ClinVar Miner

Variants with conflicting interpretations studied for Nonsyndromic Hearing Loss, Recessive

Coded as:
Minimum review status of the submission for Nonsyndromic Hearing Loss, Recessive: Collection method of the submission for Nonsyndromic Hearing Loss, Recessive:
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
103 36 0 27 39 0 0 66

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
Nonsyndromic Hearing Loss, Recessive likely benign benign
uncertain significance 31 9
likely benign 0 27

Condition to condition summary #

Total conditions: 6
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 16 0 26 28 0 0 54
not specified 0 5 0 15 11 0 0 26
Atypical Gaucher Disease 0 0 0 7 13 0 0 20
PSAP-related condition 0 0 0 0 3 0 0 3
PCDH15-related condition 0 0 0 0 2 0 0 2
CDH23-related condition 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 66
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_022124.6(CDH23):c.*349A>G rs1867978 0.77194
NM_002778.4(PSAP):c.*891G>A rs7869 0.34207
NM_001384474.1(LOXHD1):c.6183-11del rs143514947 0.23567
NM_002778.4(PSAP):c.1350+5G>A rs11000016 0.16762
NM_003690.5(PRKRA):c.-24G>A rs62176113 0.15636
NM_022124.6(CDH23):c.*204A>G rs2290022 0.13799
NM_022124.6(CDH23):c.9319+11G>A rs11000013 0.10868
NM_022124.6(CDH23):c.9873G>A (p.Thr3291=) rs2290021 0.08719
NM_022124.6(CDH23):c.*510G>A rs1054635 0.07812
NM_001145308.5(LRTOMT):c.69G>C (p.Leu23=) rs12272086 0.07159
NM_003690.5(PRKRA):c.1A>C (p.Met1Leu) rs9406386 0.04659
NM_022124.6(CDH23):c.9373T>C (p.Phe3125Leu) rs45583140 0.04021
NM_001145308.4(LRTOMT):c.-602G>A rs111537544 0.00551
NM_022124.6(CDH23):c.*361C>A rs115033851 0.00420
NM_003690.5(PRKRA):c.32C>T (p.Pro11Leu) rs62176112 0.00410
NM_022124.6(CDH23):c.*515C>A rs16929375 0.00385
NM_005422.4(TECTA):c.-1-12T>C rs145916279 0.00352
NM_022124.6(CDH23):c.10026C>T (p.Asp3342=) rs377118941 0.00185
NM_022124.6(CDH23):c.*68G>C rs527311705 0.00182
NM_022124.6(CDH23):c.*434G>A rs529522213 0.00133
NM_022124.6(CDH23):c.*430A>T rs562268606 0.00131
NM_022124.6(CDH23):c.9198+13C>T rs375384238 0.00061
NM_022124.6(CDH23):c.9942G>A (p.Thr3314=) rs376804660 0.00053
NM_022124.6(CDH23):c.*141G>A rs535544696 0.00031
NM_022124.6(CDH23):c.*104G>C rs377312107 0.00029
NM_022124.6(CDH23):c.9629T>C (p.Ile3210Thr) rs144688588 0.00026
NM_194248.3(OTOF):c.327+5G>T rs370643920 0.00024
NM_001384474.1(LOXHD1):c.5985C>T (p.Asp1995=) rs559560065 0.00016
NM_022124.6(CDH23):c.9799C>T (p.Arg3267Cys) rs201727938 0.00016
NM_001080476.3(GRXCR1):c.825G>A (p.Thr275=) rs370629848 0.00012
NM_016239.4(MYO15A):c.4038+6_4038+7insTG rs759039332 0.00007
NM_022124.6(CDH23):c.9291G>T (p.Lys3097Asn) rs368441850 0.00006
NM_000260.4(MYO7A):c.4851C>T (p.Pro1617=) rs372535399 0.00002
NM_001038603.3(MARVELD2):c.1059A>G (p.Ile353Met) rs727503158 0.00001
NM_022124.6(CDH23):c.9860G>A (p.Gly3287Asp) rs562590210 0.00001
NM_000441.2(SLC26A4):c.2320-4A>G rs727503432
NM_001256317.3(TMPRSS3):c.1192-8T>C rs751114709
NM_001384140.1(PCDH15):c.3502-10del rs750835578
NM_001384140.1(PCDH15):c.706-17_706-14del rs886047068
NM_002906.4(RDX):c.-64-6del rs61003001
NM_002906.4(RDX):c.-64-6dup rs61003001
NM_002906.4(RDX):c.468-12dup rs368429159
NM_003690.5(PRKRA):c.22_23del (p.Ala8fs) rs141354030
NM_004999.4(MYO6):c.*4113dup rs138193115
NM_004999.4(MYO6):c.*4423AATT[1] rs10547766
NM_004999.4(MYO6):c.1078+19dup rs144408691
NM_004999.4(MYO6):c.1546+7_1546+8del rs3831003
NM_013296.5(GPSM2):c.1569TTC[1] (p.Ser525del) rs35029887
NM_015404.4(WHRN):c.-608_-601del rs150944893
NM_016239.4(MYO15A):c.4038+8GT[28] rs59214589
NM_016239.4(MYO15A):c.4038+8GT[29] rs59214589
NM_016239.4(MYO15A):c.4038+8GT[30] rs59214589
NM_017433.5(MYO3A):c.1053+11_1053+12inv
NM_022124.6(CDH23):c.*588del rs148667421
NM_022124.6(CDH23):c.-197GAGCGGC[5] rs527578984
NM_022124.6(CDH23):c.-45AGGCG[2] rs71012280
NM_022124.6(CDH23):c.-45AGGCG[4] rs71012280
NM_022124.6(CDH23):c.2290-13del rs397517316
NM_022124.6(CDH23):c.5727T>C (p.Thr1909=) rs756919394
NM_022124.6(CDH23):c.9739-12G>A rs200638595
NM_024022.2(TMPRSS3):c.617-3_617-2dup rs34966432
NM_033056.4(PCDH15):c.5245CCT[3] (p.Pro1752del) rs397517462
NM_033056.4(PCDH15):c.5281GCTCCT[1] (p.1761AP[1]) rs397517465
NM_138691.3(TMC1):c.238GAA[3] (p.Glu83del) rs376040866
NM_147196.3(TMIE):c.367AAG[10] (p.Lys131dup) rs10578999
NM_182548.4(LHFPL5):c.-298AG[1] rs67478220

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