ClinVar Miner

Variants with conflicting interpretations studied for Homocystinuria due to methylene tetrahydrofolate reductase deficiency

Coded as:
Minimum review status of the submission for Homocystinuria due to methylene tetrahydrofolate reductase deficiency: Collection method of the submission for Homocystinuria due to methylene tetrahydrofolate reductase deficiency:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
694 51 0 54 16 0 20 84

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
Homocystinuria due to methylene tetrahydrofolate reductase deficiency pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 45 14 1 1
likely pathogenic 45 0 9 0 2
uncertain significance 14 9 0 14 2
likely benign 1 0 14 0 9
benign 1 2 2 9 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
Homocystinuria due to methylene tetrahydrofolate reductase deficiency 694 51 0 54 16 0 20 84
MTHFR THERMOLABILE POLYMORPHISM 0 0 0 1 1 0 2 2

All variants with conflicting interpretations #

Total variants: 84
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_005957.5(MTHFR):c.665C>T (p.Ala222Val) rs1801133 0.27446
NM_005957.5(MTHFR):c.1286A>C (p.Glu429Ala) rs1801131 0.25830
NM_005957.5(MTHFR):c.1264G>A (p.Gly422Arg) rs45571736 0.00300
NM_005957.5(MTHFR):c.348C>T (p.Ala116=) rs144921426 0.00217
NM_005957.5(MTHFR):c.1555C>T (p.Arg519Cys) rs45496998 0.00178
NM_005957.5(MTHFR):c.1761C>T (p.Ala587=) rs115049252 0.00145
NM_005957.5(MTHFR):c.708C>T (p.Phe236=) rs34279942 0.00134
NM_005957.5(MTHFR):c.1556G>T (p.Arg519Leu) rs45449298 0.00118
NM_005957.5(MTHFR):c.732C>T (p.Thr244=) rs45486194 0.00082
NM_005957.5(MTHFR):c.1719C>T (p.Thr573=) rs149585376 0.00029
NM_005957.5(MTHFR):c.3G>C (p.Met1Ile) rs373076763 0.00021
NM_005957.5(MTHFR):c.870C>T (p.Asn290=) rs141769179 0.00019
NM_005957.5(MTHFR):c.1720G>A (p.Val574Ile) rs202153689 0.00015
NM_005957.5(MTHFR):c.903G>A (p.Leu301=) rs147979890 0.00013
NM_005957.5(MTHFR):c.726A>G (p.Ala242=) rs45459991 0.00011
NM_005957.5(MTHFR):c.1003C>T (p.Arg335Cys) rs748289202 0.00010
NM_005957.5(MTHFR):c.1878C>T (p.Phe626=) rs199707466 0.00009
NM_005957.5(MTHFR):c.700G>A (p.Asp234Asn) rs45589033 0.00009
NM_005957.5(MTHFR):c.136C>T (p.Arg46Trp) rs138189536 0.00008
NM_005957.5(MTHFR):c.1004G>A (p.Arg335His) rs543016186 0.00005
NM_005957.5(MTHFR):c.1626T>C (p.Asn542=) rs190046545 0.00005
NM_005957.5(MTHFR):c.459C>G (p.Ile153Met) rs767890671 0.00005
NM_005957.5(MTHFR):c.1129C>T (p.Arg377Cys) rs121434296 0.00004
NM_005957.5(MTHFR):c.1130G>A (p.Arg377His) rs750323424 0.00004
NM_005957.5(MTHFR):c.90G>A (p.Ser30=) rs765167328 0.00004
NM_005957.5(MTHFR):c.137G>A (p.Arg46Gln) rs776483190 0.00003
NM_005957.5(MTHFR):c.1743G>A (p.Met581Ile) rs45590836 0.00003
NM_005957.5(MTHFR):c.548G>A (p.Arg183Gln) rs574132670 0.00003
NM_005957.5(MTHFR):c.330G>C (p.Met110Ile) rs781158269 0.00002
NM_005957.5(MTHFR):c.470G>A (p.Arg157Gln) rs121434295 0.00002
NM_005957.5(MTHFR):c.973C>T (p.Arg325Cys) rs371085894 0.00002
NM_005957.5(MTHFR):c.1002G>A (p.Lys334=) rs147727428 0.00001
