ClinVar Miner

Variants with conflicting interpretations studied for Nephrolithiasis/nephrocalcinosis

Coded as:
Minimum review status of the submission for Nephrolithiasis/nephrocalcinosis: Collection method of the submission for Nephrolithiasis/nephrocalcinosis:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
1261 261 0 48 63 1 10 115

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
Nephrolithiasis/nephrocalcinosis pathogenic likely pathogenic uncertain significance likely benign benign association
pathogenic 0 5 0 0 0 0
likely pathogenic 5 0 0 0 0 0
uncertain significance 2 8 0 10 0 0
likely benign 0 0 48 0 25 0
benign 0 0 5 13 0 1

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 0 118 0 27 41 0 8 74
not specified 0 85 0 24 15 0 0 38
Familial hypocalciuric hypercalcemia 1; Neonatal severe primary hyperparathyroidism; Epilepsy, idiopathic generalized, susceptibility to, 8; Autosomal dominant hypocalcemia 1 0 116 0 3 19 0 1 23
CASR-related disorder 0 40 0 3 4 0 2 9
Charcot-Marie-Tooth Neuropathy X 0 4 0 5 1 0 0 6
Familial hyperparathyroidism or Hypocalciuric hypercalcaemia 0 2 0 1 1 0 1 3
OCRL-related disorder 0 7 0 1 1 0 0 2
Developmental cataract 0 0 0 0 1 0 0 1
Serum calcium level 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 115
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000388.4(CASR):c.2956G>T (p.Ala986Ser) rs1801725 0.10965
NM_000388.4(CASR):c.2968A>G (p.Arg990Gly) rs1042636 0.08688
NM_000388.4(CASR):c.1333A>G (p.Thr445Ala) rs12493789 0.01481
NM_000388.4(CASR):c.2610G>A (p.Glu870=) rs143738711 0.01002
NM_000276.4(OCRL):c.41C>T (p.Thr14Ile) rs61752970 0.00489
NM_012203.2(GRHPR):c.962C>T (p.Pro321Leu) rs142356700 0.00442
NM_000276.4(OCRL):c.439+3A>G rs61752971 0.00248
NM_000388.4(CASR):c.2730C>A (p.Pro910=) rs34200949 0.00194
NM_000276.4(OCRL):c.1291G>A (p.Asp431Asn) rs137884245 0.00160
NM_000388.4(CASR):c.748G>A (p.Glu250Lys) rs62269092 0.00159
NM_000388.4(CASR):c.6A>C (p.Ala2=) rs112042188 0.00092
NM_000388.4(CASR):c.1631G>A (p.Arg544Gln) rs115230894 0.00086
NM_000276.4(OCRL):c.40-5C>T rs201211377 0.00082
NM_012203.2(GRHPR):c.234C>T (p.Ile78=) rs143337459 0.00080
NM_012203.2(GRHPR):c.801A>C (p.Gly267=) rs141800325 0.00077
NM_000388.4(CASR):c.1285C>T (p.His429Tyr) rs142818334 0.00066
NM_000388.4(CASR):c.3091G>A (p.Gly1031Ser) rs142704083 0.00061
NM_002764.4(PRPS1):c.942C>T (p.Ser314=) rs147731055 0.00058
NM_000388.4(CASR):c.1192G>A (p.Asp398Asn) rs201177696 0.00052
NM_000388.4(CASR):c.2064C>T (p.Phe688=) rs150869744 0.00037
NM_000388.4(CASR):c.2824G>A (p.Glu942Lys) rs76327999 0.00034
NM_002764.4(PRPS1):c.573G>A (p.Leu191=) rs770518315 0.00033
NM_000276.4(OCRL):c.954C>T (p.Arg318=) rs149646700 0.00032
