ClinVar Miner

Variants with conflicting interpretations studied for Rare genetic deafness

Coded as:
Minimum review status of the submission for Rare genetic deafness: Collection method of the submission for Rare genetic deafness:
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
278 310 0 177 2 2 54 215

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
Rare genetic deafness pathogenic likely pathogenic uncertain significance likely benign benign drug response
pathogenic 0 65 9 1 0 1
likely pathogenic 112 0 38 2 0 1
uncertain significance 1 3 0 2 1 0

Condition to condition summary #

Total conditions: 28
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 0 320 0 166 2 0 41 195
not specified 0 15 0 2 0 0 6 8
MYO7A-Related Disorders 0 1 0 3 0 0 2 5
SLC26A4-Related Disorders 0 9 0 2 0 0 1 3
Bilateral sensorineural hearing impairment 0 3 0 2 0 0 0 2
GPSM2-Related Disorders 0 1 0 2 0 0 0 2
Gentamicin response 0 0 0 0 0 2 0 2
MYO7A-related condition 0 3 0 2 0 0 0 2
OTOG-related condition 0 0 0 2 0 0 0 2
STRC-related condition 0 2 0 1 0 0 1 2
See cases 0 5 0 1 0 0 1 2
USH2A-Related Disorders 0 4 0 0 0 0 2 2
USH2A-related condition 0 3 0 2 0 0 0 2
aminoglycoside antibacterials response - Toxicity 0 0 0 0 0 2 0 2
gentamicin response - Toxicity 0 0 0 0 0 2 0 2
kanamycin response - Toxicity 0 0 0 0 0 2 0 2
streptomycin response - Toxicity 0 0 0 0 0 2 0 2
tobramycin response - Toxicity 0 0 0 0 0 2 0 2
CDH23-related condition 0 0 0 1 0 0 0 1
COL11A2-related condition 0 0 0 1 0 0 0 1
Cardiovascular phenotype 0 1 0 0 0 0 1 1
Deafness 0 2 0 1 0 0 0 1
Nonsyndromic Hearing Loss, Dominant 0 0 0 0 0 0 1 1
SLC26A4-related condition 0 5 0 1 0 0 0 1
SLC26A4-related disorder 0 2 0 1 0 0 0 1
Sensorineural deafness with hypertrophic cardiomyopathy 0 0 0 1 0 0 0 1
TMC1-related condition 0 0 0 1 0 0 0 1
amikacin response - Toxicity 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 215
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_004004.6(GJB2):c.101T>C (p.Met34Thr) rs35887622 0.00966
NM_144672.4(OTOA):c.2359G>T (p.Glu787Ter) rs200988634 0.00927
NM_001256317.3(TMPRSS3):c.413C>A (p.Ala138Glu) rs147231991 0.00146
NM_001256317.3(TMPRSS3):c.1273G>A (p.Ala425Thr) rs56264519 0.00105
NM_000441.2(SLC26A4):c.1003T>C (p.Phe335Leu) rs111033212 0.00077
NM_022124.6(CDH23):c.7823G>A (p.Arg2608His) rs202052174 0.00059
NM_138691.3(TMC1):c.1763+3A>G rs370898981 0.00056
