ClinVar Miner

Variants with conflicting interpretations studied for FGFR2-related craniosynostosis

Coded as:
Minimum review status of the submission for FGFR2-related craniosynostosis: Collection method of the submission for FGFR2-related craniosynostosis:
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
266 78 0 33 20 0 2 53

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
FGFR2-related craniosynostosis pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 5 1 0 0
likely pathogenic 2 0 0 0 0
uncertain significance 0 1 0 3 0
likely benign 0 0 13 0 2
benign 0 0 4 25 0

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 69 0 21 9 0 1 31
Isolated coronal synostosis 0 8 0 14 10 0 0 24
not specified 0 20 0 6 1 0 0 7
FGFR2-related condition 0 22 0 6 0 0 0 6
Autosomal dominant syndrome including deafness 0 0 0 0 0 0 1 1
Craniosynostosis, nonspecific 0 0 0 0 1 0 0 1
FGFR2-realated disorder 0 0 0 0 1 0 0 1
FGFR2-related craniosynostosis 391 5 0 1 0 0 0 1
Hypertelorism; High palate; Low-set ears; Cranial asymmetry; Abnormal pinna morphology; Downslanted palpebral fissures; Flat occiput; Narrow forehead; Short neck; Hydrocephalus; Brachyturricephaly; Wide anterior fontanel; Facial asymmetry; High forehead; Choanal stenosis; Shallow orbits; Abnormal posterior cranial fossa morphology; Deviated nasal septum; Lateral ventricle dilatation; Hypointensity of cerebral white matter on MRI; Abnormal zygomatic bone morphology; Mild fetal ventriculomegaly 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 53
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HGVS dbSNP gnomAD frequency
NM_000141.5(FGFR2):c.557T>C (p.Met186Thr) rs755793 0.10553
NM_000141.5(FGFR2):c.109+10T>G rs3135722 0.00799
NM_000141.5(FGFR2):c.294G>A (p.Thr98=) rs1047101 0.00776
NM_000141.5(FGFR2):c.159G>A (p.Ala53=) rs1047102 0.00414
NM_000141.5(FGFR2):c.1572A>G (p.Thr524=) rs74160613 0.00298
NM_000141.5(FGFR2):c.170C>T (p.Ser57Leu) rs56226109 0.00271
NM_000141.5(FGFR2):c.1539C>T (p.Thr513=) rs74160617 0.00234
NM_000141.5(FGFR2):c.2001C>G (p.Val667=) rs61731218 0.00187
NM_000141.5(FGFR2):c.1673-12C>T rs41293763 0.00186
NM_000141.5(FGFR2):c.454+14C>T rs112142377 0.00152
NM_000141.5(FGFR2):c.939+11T>C rs145303463 0.00134
NM_000141.5(FGFR2):c.23T>G (p.Ile8Ser) rs147307031 0.00107
NM_000141.5(FGFR2):c.759T>G (p.Pro253=) rs3135755 0.00057
NM_000141.5(FGFR2):c.34G>A (p.Val12Met) rs143978938 0.00043
NM_000141.5(FGFR2):c.2190C>T (p.Asn730=) rs55637244 0.00040
NM_000141.5(FGFR2):c.789G>A (p.Pro263=) rs138315382 0.00038
NM_000141.5(FGFR2):c.1788G>A (p.Glu596=) rs56335660 0.00036
NM_000141.5(FGFR2):c.2232C>T (p.Pro744=) rs142639988 0.00035
NM_000141.5(FGFR2):c.1986+7C>T rs199697707 0.00032
NM_000141.5(FGFR2):c.1085-13A>T rs41295573 0.00024
NM_000141.5(FGFR2):c.568C>T (p.Arg190Trp) rs147987917 0.00013
NM_000141.5(FGFR2):c.1774C>T (p.Arg592Cys) rs141929882 0.00012
NM_000141.5(FGFR2):c.289G>A (p.Ala97Thr) rs372430349 0.00011
NM_000141.5(FGFR2):c.625-10A>G rs201512833 0.00011
NM_000141.5(FGFR2):c.989G>A (p.Arg330Gln) rs199757302 0.00011
NM_000141.5(FGFR2):c.33C>T (p.Val11=) rs200562301 0.00009
NM_000141.5(FGFR2):c.942C>T (p.Ala314=) rs201717227 0.00008
NM_000141.5(FGFR2):c.2124C>T (p.Pro708=) rs140813163 0.00007
NM_000141.5(FGFR2):c.1548G>A (p.Val516=) rs200522893 0.00006
NM_000141.5(FGFR2):c.201C>T (p.Ala67=) rs200386134 0.00006
NM_000141.5(FGFR2):c.780C>T (p.Ala260=) rs778288494 0.00005
NM_000141.5(FGFR2):c.2415C>T (p.Tyr805=) rs558460047 0.00004
NM_000141.5(FGFR2):c.2195+7G>A rs377397478 0.00003
NM_000141.5(FGFR2):c.2040C>T (p.Tyr680=) rs751495618 0.00002
NM_000141.5(FGFR2):c.879C>T (p.His293=) rs55745510 0.00002
NM_000141.5(FGFR2):c.1239G>A (p.Pro413=) rs147674677 0.00001
NM_000141.5(FGFR2):c.138A>C (p.Gln46His) rs748117555 0.00001
NM_000141.5(FGFR2):c.2058-10T>C rs756377540 0.00001
NM_000141.5(FGFR2):c.755C>T (p.Ser252Leu) rs79184941 0.00001
NM_000141.5(FGFR2):c.1040C>G (p.Ser347Cys) rs121918494
NM_000141.5(FGFR2):c.1084+8C>T rs1589827584
NM_000141.5(FGFR2):c.1086G>C (p.Ala362=) rs151250769
NM_000141.5(FGFR2):c.110-22TC[3] rs773932794
NM_000141.5(FGFR2):c.1274G>A (p.Arg425Gln)
NM_000141.5(FGFR2):c.2032A>G (p.Arg678Gly) rs1845559552
NM_000141.5(FGFR2):c.2328C>T (p.Leu776=) rs148478597
NM_000141.5(FGFR2):c.2416G>A (p.Glu806Lys) rs764959117
NM_000141.5(FGFR2):c.399T>C (p.Asp133=)
NM_000141.5(FGFR2):c.758C>G (p.Pro253Arg) rs77543610
NM_000141.5(FGFR2):c.812G>T (p.Gly271Val) rs1564919048
NM_000141.5(FGFR2):c.826T>G (p.Phe276Val) rs1057519036
NM_000141.5(FGFR2):c.940G>T (p.Ala314Ser) rs1358919643
NM_000141.5(FGFR2):c.958A>G (p.Thr320Ala) rs2134260022

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