ClinVar Miner

Variants with conflicting interpretations studied for PHGDH deficiency

Coded as:
Minimum review status of the submission for PHGDH deficiency: Collection method of the submission for PHGDH deficiency:
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
665 60 0 18 20 0 5 39

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
PHGDH deficiency pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 8 3 0 0
likely pathogenic 8 0 3 0 0
uncertain significance 3 3 0 19 4
likely benign 0 0 19 0 10
benign 0 0 4 10 0

Condition to condition summary #

Total conditions: 1
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
PHGDH deficiency 665 60 0 18 20 0 5 39

All variants with conflicting interpretations #

Total variants: 39
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_006623.4(PHGDH):c.318C>T (p.Ala106=) rs115747918 0.01251
NM_006623.4(PHGDH):c.792+6T>G rs146953046 0.01118
NM_006623.4(PHGDH):c.595C>G (p.Leu199Val) rs77632964 0.00622
NM_006623.4(PHGDH):c.624T>C (p.Pro208=) rs77401816 0.00154
NM_006623.4(PHGDH):c.510+6A>G rs371736796 0.00133
NM_006623.4(PHGDH):c.1559C>A (p.Ala520Glu) rs151275800 0.00101
NM_006623.4(PHGDH):c.682G>T (p.Gly228Trp) rs139063843 0.00083
NM_006623.4(PHGDH):c.985A>T (p.Thr329Ser) rs201298102 0.00064
NM_006623.4(PHGDH):c.834C>A (p.Val278=) rs147866831 0.00051
NM_006623.4(PHGDH):c.296C>G (p.Pro99Arg) rs182600362 0.00030
NM_006623.4(PHGDH):c.412-15C>T rs368681081 0.00021
NM_006623.4(PHGDH):c.1257G>A (p.Gly419=) rs374303746 0.00016
NM_006623.4(PHGDH):c.390C>T (p.Asp130=) rs148078511 0.00012
NM_006623.4(PHGDH):c.644-12G>A rs370255821 0.00012
NM_006623.4(PHGDH):c.1543C>T (p.Leu515=) rs148721434 0.00010
NM_006623.4(PHGDH):c.422C>T (p.Thr141Ile) rs200037593 0.00009
NM_006623.4(PHGDH):c.1255G>A (p.Gly419Arg) rs145344767 0.00006
NM_006623.4(PHGDH):c.1468G>A (p.Val490Met) rs121907987 0.00006
NM_006623.4(PHGDH):c.372G>A (p.Ala124=) rs146740411 0.00005
NM_006623.4(PHGDH):c.1116C>T (p.Pro372=) rs587662790 0.00004
NM_006623.4(PHGDH):c.1129G>A (p.Gly377Ser) rs267606948 0.00002
NM_006623.4(PHGDH):c.1365A>G (p.Pro455=) rs1264262485 0.00002
NM_006623.4(PHGDH):c.374C>T (p.Thr125Met) rs764618040 0.00002
NM_006623.4(PHGDH):c.804G>A (p.Arg268=) rs587719252 0.00002
NM_006623.4(PHGDH):c.1030C>T (p.Arg344Ter) rs769256568 0.00001
NM_006623.4(PHGDH):c.1273G>A (p.Val425Met) rs121907988 0.00001
NM_006623.4(PHGDH):c.129G>A (p.Ala43=) rs587623477 0.00001
NM_006623.4(PHGDH):c.487C>T (p.Arg163Trp) rs772067625 0.00001
NM_006623.4(PHGDH):c.1078+10G>T rs374994783
NM_006623.4(PHGDH):c.1158G>A (p.Ala386=) rs144484007
NM_006623.4(PHGDH):c.1394del (p.Leu465fs)
NM_006623.4(PHGDH):c.290+2T>C rs886041874
NM_006623.4(PHGDH):c.2T>C (p.Met1Thr) rs951372478
NM_006623.4(PHGDH):c.381G>A (p.Ser127=) rs886045205
NM_006623.4(PHGDH):c.418G>A (p.Gly140Arg) rs587777770
NM_006623.4(PHGDH):c.519G>A (p.Gly173=) rs754326499
NM_006623.4(PHGDH):c.543G>A (p.Glu181=) rs886045206
NM_006623.4(PHGDH):c.781G>A (p.Val261Met) rs267606947
NM_006623.4(PHGDH):c.901del (p.Val301fs) rs1571013274

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