NM_005957.5(MTHFR):c.1013T>C (p.Met338Thr) rs368321176 0.00001
NM_005957.5(MTHFR):c.1033C>T (p.Arg345Cys) rs759031330 0.00001
NM_005957.5(MTHFR):c.1069C>T (p.Arg357Cys) rs779993607 0.00001
NM_005957.5(MTHFR):c.1070G>A (p.Arg357His) rs977038830 0.00001
NM_005957.5(MTHFR):c.1088G>A (p.Arg363His) rs786204023 0.00001
NM_005957.5(MTHFR):c.1263G>C (p.Trp421Cys) rs200688214 0.00001
NM_005957.5(MTHFR):c.1748G>A (p.Trp583Ter) rs1314085200 0.00001
NM_005957.5(MTHFR):c.1753-18G>A rs777661576 0.00001
NM_005957.5(MTHFR):c.177G>T (p.Trp59Cys) rs767789270 0.00001
NM_005957.5(MTHFR):c.202C>G (p.Arg68Gly) rs763539350 0.00001
NM_005957.5(MTHFR):c.379C>T (p.His127Tyr) rs769381688 0.00001
NM_005957.5(MTHFR):c.408G>A (p.Glu136=) rs752891093 0.00001
NM_005957.5(MTHFR):c.416C>T (p.Thr139Met) rs1057519360 0.00001
NM_005957.5(MTHFR):c.469C>T (p.Arg157Trp) rs776195746 0.00001
NM_005957.5(MTHFR):c.584C>T (p.Ala195Val) rs760161369 0.00001
NM_005957.5(MTHFR):c.767T>A (p.Ile256Asn) rs373398993 0.00001
NM_005957.5(MTHFR):c.780+1G>A rs786204020 0.00001
NM_005957.5(MTHFR):c.968T>C (p.Leu323Pro) rs121434297 0.00001
NM_005957.5(MTHFR):c.971A>G (p.Asn324Ser) rs267606887 0.00001
NM_005957.5(MTHFR):c.-13-28_-13-27del rs1553188112
NM_005957.5(MTHFR):c.1011del (p.Met338fs) rs1380686004
NM_005957.5(MTHFR):c.1015T>G (p.Trp339Gly) rs267606886
NM_005957.5(MTHFR):c.1060C>T (p.His354Tyr) rs786204022
NM_005957.5(MTHFR):c.1114A>G (p.Lys372Glu) rs786204024
NM_005957.5(MTHFR):c.1121dup (p.Tyr374Ter) rs2100527601
NM_005957.5(MTHFR):c.1228_1242del (p.Ser410_Lys414del) rs1297161027
NM_005957.5(MTHFR):c.1262G>C (p.Trp421Ser) rs200137991
NM_005957.5(MTHFR):c.1267dup (p.Glu423fs) rs1557761665
NM_005957.5(MTHFR):c.1320G>T (p.Ser440=) rs367585605
NM_005957.5(MTHFR):c.1516T>G (p.Tyr506Asp) rs786204026
NM_005957.5(MTHFR):c.1606G>T (p.Val536Phe) rs786204028
NM_005957.5(MTHFR):c.1715C>T (p.Pro572Leu) rs144508139
NM_005957.5(MTHFR):c.1750A>T (p.Lys584Ter) rs1644092513
NM_005957.5(MTHFR):c.1752+1G>T rs747846362
NM_005957.5(MTHFR):c.177G>A (p.Trp59Ter) rs767789270
NM_005957.5(MTHFR):c.1793T>C (p.Leu598Pro) rs786204034
NM_005957.5(MTHFR):c.264_302dup (p.Leu89_Pro101dup) rs786204010
NM_005957.5(MTHFR):c.273dup (p.Asp92fs) rs2100568604
NM_005957.5(MTHFR):c.288C>T (p.His96=) rs748688171
NM_005957.5(MTHFR):c.337G>A (p.Ala113Thr) rs147257424
NM_005957.5(MTHFR):c.346G>A (p.Ala116Thr) rs1056919085
NM_005957.5(MTHFR):c.469C>A (p.Arg157=) rs776195746
NM_005957.5(MTHFR):c.474A>T (p.Gly158=) rs199476142
NM_005957.5(MTHFR):c.475+1G>T rs748397580
NM_005957.5(MTHFR):c.523G>A (p.Ala175Thr) rs1182635980
NM_005957.5(MTHFR):c.531C>T (p.Asp177=) rs2100561654
NM_005957.5(MTHFR):c.604C>A (p.Pro202Thr) rs1057519361
NM_005957.5(MTHFR):c.643_645del (p.Lys215del) rs746353274
NM_005957.5(MTHFR):c.671TCA[2] (p.Ile226del) rs786204016
NM_005957.5(MTHFR):c.760C>T (p.Pro254Ser) rs786204017
NM_005957.5(MTHFR):c.831A>G (p.Pro277=) rs2522884052
NM_005957.5(MTHFR):c.860_863del (p.Ile287fs) rs1644227167

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