ClinVar Miner

Variants in gene HLCS with conflicting interpretations

See also:
Y axis minimum submission review status: Y axis collection method:
X axis minimum submission review status: X axis collection method:
Minimum conflict level:
Gene type:
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
819 63 0 43 35 0 9 80

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.

pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 27 5 0 0
likely pathogenic 27 0 8 0 0
uncertain significance 5 8 0 29 10
likely benign 0 0 29 0 16
benign 0 0 10 16 0

All variants with conflicting interpretations #

Total variants: 80
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001352514.2(HLCS):c.1275C>T (p.Ser425=) rs1065758 0.11920
NM_001352514.2(HLCS):c.727G>A (p.Val243Ile) rs61732502 0.04059
NM_001352514.2(HLCS):c.567G>T (p.Glu189Asp) rs61732504 0.03941
NM_001352514.2(HLCS):c.1969G>A (p.Gly657Arg) rs75867009 0.00642
NM_001352514.2(HLCS):c.726C>T (p.Pro242=) rs2230182 0.00587
NM_001352514.2(HLCS):c.1002C>T (p.Ala334=) rs116114362 0.00352
NM_001352514.2(HLCS):c.2113G>A (p.Glu705Lys) rs149736764 0.00315
NM_001352514.2(HLCS):c.1893-6C>T rs139904712 0.00313
NM_001352514.2(HLCS):c.1074G>A (p.Thr358=) rs116985497 0.00235
NM_001352514.2(HLCS):c.900G>A (p.Arg300=) rs146019354 0.00232
NM_001352514.2(HLCS):c.1695C>T (p.Leu565=) rs138209330 0.00087
NM_001352514.2(HLCS):c.865G>A (p.Val289Ile) rs149291867 0.00087
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 0.00014
NM_001352514.2(HLCS):c.2151C>T (p.Asn717=) rs148709879 0.00012
NM_001352514.2(HLCS):c.2345A>G (p.Tyr782Cys) rs200453837 0.00012
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.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.918A>G (p.Gly306=) rs767988985 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.569C>T (p.Pro190Leu) rs534858065 0.00003
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.1719C>T (p.Tyr573=) rs148814769 0.00001
NM_001352514.2(HLCS):c.1850T>C (p.Leu617Ser) rs1261821166 0.00001
NM_001352514.2(HLCS):c.2451-1G>A rs1158898827 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.1045G>T (p.Glu349Ter) rs148324626
NM_001352514.2(HLCS):c.1083T>A (p.Cys361Ter)
NM_001352514.2(HLCS):c.1133del (p.Gln378fs)
NM_001352514.2(HLCS):c.1151T>C (p.Leu384Pro) rs119103227
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)
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)
NM_001352514.2(HLCS):c.1646G>A (p.Trp549Ter) rs1342457304
NM_001352514.2(HLCS):c.1658_1659del (p.His553fs)
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.1869del (p.Thr624fs) rs2065031709
NM_001352514.2(HLCS):c.1977G>A (p.Val659=) rs886057075
NM_001352514.2(HLCS):c.2089G>A (p.Val697Met) rs119103231
NM_001352514.2(HLCS):c.2418C>T (p.Val806=) rs759416272
NM_001352514.2(HLCS):c.2529G>A (p.Gln843=) rs767700692
NM_001352514.2(HLCS):c.494-25TC[4] rs146532042
NM_001352514.2(HLCS):c.513dup (p.Thr172fs)
NM_001352514.2(HLCS):c.664_667del (p.Gln222fs) rs776431253
NM_001352514.2(HLCS):c.726dup (p.Val243fs)
NM_001352514.2(HLCS):c.737A>G (p.Tyr246Cys) rs765150200
NM_001352514.2(HLCS):c.863del (p.Ser288fs) rs1015594025
NM_001352514.2(HLCS):c.958del (p.Gln320fs)

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