NM_000388.4(CASR):c.1491C>T (p.Ser497=) rs150337940 0.00031
NM_000388.4(CASR):c.885C>T (p.Ala295=) rs147307274 0.00026
NM_000276.4(OCRL):c.375G>T (p.Glu125Asp) rs773022942 0.00025
NM_000388.4(CASR):c.1110G>A (p.Val370=) rs150412204 0.00024
NM_000276.4(OCRL):c.2680T>A (p.Phe894Ile) rs147629352 0.00023
NM_012203.2(GRHPR):c.391G>A (p.Glu131Lys) rs369339903 0.00023
NM_000388.4(CASR):c.537A>G (p.Gln179=) rs200129212 0.00020
NM_000388.4(CASR):c.2237C>T (p.Ala746Val) rs139417576 0.00019
NM_012203.2(GRHPR):c.343G>A (p.Ala115Thr) rs113602485 0.00016
NM_000388.4(CASR):c.1752G>A (p.Lys584=) rs138638329 0.00014
NM_000388.4(CASR):c.27C>T (p.Val9=) rs141880581 0.00014
NM_000388.4(CASR):c.546T>A (p.Ser182=) rs200545177 0.00014
NM_000388.4(CASR):c.1287C>T (p.His429=) rs746515147 0.00013
NM_000276.4(OCRL):c.2177G>T (p.Gly726Val) rs755071897 0.00012
NM_000388.4(CASR):c.2777A>G (p.Gln926Arg) rs200263975 0.00012
NM_000388.4(CASR):c.757C>A (p.Gln253Lys) rs202179597 0.00012
NM_000276.4(OCRL):c.481G>A (p.Asp161Asn) rs372298378 0.00011
NM_000388.4(CASR):c.854G>A (p.Arg285Gln) rs200039241 0.00011
NM_000388.4(CASR):c.73C>T (p.Arg25Ter) rs201633414 0.00010
NM_000388.4(CASR):c.740C>T (p.Ser247Phe) rs200382161 0.00010
NM_012203.2(GRHPR):c.380C>T (p.Pro127Leu) rs763052360 0.00010
NM_012203.2(GRHPR):c.690C>A (p.Phe230Leu) rs185747820 0.00010
NM_000388.4(CASR):c.1510G>A (p.Val504Met) rs201536450 0.00009
NM_000388.4(CASR):c.114T>C (p.Phe38=) rs61733590 0.00008
NM_000388.4(CASR):c.1188A>G (p.Thr396=) rs200312817 0.00008
NM_012203.2(GRHPR):c.357A>G (p.Leu119=) rs186922220 0.00008
NM_000388.4(CASR):c.1011C>G (p.Val337=) rs201820733 0.00007
NM_000388.4(CASR):c.2356A>G (p.Ile786Val) rs371882068 0.00007
NM_000388.4(CASR):c.3013G>A (p.Asp1005Asn) rs201990892 0.00007
NM_000388.4(CASR):c.848T>C (p.Ile283Thr) rs142745096 0.00007
NM_000388.4(CASR):c.2209G>A (p.Val737Ile) rs200318708 0.00006
NM_000276.4(OCRL):c.2563G>A (p.Val855Ile) rs376280495 0.00005
NM_000276.4(OCRL):c.50G>C (p.Gly17Ala) rs768913997 0.00005
NM_000388.4(CASR):c.165G>A (p.Pro55=) rs200018529 0.00005
NM_000388.4(CASR):c.779A>G (p.Gln260Arg) rs200386687 0.00005
NM_002764.4(PRPS1):c.288G>A (p.Arg96=) rs752194539 0.00005
NM_002764.4(PRPS1):c.444G>A (p.Glu148=) rs201285459 0.00005
NM_000388.4(CASR):c.1913G>A (p.Arg638His) rs201852643 0.00004
NM_000388.4(CASR):c.308C>T (p.Thr103Ile) rs199734455 0.00004
NM_000388.4(CASR):c.60C>T (p.Tyr20=) rs201564143 0.00004
NM_000388.4(CASR):c.705C>A (p.Ile235=) rs199887150 0.00004
NM_000388.4(CASR):c.1668G>A (p.Glu556=) rs186279271 0.00003
NM_000388.4(CASR):c.2265G>T (p.Glu755Asp) rs201366240 0.00003
NM_000276.4(OCRL):c.1852G>A (p.Glu618Lys) rs1376122843 0.00002
