ClinVar Miner

Variants with conflicting interpretations studied for Pitt-Hopkins syndrome

Coded as:
Minimum review status of the submission for Pitt-Hopkins syndrome: Y axis collection method of the submission for Pitt-Hopkins syndrome:
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
182 23 0 20 4 0 1 23

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
Pitt-Hopkins syndrome pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 5 0 0 0
likely pathogenic 5 0 1 0 0
uncertain significance 0 1 0 1 0
likely benign 0 0 4 0 13
benign 0 0 0 6 0

Condition to condition summary #

Total conditions: 6
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 7 0 13 2 0 0 15
Pitt-Hopkins syndrome 208 9 0 9 1 0 1 11
not provided 0 15 0 6 4 0 0 9
History of neurodevelopmental disorder 0 6 0 5 0 0 0 5
Intellectual disability 0 1 0 0 1 0 0 1
Severe intellectual deficiency 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 23
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HGVS dbSNP
NM_001083962.2(TCF4):c.*22G>A rs182372608
NM_001083962.2(TCF4):c.1299G>A (p.Leu433=) rs552340151
NM_001083962.2(TCF4):c.1354G>A (p.Gly452Arg) rs138570124
NM_001083962.2(TCF4):c.1419G>C (p.Pro473=) rs143944746
NM_001083962.2(TCF4):c.1487-5G>A rs749176054
NM_001083962.2(TCF4):c.1726C>T (p.Arg576Ter) rs1555710726
NM_001083962.2(TCF4):c.1738C>T (p.Arg580Trp) rs121909120
NM_001083962.2(TCF4):c.1739G>A (p.Arg580Gln) rs121909121
NM_001083962.2(TCF4):c.1741G>T (p.Val581Phe) rs587784460
NM_001083962.2(TCF4):c.1876C>T (p.Arg626Ter) rs1131691735
NM_001083962.2(TCF4):c.1905G>A (p.Ala635=) rs151150677
NM_001083962.2(TCF4):c.1923G>A (p.Glu641=) rs76956936
NM_001083962.2(TCF4):c.1965dup (p.Gly656fs) rs797046035
NM_001083962.2(TCF4):c.208-8A>G rs184943897
NM_001083962.2(TCF4):c.269A>G (p.Asn90Ser) rs143244149
NM_001083962.2(TCF4):c.5-10C>T rs552239655
NM_001083962.2(TCF4):c.504A>G (p.Val168=) rs370160994
NM_001083962.2(TCF4):c.73-3T>C rs148658897
NM_001083962.2(TCF4):c.790-9T>C rs373434281
NM_001083962.2(TCF4):c.936C>T (p.Ser312=) rs368270265
NM_001083962.2(TCF4):c.944C>T (p.Ala315Val) rs147445499
NM_001083962.2(TCF4):c.966T>C (p.Asp322=) rs142998298
NM_001083962.2(TCF4):c.990G>A (p.Ser330=) rs587784469

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