET):c.1264-5C>T rs9282835 0.02749
NM_020975.6(RET):c.2944C>T (p.Arg982Cys) rs17158558 0.01567
NM_002658.6(PLAU):c.172G>A (p.Gly58Arg) rs55744193 0.00504
NM_000110.4(DPYD):c.1905+1G>A rs3918290 0.00474
NM_020975.6(RET):c.166C>A (p.Leu56Met) rs145633958 0.00310
NM_002253.4(KDR):c.2066C>T (p.Thr689Met) rs34038364 0.00307
NM_003238.6(TGFB2):c.272G>A (p.Arg91His) rs10482721 0.00297
NM_020975.6(RET):c.1336G>C (p.Gly446Arg) rs115423919 0.00238
NM_024408.4(NOTCH2):c.7223T>A (p.Leu2408His) rs35586704 0.00228
NM_001364905.1(LRBA):c.2444A>G (p.Asn815Ser) rs140666848 0.00218
NM_003872.3(NRP2):c.1000C>T (p.Arg334Cys) rs114144673 0.00186
NM_020975.6(RET):c.2372A>T (p.Tyr791Phe) rs77724903 0.00178
NM_001377.3(DYNC2H1):c.12366+8A>G rs200404815 0.00156
NM_020975.6(RET):c.654G>A (p.Pro218=) rs137928436 0.00138
NM_000548.5(TSC2):c.1318G>A (p.Gly440Ser) rs45484298 0.00111
NM_001301130.2(POLR2F):c.453-24294G>C rs533778281 0.00095
NM_000264.5(PTCH1):c.1306G>A (p.Asp436Asn) rs142274954 0.00083
NM_007199.3(IRAK3):c.1461del (p.Asn487fs) rs776951445 0.00071
NM_020975.6(RET):c.1465G>A (p.Asp489Asn) rs9282834 0.00068
NM_020975.6(RET):c.833C>A (p.Thr278Asn) rs35118262 0.00056
NM_020975.6(RET):c.*1430A>G rs775114955 0.00053
NM_020975.6(RET):c.*29C>A rs199639914 0.00050
NM_020975.6(RET):c.3112A>G (p.Thr1038Ala) rs201740483 0.00047
NM_001620.3(AHNAK):c.7562C>G (p.Pro2521Arg) rs143391519 0.00039
NM_020975.6(RET):c.1946C>T (p.Ser649Leu) rs148935214 0.00039
NM_020975.6(RET):c.2037C>T (p.Pro679=) rs55862116 0.00039
NM_020975.6(RET):c.200G>A (p.Arg67His) rs192489011 0.00036
NM_020975.6(RET):c.1158G>A (p.Ala386=) rs373540097 0.00034
NM_020975.6(RET):c.341G>A (p.Arg114His) rs76397662 0.00029
NM_000168.6(GLI3):c.2119C>T (p.Pro707Ser) rs121917716 0.00028
NM_020975.6(RET):c.2088G>A (p.Ser696=) rs150329150 0.00024
NM_020975.6(RET):c.785T>C (p.Val262Ala) rs139790943 0.00024
NM_020975.6(RET):c.874G>A (p.Val292Met) rs34682185 0.00023
NM_020975.6(RET):c.2410G>A (p.Val804Met) rs79658334 0.00022
NM_020975.6(RET):c.2052G>A (p.Pro684=) rs145122337 0.00019
NM_020975.6(RET):c.1063+9G>A rs765463636 0.00014
NM_020975.6(RET):c.1699G>A (p.Asp567Asn) rs147219360 0.00014
NM_020975.6(RET):c.2988G>A (p.Pro996=) rs145798106 0.00014
NM_020975.6(RET):c.957C>A (p.Leu319=) rs149926238 0.00011
NM_020975.6(RET):c.1879+13C>T rs375573788 0.00008
NM_020975.6(RET):c.2081G>A (p.Arg694Gln) rs141185224 0.00008
NM_020975.6(RET):c.1438G>A (p.Glu480Lys) rs537874538 0.00004
NM_020975.6(RET):c.2976G>A (p.Pro992=) rs528823385 0.00004
NM_020975.6(RET):c.3116C>T (p.Pro1039Leu) rs79853121 0.00004
NM_020975.6(RET):c.1998G>T (p.Lys666Asn) rs146646971 0.00003
NM_020975.6(RET):c.3149G>A (p.Arg1050Gln) rs200956659 0.00003
NM_020975.6(RET):c.3185A>G (p.Tyr1062Cys) rs587778659 0.00003
NM_020975.6(RET):c.1920C>T (p.Ala640=) rs149768519 0.00002
NM_020975.6(RET):c.1941C>T (p.Ile647=) rs75225191 0.00002
NM_020975.6(RET):c.938G>A (p.Arg313Gln) rs77702891 0.00002
NM_020975.6(RET):c.1264-8C>T rs769595884 0.00001
NM_020975.6(RET):c.1890C>T (p.Cys630=) rs781145070 0.00001
NM_020975.6(RET):c.1900T>C (p.Cys634Arg) rs75076352 0.00001
NM_020975.6(RET):c.1996A>G (p.Lys666Glu) rs143795581 0.00001
NM_020975.6(RET):c.2166G>T (p.Lys722Asn) rs527726480 0.00001
NM_020975.6(RET):c.2538C>T (p.Leu846=) rs201816539 0.00001
NM_020975.6(RET):c.2982A>C (p.Lys994Asn) rs199718928 0.00001
NM_020975.6(RET):c.3332C>T (p.Thr1111Met) rs1003057639 0.00001
NM_002615.7(SERPINF1):c.643+8C>T rs149399910
NM_020975.6(RET):c.-160G>T rs567112195
NM_020975.6(RET):c.1196C>T (p.Pro399Leu) rs1554818362
NM_020975.6(RET):c.1523-7C>T rs567967877
NM_020975.6(RET):c.1858T>C (p.Cys620Arg) rs77316810
NM_020975.6(RET):c.1879+1G>A rs1588873476
NM_020975.6(RET):c.1947G>A (p.Ser649=) rs377767412
NM_020975.6(RET):c.1998G>C (p.Lys666Asn) rs146646971
NM_020975.6(RET):c.2523G>T (p.Pro841=) rs56195026
NM_020975.6(RET):c.2753T>C (p.Met918Thr) rs74799832
NM_020975.6(RET):c.538C>T (p.Arg180Ter) rs76449634
NM_020975.6(RET):c.95C>T (p.Ser32Leu) rs76764689

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