ClinVar Miner

Variants with conflicting interpretations studied for Pitt-Hopkins syndrome

Coded as:
Minimum review status of the submission for Pitt-Hopkins syndrome: 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 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
759 36 0 19 8 0 4 31

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 10 2 0 0
likely pathogenic 10 0 2 0 0
uncertain significance 2 2 0 7 1
likely benign 0 0 7 0 9
benign 0 0 1 9 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
Pitt-Hopkins syndrome 759 36 0 19 8 0 4 31

All variants with conflicting interpretations #

Total variants: 31
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001083962.2(TCF4):c.944C>T (p.Ala315Val) rs147445499 0.00066
NM_001083962.2(TCF4):c.936C>T (p.Ser312=) rs368270265 0.00043
NM_001083962.2(TCF4):c.504A>G (p.Val168=) rs370160994 0.00037
NM_001083962.2(TCF4):c.790-9T>C rs373434281 0.00036
NM_001083962.2(TCF4):c.966T>C (p.Asp322=) rs142998298 0.00034
NM_001083962.2(TCF4):c.1487-5G>A rs749176054 0.00016
NM_001083962.2(TCF4):c.816C>T (p.Asp272=) rs138403996 0.00005
NM_001083962.2(TCF4):c.945C>T (p.Ala315=) rs200115299 0.00004
NM_001083962.2(TCF4):c.1113G>A (p.Ser371=) rs148308964 0.00003
NM_001083962.2(TCF4):c.1486+4G>C rs201274415 0.00003
NM_001083962.2(TCF4):c.466C>A (p.Pro156Thr) rs200889338 0.00003
NM_001083962.2(TCF4):c.903C>T (p.Asn301=) rs781392344 0.00003
NM_001083962.2(TCF4):c.1354G>A (p.Gly452Arg) rs138570124 0.00002
NM_001083962.2(TCF4):c.584A>G (p.Asn195Ser) rs148573556 0.00001
NM_001083962.2(TCF4):c.1165C>T (p.Arg389Cys) rs2145503179
NM_001083962.2(TCF4):c.1169del (p.Arg389_Leu390insTer) rs1555764839
NM_001083962.2(TCF4):c.1486+1G>T rs2048816852
NM_001083962.2(TCF4):c.1486G>A (p.Gly496Ser) rs1599570613
NM_001083962.2(TCF4):c.1726C>T (p.Arg576Ter) rs1555710726
NM_001083962.2(TCF4):c.1732C>T (p.Arg578Cys) rs2144406630
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.1744C>T (p.Arg582Cys) rs2047109965
NM_001083962.2(TCF4):c.1817C>T (p.Thr606Ile) rs2144403104
NM_001083962.2(TCF4):c.1876C>T (p.Arg626Ter) rs1131691735
NM_001083962.2(TCF4):c.1965dup (p.Gly656fs) rs797046035
NM_001083962.2(TCF4):c.413C>G (p.Thr138Ser) rs796053416
NM_001083962.2(TCF4):c.655+1G>A rs587784465
NM_001083962.2(TCF4):c.939G>A (p.Gly313=) rs1470608351
NM_001083962.2(TCF4):c.990+12T>A rs144346949
NM_001083962.2(TCF4):c.990G>A (p.Ser330=) rs587784469

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