NM_004004.6(GJB2):c.416G>A (p.Ser139Asn) rs76434661 0.00047
NM_016239.4(MYO15A):c.9620G>A (p.Arg3207His) rs199621031 0.00026
NM_015340.4(LARS2):c.1565C>A (p.Thr522Asn) rs199589947 0.00025
NM_000260.4(MYO7A):c.3476G>T (p.Gly1159Val) rs199897298 0.00021
NM_000441.2(SLC26A4):c.349C>T (p.Leu117Phe) rs145254330 0.00017
NM_001378609.3(OTOGL):c.1078C>T (p.Arg360Ter) rs368844341 0.00016
NM_004004.6(GJB2):c.617A>G (p.Asn206Ser) rs111033294 0.00016
NM_174878.3(CLRN1):c.144T>G (p.Asn48Lys) rs111033258 0.00016
NM_004004.6(GJB2):c.110T>C (p.Val37Ala) rs141774369 0.00014
NM_016239.4(MYO15A):c.8090T>C (p.Val2697Ala) rs200451098 0.00013
NM_000441.2(SLC26A4):c.85G>C (p.Glu29Gln) rs111033205 0.00011
NM_005422.4(TECTA):c.4085G>A (p.Trp1362Ter) rs199638531 0.00011
NM_016239.4(MYO15A):c.8183G>A (p.Arg2728His) rs184435771 0.00011
NM_016239.4(MYO15A):c.9861C>T (p.Gly3287=) rs372466080 0.00011
NM_206933.4(USH2A):c.14453C>T (p.Pro4818Leu) rs143344549 0.00011
NM_001042702.5(PJVK):c.499C>T (p.Arg167Ter) rs118203989 0.00010
NM_001292063.2(OTOG):c.4984G>T (p.Gly1662Ter) rs1407028917 0.00010
NM_022124.6(CDH23):c.6442G>A (p.Asp2148Asn) rs111033271 0.00010
NM_001378609.3(OTOGL):c.1940G>A (p.Trp647Ter) rs377708973 0.00009
NM_004004.6(GJB2):c.34G>T (p.Gly12Cys) rs104894408 0.00009
NM_016239.4(MYO15A):c.6764+2T>A rs763975867 0.00009
NM_017433.5(MYO3A):c.315del (p.Gly106fs) rs777580042 0.00009
NM_004004.6(GJB2):c.283G>A (p.Val95Met) rs111033299 0.00008
NM_000260.4(MYO7A):c.287C>T (p.Thr96Met) rs781811444 0.00007
NM_001292063.2(OTOG):c.7418del (p.Arg2473fs) rs751369871 0.00007
NM_000260.4(MYO7A):c.5618G>A (p.Arg1873Gln) rs397516322 0.00006
NM_000260.4(MYO7A):c.652G>A (p.Asp218Asn) rs201539845 0.00006
NM_000441.2(SLC26A4):c.-4+5G>A rs727503425 0.00006
NM_000441.2(SLC26A4):c.1541A>G (p.Gln514Arg) rs111033316 0.00006
NM_006005.3(WFS1):c.1886G>A (p.Arg629Gln) rs146670741 0.00006
NM_016239.4(MYO15A):c.8714-1G>A rs377015931 0.00006
NM_022124.6(CDH23):c.7362G>A (p.Thr2454=) rs370983472 0.00006
NM_153700.2(STRC):c.4219-1G>A rs748854592 0.00006
NM_206933.4(USH2A):c.1036A>C (p.Asn346His) rs369522997 0.00006
NM_206933.4(USH2A):c.956G>A (p.Cys319Tyr) rs121912599 0.00006
NM_000441.2(SLC26A4):c.706C>G (p.Leu236Val) rs111033242 0.00005
NM_001378609.3(OTOGL):c.975del (p.Leu325fs) rs766753922 0.00005
NM_016239.4(MYO15A):c.5925G>A (p.Trp1975Ter) rs375290498 0.00005
NM_016239.4(MYO15A):c.6046+1G>A rs201978571 0.00005
NM_138691.3(TMC1):c.1333C>T (p.Arg445Cys) rs372710475 0.00005
