ClinVar Miner

Variants with conflicting interpretations studied for Classic homocystinuria

Coded as:
Minimum review status of the submission for Classic homocystinuria: Collection method of the submission for Classic homocystinuria:
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
121 135 0 79 26 0 23 121

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
Classic homocystinuria pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 39 4 0 0
likely pathogenic 62 0 13 0 0
uncertain significance 9 14 0 25 3
likely benign 0 0 6 0 13
benign 0 0 1 5 0

Condition to condition summary #

Total conditions: 2
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
HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED 0 128 0 77 26 0 22 120
Classic homocystinuria 257 67 0 40 6 0 10 53

All variants with conflicting interpretations #

Total variants: 121
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000071.3(CBS):c.304A>C (p.Lys102Gln) rs34040148 0.01138
NM_000071.3(CBS):c.1145+7C>T rs201158177 0.00620
NM_000071.3(CBS):c.531+11G>A rs186114513 0.00479
NM_000071.3(CBS):c.954+8G>A rs76292057 0.00188
NM_000071.3(CBS):c.1059G>A (p.Thr353=) rs61735859 0.00162
NM_000071.3(CBS):c.1359-14C>T rs115185587 0.00137
NM_000071.3(CBS):c.1643G>A (p.Arg548Gln) rs150828989 0.00105
NM_000071.3(CBS):c.52C>T (p.Arg18Cys) rs201827340 0.00086
NM_000071.3(CBS):c.829-13G>A rs201106576 0.00067
NM_000071.3(CBS):c.215A>T (p.Lys72Ile) rs192232907 0.00056
NM_000071.3(CBS):c.1479G>A (p.Thr493=) rs143225442 0.00029
NM_000071.3(CBS):c.600G>A (p.Pro200=) rs181472622 0.00029
NM_000071.3(CBS):c.1330G>A (p.Asp444Asn) rs28934891 0.00026
NM_000071.3(CBS):c.33G>A (p.Gly11=) rs567323664 0.00025
NM_000071.3(CBS):c.829-11G>T rs371619788 0.00025
NM_000071.3(CBS):c.146C>T (p.Pro49Leu) rs148865119 0.00013
NM_000071.3(CBS):c.1146-12C>T rs199550738 0.00010
NM_000071.3(CBS):c.1632C>T (p.Ala544=) rs566810122 0.00010
NM_000071.3(CBS):c.362G>A (p.Arg121His) rs770095972 0.00010
NM_000071.3(CBS):c.770C>T (p.Thr257Met) rs758236584 0.00010
NM_000071.3(CBS):c.894G>A (p.Gln298=) rs370514077 0.00010
NM_000071.3(CBS):c.888G>A (p.Thr296=) rs769593715 0.00007
NM_000071.3(CBS):c.1161C>T (p.Ser387=) rs149280976 0.00006
NM_000071.3(CBS):c.1425G>A (p.Pro475=) rs147885808 0.00006
NM_000071.3(CBS):c.572C>T (p.Thr191Met) rs121964973 0.00006
NM_000071.3(CBS):c.786G>A (p.Thr262=) rs551782391 0.00006
NM_000071.3(CBS):c.1281G>A (p.Pro427=) rs563330591 0.00004
NM_000071.3(CBS):c.1499C>T (p.Ser500Leu) rs755106884 0.00004