NM_000388.4(CASR):c.2638G>T (p.Ala880Ser) rs763865303 0.00002
NM_000388.4(CASR):c.445G>A (p.Val149Ile) rs749288251 0.00002
NM_000388.4(CASR):c.492+5T>A rs200277155 0.00002
NM_000388.4(CASR):c.57C>T (p.Ala19=) rs761576251 0.00002
NM_002764.4(PRPS1):c.705-6C>T rs199740956 0.00002
NM_000388.4(CASR):c.106G>A (p.Gly36Arg) rs193922420 0.00001
NM_000388.4(CASR):c.1297G>C (p.Asp433His) rs199511990 0.00001
NM_000388.4(CASR):c.1371G>A (p.Ala457=) rs766477389 0.00001
NM_000388.4(CASR):c.1393C>T (p.Arg465Trp) rs751217000 0.00001
NM_000388.4(CASR):c.206G>A (p.Arg69His) rs193922432 0.00001
NM_000388.4(CASR):c.2303G>T (p.Gly768Val) rs201858689 0.00001
NM_000388.4(CASR):c.2829G>A (p.Gln943=) rs764614440 0.00001
NM_000388.4(CASR):c.2910C>T (p.Ser970=) rs200686461 0.00001
NM_000388.4(CASR):c.3132G>A (p.Val1044=) rs755277801 0.00001
NM_000388.4(CASR):c.40A>G (p.Thr14Ala) rs199515839 0.00001
NM_000388.4(CASR):c.427G>A (p.Gly143Arg) rs769256610 0.00001
NM_000388.4(CASR):c.888C>T (p.Ser296=) rs759988398 0.00001
NM_000388.4(CASR):c.98T>G (p.Ile33Ser) rs758232331 0.00001
NM_012203.2(GRHPR):c.578C>T (p.Ala193Val) rs771231175 0.00001
NM_000194.3(HPRT1):c.134+6_134+9del rs794727238
NM_000276.4(OCRL):c.101A>G (p.Gln34Arg) rs751244947
NM_000388.4(CASR):c.1108G>A (p.Val370Met) rs2074634164
NM_000388.4(CASR):c.1163C>G (p.Ser388Trp) rs377282860
NM_000388.4(CASR):c.1209T>C (p.Ser403=) rs387907400
NM_000388.4(CASR):c.1250C>G (p.Ser417Cys) rs1576859379
NM_000388.4(CASR):c.1394G>A (p.Arg465Gln) rs104893716
NM_000388.4(CASR):c.1395G>A (p.Arg465=) rs387907391
NM_000388.4(CASR):c.1608+4G>T rs878853974
NM_000388.4(CASR):c.1664T>C (p.Ile555Thr) rs1576875819
NM_000388.4(CASR):c.1665T>C (p.Ile555=) rs201955278
NM_000388.4(CASR):c.197G>A (p.Arg66His) rs1276839362
NM_000388.4(CASR):c.2056A>G (p.Ile686Val) rs753013993
NM_000388.4(CASR):c.2229C>T (p.Leu743=) rs372578790
NM_000388.4(CASR):c.2770_2777del (p.Phe924fs) rs2473281810
NM_000388.4(CASR):c.2901C>A (p.Ile967=) rs199594582
NM_000388.4(CASR):c.3025C>T (p.Arg1009Ter) rs1256856876
NM_000388.4(CASR):c.3040C>A (p.Leu1014Ile) rs202219108
NM_000388.4(CASR):c.3223G>T (p.Val1075Leu) rs748855270
NM_000388.4(CASR):c.3234A>T (p.Ser1078=) rs556263764
NM_000388.4(CASR):c.346G>A (p.Ala116Thr) rs104893691
NM_000388.4(CASR):c.379G>A (p.Glu127Lys) rs2074565202
NM_000388.4(CASR):c.413C>T (p.Thr138Met) rs121909263
NM_000388.4(CASR):c.61G>A (p.Gly21Arg) rs1064794290
NM_000388.4(CASR):c.649G>T (p.Asp217Tyr) rs201091657
NM_000388.4(CASR):c.664G>A (p.Gly222Arg) rs2107632066
NM_000388.4(CASR):c.680G>A (p.Arg227Gln) rs28936684
NM_000388.4(CASR):c.99C>T (p.Ile33=) rs387907398
NM_002764.4(PRPS1):c.705-4C>T rs1925730100

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