NM_000260.4(MYO7A):c.1A>G (p.Met1Val) rs797044518 0.00004
NM_000260.4(MYO7A):c.6326C>T (p.Thr2109Ile) rs377670513 0.00004
NM_001039876.3(SYNE4):c.559C>T (p.Arg187Ter) rs750797779 0.00004
NM_001292063.2(OTOG):c.3457C>T (p.Arg1153Ter) rs772430523 0.00004
NM_013296.5(GPSM2):c.1492C>T (p.Arg498Ter) rs370907055 0.00004
NM_174878.3(CLRN1):c.127G>A (p.Gly43Arg) rs111033434 0.00004
NM_000219.6(KCNE1):c.137A>G (p.Tyr46Cys) rs1402178514 0.00003
NM_000260.4(MYO7A):c.401T>A (p.Ile134Asn) rs111033181 0.00003
NM_000260.4(MYO7A):c.6439-2A>G rs397516330 0.00003
NM_000441.2(SLC26A4):c.2171A>G (p.Asp724Gly) rs757820624 0.00003
NM_000441.2(SLC26A4):c.554G>C (p.Arg185Thr) rs542620119 0.00003
NM_001039141.3(TRIOBP):c.5317C>T (p.Arg1773Ter) rs368112491 0.00003
NM_001384474.1(LOXHD1):c.2497C>T (p.Arg833Ter) rs188119157 0.00003
NM_004004.6(GJB2):c.44A>C (p.Lys15Thr) rs111033217 0.00003
NM_006383.4(CIB2):c.300_309del (p.Glu100fs) rs765741202 0.00003
NM_138691.3(TMC1):c.1141T>A (p.Tyr381Asn) rs749491943 0.00003
NM_206933.4(USH2A):c.949C>A (p.Arg317=) rs111033272 0.00003
NM_000260.4(MYO7A):c.3827C>T (p.Ser1276Leu) rs369458838 0.00002
NM_000260.4(MYO7A):c.5660C>T (p.Pro1887Leu) rs199606180 0.00002
NM_000260.4(MYO7A):c.5824G>T (p.Gly1942Ter) rs111033192 0.00002
NM_000260.4(MYO7A):c.5899C>T (p.Arg1967Ter) rs376764423 0.00002
NM_000260.4(MYO7A):c.722G>A (p.Arg241His) rs111033284 0.00002
NM_001199107.2(TBC1D24):c.457G>A (p.Glu153Lys) rs376712059 0.00002
NM_001384140.1(PCDH15):c.3316C>T (p.Arg1106Ter) rs202033121 0.00002
NM_001393500.2(TOMT):c.259+4A>C rs545947177 0.00002
NM_004004.6(GJB2):c.194A>G (p.Tyr65Cys) rs111033203 0.00002
NM_004999.4(MYO6):c.826C>T (p.Arg276Ter) rs727503326 0.00002
NM_005422.4(TECTA):c.5977C>T (p.Arg1993Ter) rs760574657 0.00002
NM_016239.4(MYO15A):c.8341-2A>C rs778404517 0.00002
NM_138691.3(TMC1):c.1939T>C (p.Ser647Pro) rs138527651 0.00002
NM_194248.3(OTOF):c.4718T>C (p.Ile1573Thr) rs111033405 0.00002
NM_194248.3(OTOF):c.5713-2A>G rs111033455 0.00002
NM_206933.4(USH2A):c.5581G>A (p.Gly1861Ser) rs375668376 0.00002
NM_206933.4(USH2A):c.5857+2T>C rs397518022 0.00002
NM_000260.4(MYO7A):c.1097T>C (p.Leu366Pro) rs397516281 0.00001
NM_000260.4(MYO7A):c.1208A>G (p.Tyr403Cys) rs797044511 0.00001
NM_000260.4(MYO7A):c.2187+1G>A rs111033290 0.00001
NM_000260.4(MYO7A):c.2863G>A (p.Gly955Ser) rs781988557 0.00001
NM_000260.4(MYO7A):c.4065del (p.His1355fs) rs111033202 0.00001