NM_000071.3(CBS):c.1512G>A (p.Glu504=) rs149170219 0.00004
NM_000071.3(CBS):c.341C>T (p.Ala114Val) rs121964964 0.00004
NM_000071.3(CBS):c.1039G>A (p.Gly347Ser) rs771298943 0.00003
NM_000071.3(CBS):c.1058C>T (p.Thr353Met) rs121964972 0.00003
NM_000071.3(CBS):c.1135C>T (p.Arg379Trp) rs769080151 0.00003
NM_000071.3(CBS):c.1280C>T (p.Pro427Leu) rs863223434 0.00003
NM_000071.3(CBS):c.1316G>A (p.Arg439Gln) rs756467921 0.00003
NM_000071.3(CBS):c.374G>A (p.Arg125Gln) rs781444670 0.00003
NM_000071.3(CBS):c.737-1G>C rs757428597 0.00003
NM_000071.3(CBS):c.775G>A (p.Gly259Ser) rs143124288 0.00003
NM_000071.3(CBS):c.785C>T (p.Thr262Met) rs149119723 0.00003
NM_000071.3(CBS):c.924C>T (p.Tyr308=) rs149809170 0.00003
NM_000071.3(CBS):c.1006C>T (p.Arg336Cys) rs398123151 0.00002
NM_000071.3(CBS):c.301C>G (p.Leu101Val) rs369644531 0.00002
NM_000071.3(CBS):c.325T>C (p.Cys109Arg) rs778220779 0.00002
NM_000071.3(CBS):c.361C>T (p.Arg121Cys) rs775992753 0.00002
NM_000071.3(CBS):c.430G>A (p.Glu144Lys) rs121964966 0.00002
NM_000071.3(CBS):c.689del (p.Leu230fs) rs775351239 0.00002
NM_000071.3(CBS):c.959T>C (p.Val320Ala) rs781567152 0.00002
NM_000071.3(CBS):c.1007G>A (p.Arg336His) rs760417941 0.00001
NM_000071.3(CBS):c.1065G>A (p.Ala355=) rs748552493 0.00001
NM_000071.3(CBS):c.1109G>A (p.Cys370Tyr) rs757920190 0.00001
NM_000071.3(CBS):c.1111G>A (p.Val371Met) rs372010465 0.00001
NM_000071.3(CBS):c.1136G>A (p.Arg379Gln) rs763036586 0.00001
NM_000071.3(CBS):c.1397C>T (p.Ser466Leu) rs121964971 0.00001
NM_000071.3(CBS):c.1551G>A (p.Gln517=) rs750311684 0.00001
NM_000071.3(CBS):c.28del (p.Val10fs) rs779250698 0.00001
NM_000071.3(CBS):c.373C>T (p.Arg125Trp) rs886057100 0.00001
NM_000071.3(CBS):c.442G>A (p.Gly148Arg) rs755952006 0.00001
NM_000071.3(CBS):c.797G>A (p.Arg266Lys) rs121964969 0.00001
NM_000071.3(CBS):c.828+1G>A rs763290176 0.00001
NM_000071.3(CBS):c.982G>A (p.Asp328Asn) rs758447354 0.00001
NC_000021.9:g.(?_43060421)_(43062415_?)dup
NM_000071.2(CBS):c.832_833insCTGGGGTGGATCATCCAGGTGGGGCTTTTGCTGGGCTTGAGCCCTGAAGCCGCGCCCTCTGCAGATCA
NM_000071.3(CBS):c.1007G>C (p.Arg336Pro) rs760417941
NM_000071.3(CBS):c.1017C>T (p.Ile339=) rs773933333
NM_000071.3(CBS):c.1071C>T (p.Ala357=) rs368206976
NM_000071.3(CBS):c.1145+1G>A
NM_000071.3(CBS):c.1146-6C>T rs1981696579
NM_000071.3(CBS):c.1218del (p.Lys406fs) rs794727083
NM_000071.3(CBS):c.1221del (p.Trp408fs) rs1361324844
NM_000071.3(CBS):c.1265C>T (p.Pro422Leu) rs28934892
NM_000071.3(CBS):c.1358+15C>G rs186497436
NM_000071.3(CBS):c.1358+1G>A rs786204679
