ClinVar Miner

Variants with conflicting interpretations studied for Holocarboxylase synthetase deficiency

Coded as:
Minimum review status of the submission for Holocarboxylase synthetase deficiency: Collection method of the submission for Holocarboxylase synthetase deficiency:
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
768 65 0 42 35 0 10 84

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
Holocarboxylase synthetase deficiency pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 34 3 0 0
likely pathogenic 34 0 8 0 0
uncertain significance 3 8 0 28 9
likely benign 0 0 28 0 8
benign 0 0 9 8 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
Holocarboxylase synthetase deficiency 768 65 0 42 35 0 10 84

All variants with conflicting interpretations #

Total variants: 84
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001352514.2(HLCS):c.726C>T (p.Pro242=) rs2230182 0.00548
NM_001352514.2(HLCS):c.1002C>T (p.Ala334=) rs116114362 0.00326
NM_001352514.2(HLCS):c.2113G>A (p.Glu705Lys) rs149736764 0.00315
NM_001352514.2(HLCS):c.1074G>A (p.Thr358=) rs116985497 0.00235
NM_001352514.2(HLCS):c.865G>A (p.Val289Ile) rs149291867 0.00087
NM_001352514.2(HLCS):c.1695C>T (p.Leu565=) rs138209330 0.00076
NM_001352514.2(HLCS):c.1331G>A (p.Arg444Gln) rs146030669 0.00074
NM_001352514.2(HLCS):c.1347G>C (p.Arg449Ser) rs142621386 0.00043
NM_001352514.2(HLCS):c.1390G>T (p.Val464Leu) rs144705277 0.00043
NM_001352514.2(HLCS):c.1811G>A (p.Arg604His) rs74574054 0.00036
NM_001352514.2(HLCS):c.1621-12T>C rs367728041 0.00032
NM_001352514.2(HLCS):c.1073C>T (p.Thr358Met) rs142524025 0.00026
NM_001352514.2(HLCS):c.2465A>G (p.His822Arg) rs148868421 0.00026
NM_001352514.2(HLCS):c.2615G>A (p.Arg872Gln) rs147474255 0.00018
NM_001352514.2(HLCS):c.1843G>C (p.Val615Leu) rs376210604 0.00015
NM_001352514.2(HLCS):c.2345A>G (p.Tyr782Cys) rs200453837 0.00012
NM_001352514.2(HLCS):c.2151C>T (p.Asn717=) rs148709879 0.00011
NM_001352514.2(HLCS):c.2416G>A (p.Val806Ile) rs368124997 0.00011
NM_001352514.2(HLCS):c.951C>T (p.Ser317=) rs185480832 0.00011
NM_001352514.2(HLCS):c.1974dup (p.Val659fs) rs767533946 0.00009
NM_001352514.2(HLCS):c.569C>T (p.Pro190Leu) rs534858065 0.00007
NM_001352514.2(HLCS):c.1278G>A (p.Glu426=) rs548505968 0.00006
NM_001352514.2(HLCS):c.2352C>T (p.Ile784=) rs150263699 0.00006
NM_001352514.2(HLCS):c.1857C>A (p.Ala619=) rs759178651 0.00005
NM_001352514.2(HLCS):c.2260dup (p.Ser754fs) rs766163167 0.00004
NM_001352514.2(HLCS):c.2341G>A (p.Asp781Asn) rs149399432 0.00004
NM_001352514.2(HLCS):c.2434C>T (p.Arg812Ter) rs146448211 0.00004
NM_001352514.2(HLCS):c.2583C>T (p.Phe861=) rs532108774 0.00004
NM_001352514.2(HLCS):c.494-9A>G rs376397597 0.00004
NM_001352514.2(HLCS):c.574C>G (p.Pro192Ala) rs200950813 0.00004
NM_001352514.2(HLCS):c.1821G>A (p.Leu607=) rs147495853 0.00003
NM_001352514.2(HLCS):c.1960+5G>A rs753887925 0.00003
NM_001352514.2(HLCS):c.2121+1G>A rs1175936807 0.00003
NM_001352514.2(HLCS):c.2182G>A (p.Gly728Ser) rs119103230 0.00003
