ClinVar Miner

Variants with conflicting interpretations studied for Holt-Oram syndrome

Coded as:
Minimum review status of the submission for Holt-Oram syndrome: Y axis collection method of the submission for Holt-Oram 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
162 28 0 17 8 0 3 25

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
Holt-Oram syndrome pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 3 0 0 0
likely pathogenic 3 0 1 0 0
uncertain significance 1 2 0 1 0
likely benign 0 0 4 0 6
benign 0 0 3 7 0

Condition to condition summary #

Total conditions: 11
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
Cardiovascular phenotype 0 10 0 8 4 0 2 14
not specified 0 12 0 7 2 0 0 9
not provided 0 18 0 5 2 0 0 7
Aortic valve disease 2 0 6 0 4 0 0 1 5
Loeys-Dietz syndrome 0 3 0 5 0 0 0 5
Loeys-Dietz syndrome 4 0 2 0 1 2 0 1 4
Holt-Oram syndrome 210 2 0 2 0 0 1 3
Connective tissue disorder 0 0 0 2 0 0 0 2
Thoracic aortic aneurysm and aortic dissection 0 3 0 1 2 0 0 2
Aortic aneurysm 0 0 0 0 1 0 0 1
Hirschsprung disease 1 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 25
Download table as spreadsheet
HGVS dbSNP
NM_000192.3(TBX5):c.114C>T (p.Ser38=) rs34014008
NM_000192.3(TBX5):c.316A>G (p.Ile106Val) rs147710408
NM_000192.3(TBX5):c.331G>T (p.Asp111Tyr) rs77357563
NM_000192.3(TBX5):c.510+5G>A rs1555226301
NM_000192.3(TBX5):c.55G>T (p.Ala19Ser) rs200461617
NM_000192.3(TBX5):c.668C>T (p.Thr223Met) rs1555225344
NM_000192.3(TBX5):c.710G>A (p.Arg237Gln) rs104894378
NM_000192.3(TBX5):c.786C>T (p.Thr262=) rs375955080
NM_000192.3(TBX5):c.787G>A (p.Val263Met) rs147405081
NM_001135599.3(TGFB2):c.114G>A (p.Glu38=) rs149215818
NM_001135599.3(TGFB2):c.272G>A (p.Arg91His) rs10482721
NM_001135599.3(TGFB2):c.475C>T (p.Arg159Ter) rs869025531
NM_001135599.3(TGFB2):c.703G>C (p.Val235Leu) rs10482810
NM_001135599.3(TGFB2):c.728-4C>T rs11466408
NM_003238.5(TGFB2):c.1140C>T (p.Cys380=) rs201129153
NM_003238.5(TGFB2):c.1239C>T (p.Cys413=) rs141225367
NM_003238.5(TGFB2):c.294_308del (p.Ala100_Tyr104del) rs398122883
NM_003238.5(TGFB2):c.303G>A (p.Lys101=) rs147052890
NM_003238.5(TGFB2):c.356C>T (p.Pro119Leu) rs149533093
NM_003238.5(TGFB2):c.357G>A (p.Pro119=) rs138514914
NM_003238.5(TGFB2):c.588C>T (p.Gly196=) rs192335285
NM_003238.5(TGFB2):c.823A>G (p.Ser275Gly) rs139825195
NM_003238.5(TGFB2):c.895C>T (p.Arg299Trp) rs863223792
NM_003238.5(TGFB2):c.904C>T (p.Arg302Cys) rs869312903
NM_003238.5(TGFB2):c.905G>A (p.Arg302His) rs1553303213

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