NM_000071.3(CBS):c.1498_1499del (p.Ser500fs) rs1555871188
NM_000071.3(CBS):c.153_165del (p.Arg51fs) rs1555876784
NM_000071.3(CBS):c.1566del (p.Lys523fs) rs786204466
NM_000071.3(CBS):c.1576C>T (p.Gln526Ter) rs1555869958
NM_000071.3(CBS):c.1616T>C (p.Leu539Ser) rs121964968
NM_000071.3(CBS):c.162G>A (p.Trp54Ter) rs199948079
NM_000071.3(CBS):c.209+1G>C rs751464024
NM_000071.3(CBS):c.210-1G>C rs2146414477
NM_000071.3(CBS):c.233C>G (p.Pro78Arg) rs786204608
NM_000071.3(CBS):c.262C>G (p.Pro88Ala)
NM_000071.3(CBS):c.262C>T (p.Pro88Ser) rs2146413970
NM_000071.3(CBS):c.284T>C (p.Ile95Thr) rs1347662650
NM_000071.3(CBS):c.302T>C (p.Leu101Pro) rs786204757
NM_000071.3(CBS):c.306G>C (p.Lys102Asn) rs786204609
NM_000071.3(CBS):c.313C>G (p.Leu105Val) rs1601375543
NM_000071.3(CBS):c.346G>A (p.Gly116Arg) rs760214620
NM_000071.3(CBS):c.359A>G (p.Asp120Gly) rs1982750491
NM_000071.3(CBS):c.362G>T (p.Arg121Leu) rs770095972
NM_000071.3(CBS):c.371_374dup (p.Met126fs) rs755625628
NM_000071.3(CBS):c.402del (p.Thr135fs) rs1057517083
NM_000071.3(CBS):c.429C>G (p.Ile143Met) rs370167302
NM_000071.3(CBS):c.430G>C (p.Glu144Gln) rs121964966
NM_000071.3(CBS):c.434C>T (p.Pro145Leu) rs121964963
NM_000071.3(CBS):c.457G>A (p.Gly153Arg) rs745704046
NM_000071.3(CBS):c.481del (p.Arg161fs) rs2146387904
NM_000071.3(CBS):c.493T>G (p.Cys165Gly) rs1234354755
NM_000071.3(CBS):c.502G>A (p.Val168Met) rs121964970
NM_000071.3(CBS):c.536_553del (p.Asp179_Leu184del) rs794727835
NM_000071.3(CBS):c.580_599del (p.Asn194fs)
NM_000071.3(CBS):c.612G>T (p.Val204=) rs539670390
NM_000071.3(CBS):c.667-14C>G rs1388184910
NM_000071.3(CBS):c.667-14_667-7del rs764160782
NM_000071.3(CBS):c.676G>A (p.Ala226Thr) rs763835246
NM_000071.3(CBS):c.683A>G (p.Asn228Ser) rs1555874803
NM_000071.3(CBS):c.732_733del (p.Cys244_Asp245delinsTer)
NM_000071.3(CBS):c.738del rs766453711
NM_000071.3(CBS):c.752T>C (p.Leu251Pro) rs1176770868
NM_000071.3(CBS):c.753G>T (p.Leu251=) rs2146375662
NM_000071.3(CBS):c.808_810del (p.Glu270del) rs760710691
NM_000071.3(CBS):c.816T>A (p.Cys272Ter) rs528689432
NM_000071.3(CBS):c.825C>T (p.Cys275=) rs764638041
NM_000071.3(CBS):c.829-8C>G rs750081937
NM_000071.3(CBS):c.862G>A (p.Ala288Thr) rs141502207
NM_000071.3(CBS):c.889G>T (p.Glu297Ter)
NM_000071.3(CBS):c.949A>G (p.Arg317Gly)
NM_000071.3(CBS):c.954+1G>A rs1057517373
NM_000071.3(CBS):c.969G>A (p.Trp323Ter) rs863223432
NM_000071.3(CBS):c.98del (p.Pro33fs) rs2146428203
NM_000071.3(CBS):c.992C>A (p.Ala331Glu) rs777919630

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