NM_000260.4(MYO7A):c.5573T>C (p.Leu1858Pro) rs368657015 0.00001
NM_000260.4(MYO7A):c.5804T>C (p.Leu1935Pro) rs397516323 0.00001
NM_000441.2(SLC26A4):c.1231G>C (p.Ala411Pro) rs1293971731 0.00001
NM_000441.2(SLC26A4):c.1694G>A (p.Cys565Tyr) rs111033257 0.00001
NM_000441.2(SLC26A4):c.845G>A (p.Cys282Tyr) rs111033454 0.00001
NM_001256317.3(TMPRSS3):c.1340T>C (p.Met447Thr) rs201018751 0.00001
NM_001256317.3(TMPRSS3):c.727G>A (p.Gly243Arg) rs372526764 0.00001
NM_001378609.3(OTOGL):c.4341del (p.Met1447fs) rs766971906 0.00001
NM_004004.6(GJB2):c.19C>T (p.Gln7Ter) rs111033451 0.00001
NM_004004.6(GJB2):c.239A>C (p.Gln80Pro) rs727504302 0.00001
NM_004004.6(GJB2):c.279G>A (p.Met93Ile) rs397516871 0.00001
NM_004004.6(GJB2):c.365A>T (p.Lys122Ile) rs111033295 0.00001
NM_004700.4(KCNQ4):c.961G>A (p.Gly321Ser) rs28939710 0.00001
NM_005422.4(TECTA):c.2719C>T (p.Arg907Ter) rs764424917 0.00001
NM_005422.4(TECTA):c.5597C>T (p.Thr1866Met) rs140236996 0.00001
NM_016239.4(MYO15A):c.4252G>A (p.Gly1418Arg) rs753790346 0.00001
NM_016239.4(MYO15A):c.6437G>A (p.Arg2146Gln) rs760980785 0.00001
NM_016239.4(MYO15A):c.7893+1G>A rs727503316 0.00001
NM_022124.6(CDH23):c.1369C>T (p.Arg457Trp) rs727504455 0.00001
NM_022124.6(CDH23):c.3016G>A (p.Glu1006Lys) rs745571683 0.00001
NM_022124.6(CDH23):c.5712G>A (p.Thr1904=) rs397517342 0.00001
NM_022124.6(CDH23):c.6049G>A (p.Gly2017Ser) rs183431253 0.00001
NM_022124.6(CDH23):c.6614C>T (p.Pro2205Leu) rs397517349 0.00001
NM_032119.4(ADGRV1):c.14365C>T (p.Arg4789Trp) rs1131691924 0.00001
NM_133261.3(GIPC3):c.122C>A (p.Thr41Lys) rs727503062 0.00001
NM_144672.4(OTOA):c.1880+1G>A rs148690740 0.00001
NM_153700.2(STRC):c.4425G>C (p.Trp1475Cys) rs727503443 0.00001
NM_173477.5(USH1G):c.1373A>T (p.Asp458Val) rs397517925 0.00001
NM_194248.3(OTOF):c.3864+1G>A rs758918226 0.00001
NM_194248.3(OTOF):c.5375G>A (p.Arg1792His) rs111033349 0.00001
NM_206933.4(USH2A):c.1055C>T (p.Thr352Ile) rs780308389 0.00001
NM_206933.4(USH2A):c.10712C>T (p.Thr3571Met) rs202175091 0.00001
NM_206933.4(USH2A):c.10724G>A (p.Cys3575Tyr) rs111033265 0.00001
NM_206933.4(USH2A):c.13130C>A (p.Ser4377Ter) rs111033385 0.00001
NM_206933.4(USH2A):c.3408T>A (p.Ser1136Arg) rs1064793287 0.00001
NM_206933.4(USH2A):c.653T>A (p.Val218Glu) rs397518026 0.00001
NM_206933.4(USH2A):c.9799T>C (p.Cys3267Arg) rs111033263 0.00001
NC_012920.1(MT-ND1):m.1494C>T rs267606619
NC_012920.1(MT-ND1):m.1555A>G rs267606617
NM_000152.5(GAA):c.1841C>T (p.Thr614Met) rs369531647