NM_001352514.2(HLCS):c.918A>G (p.Gly306=) rs767988985 0.00003
NM_001352514.2(HLCS):c.1045G>T (p.Glu349Ter) rs148324626 0.00002
NM_001352514.2(HLCS):c.1529T>A (p.Val510Asp) rs769499327 0.00002
NM_001352514.2(HLCS):c.1808A>G (p.Tyr603Cys) rs781603756 0.00002
NM_001352514.2(HLCS):c.1985G>A (p.Ser662Asn) rs773398782 0.00002
NM_001352514.2(HLCS):c.2152G>A (p.Asp718Asn) rs119103228 0.00002
NM_001352514.2(HLCS):c.2340C>T (p.Ala780=) rs760265551 0.00002
NM_001352514.2(HLCS):c.1088T>G (p.Leu363Arg) rs28934602 0.00001
NM_001352514.2(HLCS):c.1151T>C (p.Leu384Pro) rs119103227 0.00001
NM_001352514.2(HLCS):c.1646G>A (p.Trp549Ter) rs1342457304 0.00001
NM_001352514.2(HLCS):c.1658_1659del (p.His553fs) rs751956557 0.00001
NM_001352514.2(HLCS):c.1719C>T (p.Tyr573=) rs148814769 0.00001
NM_001352514.2(HLCS):c.1850T>C (p.Leu617Ser) rs1261821166 0.00001
NM_001352514.2(HLCS):c.2089G>A (p.Val697Met) rs119103231 0.00001
NM_001352514.2(HLCS):c.2451-1G>A rs1158898827 0.00001
NM_001352514.2(HLCS):c.2519G>C (p.Gly840Ala) rs764148793 0.00001
NM_001352514.2(HLCS):c.2529G>A (p.Gln843=) rs767700692 0.00001
NM_001352514.2(HLCS):c.2567C>T (p.Pro856Leu) rs1260631800 0.00001
NM_001352514.2(HLCS):c.2585A>C (p.Asp862Ala) rs752737867 0.00001
NM_001352514.2(HLCS):c.609C>T (p.Asp203=) rs370118884 0.00001
NM_001352514.2(HLCS):c.723C>A (p.Gly241=) rs886057077 0.00001
NM_001352514.2(HLCS):c.840C>T (p.Tyr280=) rs779907293 0.00001
NM_001352514.2(HLCS):c.1063_1064del (p.Asp355fs) rs2517578591
NM_001352514.2(HLCS):c.1083T>A (p.Cys361Ter) rs568871363
NM_001352514.2(HLCS):c.1133del (p.Gln378fs) rs2066903607
NM_001352514.2(HLCS):c.1418G>A (p.Gly473Glu)
NM_001352514.2(HLCS):c.1418dup (p.Glu474fs) rs1555955827
NM_001352514.2(HLCS):c.1576C>T (p.Gln526Ter) rs1393866282
NM_001352514.2(HLCS):c.1600_1604del (p.Tyr534fs) rs2517546301
NM_001352514.2(HLCS):c.1620+7del rs140568778
NM_001352514.2(HLCS):c.1621-13_1621-10del rs377641674
NM_001352514.2(HLCS):c.1631del (p.Asp544fs) rs2517424327
NM_001352514.2(HLCS):c.1668C>A (p.Ser556=) rs771923409
NM_001352514.2(HLCS):c.1699_1700del (p.Ser566_Leu567insTer) rs1555930523
NM_001352514.2(HLCS):c.1769dup (p.Met590fs) rs1370055698
NM_001352514.2(HLCS):c.1869del (p.Thr624fs) rs2065031709
NM_001352514.2(HLCS):c.1954G>C (p.Gly652Arg) rs1555885056
NM_001352514.2(HLCS):c.1977G>A (p.Val659=) rs886057075
NM_001352514.2(HLCS):c.2144G>A (p.Trp715Ter) rs1174060268
NM_001352514.2(HLCS):c.2224del (p.Tyr742fs) rs2516853033
NM_001352514.2(HLCS):c.2418C>T (p.Val806=) rs759416272
NM_001352514.2(HLCS):c.494-25TC[4] rs146532042
NM_001352514.2(HLCS):c.513dup (p.Thr172fs) rs2517583431
NM_001352514.2(HLCS):c.664C>T (p.Gln222Ter) rs1555957134
NM_001352514.2(HLCS):c.664_667del (p.Gln222fs) rs776431253
NM_001352514.2(HLCS):c.726dup (p.Val243fs) rs1388238708
NM_001352514.2(HLCS):c.737A>G (p.Tyr246Cys) rs765150200
NM_001352514.2(HLCS):c.863del (p.Ser288fs) rs1015594025
NM_001352514.2(HLCS):c.958C>T (p.Gln320Ter) rs1288729804
NM_001352514.2(HLCS):c.958del (p.Gln320fs) rs2517579694

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