ClinVar Miner

Variants with conflicting interpretations studied for Disorders of Intracellular Cobalamin Metabolism

Coded as:
Minimum review status of the submission for Disorders of Intracellular Cobalamin Metabolism: Collection method of the submission for Disorders of Intracellular Cobalamin Metabolism:
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
378 84 0 34 32 2 2 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
Disorders of Intracellular Cobalamin Metabolism pathogenic likely pathogenic uncertain significance likely benign benign drug response risk factor
likely pathogenic 1 0 0 0 0 0 0
uncertain significance 2 1 0 26 3 0 0
likely benign 0 0 5 0 11 0 0
benign 0 0 0 22 0 1 2

Condition to condition summary #

Total conditions: 9
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 62 0 22 13 0 2 37
not specified 0 55 0 11 16 0 0 26
MTR-related condition 0 5 0 2 5 0 0 7
Methylmalonic acidemia with homocystinuria cblC 0 10 0 1 5 0 0 6
MMACHC-related condition 0 3 0 0 2 0 1 3
MTRR-related condition 0 2 0 1 2 0 0 3
Neural tube defects, folate-sensitive, susceptibility to 0 0 0 0 0 2 0 2
Down syndrome, susceptibility to 0 0 0 0 0 1 0 1
Methotrexate response 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 68
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_002454.3(MTRR):c.66A>G (p.Ile22Met) rs1801394 0.44947
NM_000254.3(MTR):c.2756A>G (p.Asp919Gly) rs1805087 0.21137
NM_015506.3(MMACHC):c.811A>G (p.Ser271Gly) rs35219601 0.04960
NM_018368.3(LMBRD1):c.-250G>C rs112053239 0.02394
NM_002454.3(MTRR):c.*151A>G rs112465197 0.01706
NM_002454.3(MTRR):c.*49A>G rs142538539 0.01601
NM_000254.3(MTR):c.-201C>G rs111840642 0.01495
NM_015506.3(MMACHC):c.*269A>G rs35067820 0.01308
NM_002454.3(MTRR):c.*167A>G rs115253331 0.01048
NM_000254.3(MTR):c.-151C>T rs41305572 0.00828
NM_000254.3(MTR):c.-111C>T rs113809927 0.00822
NM_015702.3(MMADHC):c.87A>C (p.Lys29Asn) rs61750442 0.00751
NM_015702.3(MMADHC):c.473G>A (p.Arg158Gln) rs114276563 0.00611
NM_000254.3(MTR):c.858C>T (p.Pro286=) rs146019467 0.00576
NM_000254.3(MTR):c.1033G>A (p.Val345Ile) rs145006491 0.00514
NM_000254.3(MTR):c.3474G>A (p.Leu1158=) rs142113735 0.00510
NM_002454.3(MTRR):c.288C>T (p.Leu96=) rs35587995 0.00500
NM_000254.3(MTR):c.155G>A (p.Arg52Gln) rs12749581 0.00417
NM_002454.3(MTRR):c.1468A>G (p.Thr490Ala) rs41283145 0.00414
NM_000254.3(MTR):c.2815G>C (p.Gly939Arg) rs113042166 0.00401
NM_018368.3(LMBRD1):c.-276A>G rs148064952 0.00387
NM_002454.3(MTRR):c.1819G>A (p.Val607Ile) rs114259126 0.00366
NM_002454.3(MTRR):c.876C>T (p.Thr292=) rs144724549 0.00341
NM_000254.3(MTR):c.1076-8C>T rs115186224 0.00321
NM_002454.3(MTRR):c.210C>G (p.Arg70=) rs41282641 0.00303
NM_015702.3(MMADHC):c.-8C>T rs180812156 0.00282
NM_002454.3(MTRR):c.1326C>T (p.Leu442=) rs144781389 0.00274
NM_000254.3(MTR):c.1485G>A (p.Met495Ile) rs2229275 0.00265
NM_000254.3(MTR):c.3079C>T (p.Arg1027Trp) rs116836001 0.00235
NM_002454.3(MTRR):c.1982A>G (p.His661Arg) rs148909799 0.00196
NM_015702.3(MMADHC):c.646C>G (p.Arg216Gly) rs141093638 0.00181
NM_002454.3(MTRR):c.177C>G (p.Thr59=) rs142098262 0.00147
NM_015702.3(MMADHC):c.578T>C (p.Val193Ala) rs147370143 0.00117
NM_000254.3(MTR):c.1141G>A (p.Ala381Thr) rs144777709 0.00073
NM_000254.3(MTR):c.2622G>A (p.Pro874=) rs141919148 0.00064
NM_015702.3(MMADHC):c.617A>G (p.Asn206Ser) rs138607412 0.00051
NM_002454.3(MTRR):c.540G>A (p.Val180=) rs149037732 0.00046
NM_015506.3(MMACHC):c.277-4C>G rs199889403 0.00045
NM_000254.3(MTR):c.1080A>G (p.Leu360=) rs141861479 0.00043
NM_000254.3(MTR):c.1977A>G (p.Lys659=) rs144767461 0.00038
NM_015506.3(MMACHC):c.691T>C (p.Leu231=) rs373198842 0.00038
NM_000254.3(MTR):c.3712-7T>G rs151081130 0.00036
NM_015506.3(MMACHC):c.440G>C (p.Gly147Ala) rs140522266 0.00034
NM_000254.3(MTR):c.3583A>G (p.Ile1195Val) rs149476106 0.00026
NM_015506.3(MMACHC):c.389A>G (p.Tyr130Cys) rs200094982 0.00014
NM_015506.3(MMACHC):c.799C>T (p.Arg267Trp) rs34258482 0.00013
NM_015702.3(MMADHC):c.-60G>A rs886054923 0.00013
NM_000254.3(MTR):c.3552C>T (p.Thr1184=) rs760793648 0.00010
NM_000254.3(MTR):c.866-10C>G rs368755647 0.00010
NM_002454.3(MTRR):c.-26+14C>T rs368193742 0.00010
NM_002454.3(MTRR):c.1020C>T (p.Cys340=) rs201348649 0.00010
NM_015702.3(MMADHC):c.-16A>G rs144111552 0.00009
NM_000254.3(MTR):c.3126C>T (p.Asp1042=) rs529430607 0.00008
NM_015506.3(MMACHC):c.458G>A (p.Arg153Gln) rs200276195 0.00006
NM_000254.3(MTR):c.2994C>T (p.Asn998=) rs778549407 0.00005
NM_002454.3(MTRR):c.346C>A (p.Gln116Lys) rs202110383 0.00005
NM_000254.3(MTR):c.1722T>C (p.Ser574=) rs142857114 0.00004
NM_002454.3(MTRR):c.27T>C (p.Ala9=) rs114748706 0.00004
NM_000254.3(MTR):c.2772C>G (p.Leu924=) rs533541925 0.00002
NM_000254.3(MTR):c.181A>C (p.Arg61=) rs886046217 0.00001
NM_000254.3(MTR):c.34+10C>T rs376679817 0.00001
NM_000254.3(MTR):c.*16del rs67705775
NM_000254.3(MTR):c.742G>A (p.Val248Met) rs142648132
NM_002454.3(MTRR):c.1678_1681del (p.Glu560Asnfs) rs768980918
NM_002454.3(MTRR):c.1875G>T (p.Val625=) rs12347
NM_015506.3(MMACHC):c.848G>C (p.Ter283Ser) rs201025783
NM_015702.3(MMADHC):c.-145A>G rs12477482
NM_018368.4(LMBRD1):c.981-10dup rs202207965

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