NM_000260.4(MYO7A):c.1200+1G>A rs397516283
NM_000260.4(MYO7A):c.132+5G>A rs397516284
NM_000260.4(MYO7A):c.1690+1G>A rs111033389
NM_000260.4(MYO7A):c.2094+1G>A rs111033404
NM_000260.4(MYO7A):c.2283-1G>T rs397516295
NM_000260.4(MYO7A):c.247C>A (p.Arg83Ser) rs781790246
NM_000260.4(MYO7A):c.285+2T>C rs782292032
NM_000260.4(MYO7A):c.2904G>A (p.Glu968=) rs111033233
NM_000260.4(MYO7A):c.3532del (p.Gln1178fs) rs111033239
NM_000260.4(MYO7A):c.3543_3544dup (p.Asn1182fs) rs111033390
NM_000260.4(MYO7A):c.3591_3592del (p.Cys1198fs) rs1555090368
NM_000260.4(MYO7A):c.3892G>A (p.Gly1298Arg) rs727503329
NM_000260.4(MYO7A):c.3979G>A (p.Glu1327Lys) rs373169422
NM_000260.4(MYO7A):c.397C>T (p.His133Tyr) rs111033403
NM_000260.4(MYO7A):c.397dup (p.His133fs) rs111033187
NM_000260.4(MYO7A):c.4411T>C (p.Ser1471Pro) rs397516310
NM_000260.4(MYO7A):c.4544_4551delinsCA (p.Glu1515_Met1517delinsAla) rs111033259
NM_000260.4(MYO7A):c.5208dup (p.Lys1737fs) rs111033276
NM_000260.4(MYO7A):c.5327-11A>G rs397516316
NM_000260.4(MYO7A):c.6062A>G (p.Lys2021Arg) rs876657655
NM_000260.4(MYO7A):c.689C>T (p.Ala230Val) rs797044512
NM_000260.4(MYO7A):c.977T>A (p.Leu326Gln) rs797044491
NM_000307.5(POU3F4):c.341G>A (p.Trp114Ter) rs111033343
NM_000441.2(SLC26A4):c.1204G>A (p.Val402Met) rs397516414
NM_000441.2(SLC26A4):c.1264-1G>C rs111033311
NM_000441.2(SLC26A4):c.1281TGC[1] (p.Ala429del) rs111033306
NM_000441.2(SLC26A4):c.1437+2T>G rs397516418
NM_000441.2(SLC26A4):c.1707+6T>C rs727505230
NM_000441.2(SLC26A4):c.170C>G (p.Ser57Ter) rs111033200
NM_000441.2(SLC26A4):c.2027T>A (p.Leu676Gln) rs111033318
NM_000441.2(SLC26A4):c.2145G>T (p.Lys715Asn) rs397516427
NM_000441.2(SLC26A4):c.589G>A (p.Gly197Arg) rs111033380
NM_000441.2(SLC26A4):c.716T>A (p.Val239Asp) rs111033256
NM_000441.2(SLC26A4):c.765+2T>C rs397516432
NM_000441.2(SLC26A4):c.85G>T (p.Glu29Ter) rs111033205
NM_000441.2(SLC26A4):c.918+1G>T rs111033245
NM_001039141.3(TRIOBP):c.1195C>T (p.Arg399Ter) rs750078356
NM_001128228.3(TPRN):c.107del (p.Gly36fs) rs1011757302
NM_001292063.2(OTOG):c.2453_2454insACTGGACACCCA (p.Tyr818Ter) rs876657656
NM_001292063.2(OTOG):c.3187C>T (p.Arg1063Ter)
NM_001292063.2(OTOG):c.499del (p.Val167fs) rs876657657
NM_001292063.2(OTOG):c.5194C>T (p.Gln1732Ter)
NM_001292063.2(OTOG):c.5926dup (p.Gln1976fs) rs34547529
NM_001292063.2(OTOG):c.7353dup (p.Ala2452fs) rs1157646266
NM_001378609.3(OTOGL):c.841_842del (p.Met281fs) rs876657658
