ClinVar Miner

Variants with conflicting interpretations studied for Cystinuria

Coded as:
Minimum review status of the submission for Cystinuria: Collection method of the submission for Cystinuria:
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
323 52 0 18 20 0 11 46

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
Cystinuria pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 15 9 0 1
likely pathogenic 15 0 4 0 0
uncertain significance 9 4 0 15 5
likely benign 0 0 15 0 3
benign 1 0 5 3 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
Cystinuria 323 52 0 18 20 0 11 46

All variants with conflicting interpretations #

Total variants: 46
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000341.4(SLC3A1):c.892-6C>G rs114640930 0.00651
NM_000341.4(SLC3A1):c.1035G>A (p.Glu345=) rs78795495 0.00357
NM_000341.4(SLC3A1):c.300C>T (p.Leu100=) rs115030299 0.00351
NM_014270.5(SLC7A9):c.978-17G>A rs45628833 0.00315
NM_000341.4(SLC3A1):c.566C>T (p.Thr189Met) rs140317484 0.00287
NM_000341.4(SLC3A1):c.797T>C (p.Phe266Ser) rs141587158 0.00273
NM_000341.4(SLC3A1):c.231T>A (p.Ser77=) rs146630359 0.00260
NM_014270.5(SLC7A9):c.544G>A (p.Ala182Thr) rs79389353 0.00238
NM_000341.4(SLC3A1):c.1398C>T (p.Asn466=) rs140821819 0.00211
NM_000341.4(SLC3A1):c.1400T>C (p.Met467Thr) rs121912691 0.00175
NM_000341.4(SLC3A1):c.788G>C (p.Ser263Thr) rs139310305 0.00076
NM_000341.4(SLC3A1):c.1126G>A (p.Gly376Ser) rs143068960 0.00073
NM_000341.4(SLC3A1):c.1767C>T (p.Ile589=) rs142141929 0.00056
NM_000341.4(SLC3A1):c.592del (p.Ala198fs) rs778000327 0.00028
NM_000341.4(SLC3A1):c.1473C>T (p.Ala491=) rs144065614 0.00026
NM_000341.4(SLC3A1):c.66C>T (p.Asn22=) rs149507807 0.00026
NM_014270.5(SLC7A9):c.368C>T (p.Thr123Met) rs79987078 0.00023
NM_014270.5(SLC7A9):c.313G>A (p.Gly105Arg) rs121908480 0.00017
NM_000341.4(SLC3A1):c.417C>T (p.Asn139=) rs150870922 0.00012
NM_014270.5(SLC7A9):c.695A>G (p.Tyr232Cys) rs121908487 0.00012
NM_000341.4(SLC3A1):c.1973G>A (p.Arg658His) rs370262167 0.00011
NM_000341.4(SLC3A1):c.1717T>C (p.Leu573=) rs148703534 0.00009
NM_000341.4(SLC3A1):c.1799G>A (p.Gly600Glu) rs141944551 0.00009
NM_000341.4(SLC3A1):c.1889G>A (p.Gly630Asp) rs150557210 0.00009
NM_000341.4(SLC3A1):c.647C>T (p.Thr216Met) rs369641941 0.00009
NM_000341.4(SLC3A1):c.1354C>T (p.Arg452Trp) rs201502095 0.00007
NM_000341.4(SLC3A1):c.1084C>T (p.Arg362Cys) rs375399468 0.00006
NM_014270.5(SLC7A9):c.671C>T (p.Ala224Val) rs140873167 0.00006
NM_000341.4(SLC3A1):c.1093C>T (p.Arg365Trp) rs765828196 0.00005
NM_000341.4(SLC3A1):c.1137-3T>C rs555017366 0.00005
NM_014270.5(SLC7A9):c.604+2T>C rs763110287 0.00005
NM_000341.4(SLC3A1):c.1125C>T (p.Pro375=) rs760943092 0.00004
NM_014270.5(SLC7A9):c.997C>T (p.Arg333Trp) rs121908484 0.00004
NM_000341.4(SLC3A1):c.1826A>G (p.Asn609Ser) rs200592320 0.00003
NM_000341.4(SLC3A1):c.1085G>A (p.Arg362His) rs121912697 0.00001
NM_000341.4(SLC3A1):c.1269C>T (p.Ser423=) rs557669708 0.00001
NM_000341.4(SLC3A1):c.2020dup (p.Tyr674fs) rs777149216 0.00001
NM_014270.5(SLC7A9):c.605-3C>A rs749913021 0.00001
NM_000341.4(SLC3A1):c.1094G>T (p.Arg365Leu) rs567478582
NM_000341.4(SLC3A1):c.1136+3del rs796262035
NM_000341.4(SLC3A1):c.1200A>G (p.Pro400=) rs886056069
NM_000341.4(SLC3A1):c.1400T>A (p.Met467Lys) rs121912691
NM_000341.4(SLC3A1):c.1603_1604del (p.Thr535fs) rs767801148
NM_000341.4(SLC3A1):c.1640C>T (p.Ser547Leu) rs368796166
NM_000341.4(SLC3A1):c.1750del (p.Arg584fs) rs775827496
NM_000341.4(SLC3A1):c.1854G>A (p.Met618Ile) rs698761

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