NM_001384140.1(PCDH15):c.1998-2A>G rs397517452
NM_001384474.1(LOXHD1):c.1537_1538del (p.Leu513fs) rs1555683951
NM_001384474.1(LOXHD1):c.4714C>T (p.Arg1572Ter) rs75949023
NM_001384474.1(LOXHD1):c.610+2T>A
NM_004004.6(GJB2):c.35G>T (p.Gly12Val) rs1801002
NM_004004.6(GJB2):c.389G>C (p.Gly130Ala) rs779018464
NM_004004.6(GJB2):c.456C>A (p.Tyr152Ter) rs111033420
NM_004004.6(GJB2):c.56G>C (p.Ser19Thr) rs80338941
NM_004004.6(GJB2):c.9G>A (p.Trp3Ter) rs111033401
NM_004999.4(MYO6):c.737A>G (p.His246Arg) rs121912560
NM_005422.4(TECTA):c.5692T>C (p.Cys1898Arg) rs1591464207
NM_006005.3(WFS1):c.2146G>A (p.Ala716Thr) rs28937893
NM_006005.3(WFS1):c.2389G>A (p.Asp797Asn) rs1553879004
NM_013296.5(GPSM2):c.742del (p.Gly249fs) rs528069912
NM_016239.4(MYO15A):c.10247CCT[1] (p.Ser3417del) rs760069953
NM_016239.4(MYO15A):c.3006del (p.Lys1003fs) rs1162296750
NM_016239.4(MYO15A):c.9303+1G>T rs876657708
NM_022124.6(CDH23):c.1246_1266del (p.Ala416_Glu422del) rs397517305
NM_022124.6(CDH23):c.5712+1G>A rs397517341
NM_022124.6(CDH23):c.7483-1G>C rs876657682
NM_032119.4(ADGRV1):c.1180del (p.Ser394fs) rs1400695342
NM_032119.4(ADGRV1):c.17303_17315del (p.Gly5768fs) rs727504644
NM_080680.3(COL11A2):c.3100C>T (p.Arg1034Cys) rs121912947
NM_133261.3(GIPC3):c.85del (p.Ala29fs)
NM_138691.3(TMC1):c.741+1G>A rs1588067173
NM_144672.4(OTOA):c.746_751delinsA (p.Ser249fs) rs876657716
NM_144672.4(OTOA):c.806C>A (p.Ser269Ter)
NM_153700.2(STRC):c.3502_3503del (p.Gln1168fs) rs764864372
NM_153700.2(STRC):c.5125A>G (p.Thr1709Ala) rs1336307815
NM_194248.3(OTOF):c.1927G>T (p.Glu643Ter) rs200864338
NM_194248.3(OTOF):c.828C>A (p.Cys276Ter) rs111033447
NM_194323.3(OTOF):c.3624del (p.Leu1209fs) rs727505359
NM_206933.4(USH2A):c.10450C>T (p.Arg3484Ter) rs111033379
NM_206933.4(USH2A):c.10759C>T (p.Gln3587Ter) rs111033418
NM_206933.4(USH2A):c.12294+1G>C rs111033526
NM_206933.4(USH2A):c.13010C>T (p.Thr4337Met) rs527236137
NM_206933.4(USH2A):c.13313G>A (p.Trp4438Ter) rs111033417
NM_206933.4(USH2A):c.14287G>A (p.Gly4763Arg) rs397517990
NM_206933.4(USH2A):c.2809+2T>A rs1553320397
NM_206933.4(USH2A):c.3547_3548del (p.Ile1183fs) rs397518013
NM_206933.4(USH2A):c.4189_4193dup (p.Ile1399fs) rs1553313308
NM_206933.4(USH2A):c.5788C>T (p.Arg1930Ter) rs397518021
NM_206933.4(USH2A):c.6289_6302del (p.Leu2096_Ile2097insTer) rs111033268
NM_206933.4(USH2A):c.6795_6797del (p.Glu2265_Tyr2266delinsAsp) rs727503723

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